Fabian Joachim Theis

ORCID: 0000-0002-2419-1943

Also affiliated with Munich School of Philosophy, Helmholtz Munich, Institute of Bioinformatics and Systems Biology, Helmholtz Institute Mainz, Centre National des Sciences et Technologies Nucléaires, Technical University of Munich

Biochemistry, Genetics and Molecular BiologyComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

75.0Author DataRank

Indexed papers

87in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 87 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Genome Biology(2010)10.1186/gb-2010-11-1-r6

Top 2%

7.2DataRank

Top 2%290 citations

Andreas Kowarsch, Daniel Schmidl, Felix Buggenthin, Barbara Brauner, Irmtraud Dunger +6 more

Papers

Driven by 802 papers — median percentile 22. Top paper: “SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues”.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Cell(2020)10.1016/j.cell.2020.04.035

N/A

14.1DataRank · unranked

2492 citations

Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas +92 more

Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer

Molecular Cancer(2015)10.1186/s12943-015-0401-6

N/A

9.8DataRank · unranked

206 citations

Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann +14 more

A Python library for probabilistic analysis of single-cell omics data

Nature Biotechnology(2022)10.1038/s41587-021-01206-w

N/A

9.4DataRank · unranked

825 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong +24 more

The Structure of Borders in a Small World

PLoS ONE(2010)10.1371/journal.pone.0015422

N/A

9.2DataRank · unranked

174 citations

Daniel Grady, Rafael Brune, Dirk Brockmann, Fabian Joachim Theis, Christian Thiemann

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Genome Biology(2010)10.1186/gb-2010-11-1-r6

Top 2%

7.2DataRank

Top 2%290 citations

Andreas Kowarsch, Daniel Schmidl, Felix Buggenthin, Barbara Brauner, Irmtraud Dunger +6 more

A geometric algorithm for overcomplete linear ICA

Neurocomputing(2004)10.1016/j.neucom.2003.09.008

N/A

6.8DataRank · unranked

100 citations

Elmar W. Lang, Carlos G. Puntonet, Fabian Joachim Theis

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy

BMC Bioinformatics(2013)10.1186/1471-2105-14-297

N/A

6.7DataRank · unranked

162 citations

Carsten Marr, Michael Schwarzfischer, Philipp S. Hoppe, Oliver Hilsenbeck, Fabian Joachim Theis +1 more

Benchmarking atlas-level data integration in single-cell genomics

Nature Methods(2021)10.1038/s41592-021-01336-8

Top 3%

6.5DataRank

Top 3%1462 citations

Maren Büttner, Kridsadakorn Chaichoompu, M. F. Mueller, Fabian Joachim Theis, Anna Danese +7 more

Software tools for single-cell tracking and quantification of cellular and molecular properties

Nature Biotechnology(2016)10.1038/nbt.3626

N/A

6.1DataRank · unranked

176 citations

Michael Schwarzfischer, Stavroula Skylaki, Bernhard Schauberger, Philipp S. Hoppe, Dirk Loeffler +14 more

Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes

Diabetologia(2014)10.1007/s00125-014-3362-1

N/A

6.0DataRank · unranked

135 citations

Jan Krumsiek, Florian Buettner, Christof Angermüller, Eleni Z. Giannopoulou, Fabian Joachim Theis +4 more

Cloning and Sequencing of the Genes Encoding the Periplasmic-CytochromeB-Containing Selenate Reductase ofThauera selenatis

DNA Sequence(2000)10.3109/10425170009015604

N/A

5.5DataRank · unranked

118 citations

Ashley Bowen, Joan M. Macy, A. R. Bowen, Fabian Joachim Theis, Torsten Krafft

The scverse project provides a computational ecosystem for single-cell omics data analysis

Nature Biotechnology(2023)10.1038/s41587-023-01733-8

Top 4%

5.4DataRank

Top 4%353 citations

Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso +29 more

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

Proceedings of the National Academy of Sciences(2017)10.1073/pnas.1708341114

N/A

5.4DataRank · unranked

178 citations

Dmitry Shaposhnikov, Valentyna Rishko, Chaido Ori, Christoph Ziegenhain, Steffen Sass +10 more

Benchmarking atlas-level data integration in single-cell genomics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.22.111161

N/A

5.3DataRank · unranked

122 citations

Maren Büttner, Kridsadakorn Chaichoompu, Marta Interlandi, Michaela Müller, Daniel Strobl +6 more

Erythropoietin enhances hippocampal long-term potentiation and memory

BMC Biology(2008)10.1186/1741-7007-6-37

N/A

5.0DataRank · unranked

166 citations

Derya Sargin, Alicja Stradomska, Lucian Medrihan, Christoph Gertler, Mingyue Zhang +16 more

An integrated cell atlas of the lung in health and disease

Nature Medicine(2023)10.1038/s41591-023-02327-2

Top 4%

5.0DataRank

Top 4%781 citations

Ciro Ramírez-Suástegui, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov +87 more

Atrx promotes heterochromatin formation at retrotransposons

EMBO reports(2015)10.15252/embr.201439937

N/A

4.8DataRank · unranked

183 citations

Katharina Schmidt, Sophia Groh, Ivan Kondofersky, Joachim Ellwart, Christiane Fuchs +4 more

The proteome landscape of the kingdoms of life

Nature(2020)10.1038/s41586-020-2402-x

Top 5%

4.7DataRank

Top 5%224 citations

Philipp E. Geyer, Ana R. Colaço, Peter V. Treit, Maximilian T. Strauss, Mario Oroshi +9 more

Odefy - From discrete to continuous models

BMC Bioinformatics(2010)10.1186/1471-2105-11-233

N/A

4.6DataRank · unranked

121 citations

Sebastian Pölsterl, Dominik M. Wittmann, Fabian Joachim Theis, Jan Krumsiek

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.22.423933

N/A

4.6DataRank · unranked

123 citations

Marvin Thielert, Catherine G. Vasilopoulou, Constantin Ammar, Fabian Coscia, Andreas Mund +13 more

Network plasticity of pluripotency transcription factors in embryonic stem cells

Nature Cell Biology(2015)10.1038/ncb3237

N/A

4.5DataRank · unranked

141 citations

Carsten Marr, Simon Hastreiter, Justin Feigelman, Michael Schwarzfischer, Philipp S. Hoppe +10 more

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

Molecular Systems Biology(2021)10.15252/msb.20209923

Top 5%

4.4DataRank

Top 5%380 citations

Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio‐Escat, Michal Klein, Olga Ivanova +7 more

Body Fat Free Mass Is Associated with the Serum Metabolite Profile in a Population-Based Study

PLoS ONE(2012)10.1371/journal.pone.0040009

N/A

4.4DataRank · unranked

109 citations

Ann-Kristin Petersen, Christian Gieger, Angela Döring, Thomas Illig, Rui Wang-Sattler +16 more

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

Genome Biology(2021)10.1186/s13059-021-02519-4

Top 5%

4.2DataRank

Top 5%200 citations

Fabian Joachim Theis, Luke Zappia

Method of conditional moments (MCM) for the Chemical Master Equation

Journal of Mathematical Biology(2013)10.1007/s00285-013-0711-5

N/A

4.2DataRank · unranked

113 citations

V. Wolf, Christiane Fuchs, Verena Wolf, Atefeh Kazeroonian, Fabian Joachim Theis

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PLOS Computational Biology(2017)10.1371/journal.pcbi.1005331

N/A

4.2DataRank · unranked

162 citations

Barbara Kaltenbacher, Fabian Joachim Theis, Christiane Fuchs, Fabian Fröhlich

Towards a general independent subspace analysis

Advances in Neural Information Processing Systems 19(2007)10.7551/mitpress/7503.003.0175

N/A

4.1DataRank · unranked

91 citations

Fabian Joachim Theis

Inhibition of LTβR signalling activates WNT-induced regeneration in lung

Nature(2020)10.1038/s41586-020-2882-8

N/A

4.1DataRank · unranked

178 citations

Gerrit John-Schuster, Danijela Heide, Dominik Pfister, Mareike Lehmann, Yan Hu +47 more

A Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2/E2F3 Controls Neural Progenitor Cell-Cycle Exit and Differentiation

The Journal of Neuroscience(2012)10.1523/jneurosci.2124-12.2012

N/A

4.0DataRank · unranked

97 citations

Na Li, Yen-Kar Ng, Jingzhong Zhang, Florian Meier, Fabian Joachim Theis +5 more

Inferring Interaction Networks From Multi-Omics Data

Frontiers in Genetics(2019)10.3389/fgene.2019.00535

N/A

3.9DataRank · unranked

151 citations

Fabian Joachim Theis, Matthias Heinig, Johann S. Hawe

Machine learning for perturbational single-cell omics

Cell Systems(2021)10.1016/j.cels.2021.05.016

N/A

3.6DataRank · unranked

136 citations

Mohammad Lotfollahi, Francesca Finotello, Fabian Joachim Theis, Florian Wolf, Yuge Ji

Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy

Nature Machine Intelligence(2020)10.1038/s42256-020-00247-1

N/A

3.5DataRank · unranked

87 citations

Niklas D. Köhler, Jakob Siedlecki, Tina Herold, Leonie Keidel, Ben Asani +6 more

PhenomiR: MicroRNAs in Human Diseases and Biological Processes

Methods in Molecular Biology(2011)10.1007/978-1-61779-427-8_17

Top 6%

3.5DataRank

Top 6%81 citations

Andreas Kowarsch, Fabian Joachim Theis, Andreas Ruepp

Metabolite profiling reveals new insights into the regulation of serum urate in humans

Metabolomics(2013)10.1007/s11306-013-0565-2

N/A

3.4DataRank · unranked

71 citations

Melanie Waldenberger, Jan Krumsiek, Anne M. Evans, Ulli Jeratsch, Michaela Breier +19 more

Uniqueness of complex and multidimensional independent component analysis

Signal Processing(2004)10.1016/j.sigpro.2004.01.008

N/A

3.4DataRank · unranked

62 citations

Fabian Joachim Theis

Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model

Cell Systems(2018)10.1016/j.cels.2018.10.013

N/A

3.4DataRank · unranked

156 citations

Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache, Artur Muradyan +11 more

Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma

Cell(2024)10.1016/j.cell.2023.11.032

N/A

3.4DataRank · unranked

195 citations

Ken Xie, Florian Ingelfinger, Yonatan Katzenelenbogen, Kathleen Abadie, Thomas Look +24 more

Single cell RNA-seq denoising using a deep count autoencoder

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/300681

N/A

3.3DataRank · unranked

86 citations

Lukas M. Simon, Maria Mircea, Nikola S. Mueller, Fabian Joachim Theis, Gökçen Eraslan

Linear Geometric ICA: Fundamentals and Algorithms

Neural Computation(2003)10.1162/089976603762552979

N/A

3.2DataRank · unranked

69 citations

Andreas Jung, Carlos G. Puntonet, Elmar W. Lang, Fabian Joachim Theis

Blind signal separation into groups of dependent signals using joint block diagonalization

University of Regensburg Publication Server (University of Regensburg)(2005)10.1109/iscas.2005.1465976

N/A

3.2DataRank · unranked

59 citations

Fabian Joachim Theis

Inferring population dynamics from single-cell RNA-sequencing time series data

Nature Biotechnology(2019)10.1038/s41587-019-0088-0

N/A

3.2DataRank · unranked

124 citations

Anna K. Fiedler, Eric M. Kernfeld, Ryan M. J. Genga, Aimée Bastidas-Ponce, Mostafa Bakhti +6 more

Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate

The EMBO Journal(2018)10.15252/embj.201899518

N/A

3.2DataRank · unranked

108 citations

Wolfram H. Gruhn, Ricardo Ramnarine, Edward S. Allgeyer, Florian Buettner, Carsten Marr +7 more

Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas

Molecular Metabolism(2017)10.1016/j.molmet.2017.06.021

N/A

3.2DataRank · unranked

116 citations

Fabian Joachim Theis, Heiko Lickert, Anika Böttcher, Sophie Tritschler

anndata: Access and store annotated data matrices

Journal of Open Source Software(2024)10.21105/joss.04371

Top 7%

3.1DataRank

Top 7%203 citations

Sergei Rybakov, Fabian Joachim Theis, Philipp Angerer, Francesca Finotello, Valeh Valiollah Pour Amiri

Post-surgical adhesions are triggered by calcium-dependent membrane bridges between mesothelial surfaces

Nature Communications(2020)10.1038/s41467-020-16893-3

N/A

3.1DataRank · unranked

80 citations

Tim Koopmans, Pushkar Ramesh, Simon Christ, Maximilian Strunz, Juliane Wannemacher +12 more

Conditional out-of-distribution generation for unpaired data using transfer VAE

Bioinformatics(2020)10.1093/bioinformatics/btaa800

N/A

3.1DataRank · unranked

139 citations

Mohsen Naghipourfar, Fabian Joachim Theis, Francesca Finotello, Florian Wolf, Mohammad Lotfollahi

Origin and function of activated fibroblast states during zebrafish heart regeneration

Nature Genetics(2022)10.1038/s41588-022-01129-5

N/A

3.1DataRank · unranked

143 citations

Sara Lelek, Bastiaan Spanjaard, Hadil El-Sammak, Mariana Guedes Simões, Janita Mintcheva +8 more

miTALOS v2: Analyzing Tissue Specific microRNA Function

PLOS ONE(2016)10.1371/journal.pone.0151771

Top 7%

3.1DataRank

Top 7%77 citations

Fabian Joachim Theis, Nikola S. Mueller, Martin Preusse

Distinct molecular profiles of skull bone marrow in health and neurological disorders

Cell(2023)10.1016/j.cell.2023.07.009

N/A

3.1DataRank · unranked

166 citations

Louis Benedikt Kuemmerle, Robert Perneczky, Benjamin Förstera, Selin Ulukaya, Mayar Ali +90 more

Squidpy: a scalable framework for spatial single cell analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.19.431994

N/A

3.0DataRank · unranked

71 citations

Hannah Spitzer, Michal Klein, David S. Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle +8 more

Multi-omic signature of body weight change: results from a population-based cohort study

BMC Medicine(2015)10.1186/s12916-015-0282-y

N/A

2.9DataRank · unranked

81 citations

Susanne Vogt, Ferdinand Stückler, Jan Krumsiek, Jörg Bartel, Tim Kacprowski +27 more

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

EMBO Molecular Medicine(2021)10.15252/emmm.202012871

Top 7%

2.9DataRank

Top 7%105 citations

Lukas M. Simon, Gabriela Leuschner, Meshal Ansari, Philipp E. Geyer, Ilias Angelidis +18 more

Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting

PLoS ONE(2014)10.1371/journal.pone.0101814

N/A

2.9DataRank · unranked

39 citations

Stefanie Eyerich, Bettina Knapp, Francesca Nasorri, Claudia Scarponi, Martina Mattii +16 more

miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs

RNA(2011)10.1261/rna.2474511

N/A

2.9DataRank · unranked

61 citations

Martin Preusse, Carsten Marr, Fabian Joachim Theis, Andreas Kowarsch

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Histochemistry and Cell Biology(2023)10.1007/s00418-023-02209-1

N/A

2.8DataRank · unranked

123 citations

Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva Maxfield Brown +64 more

Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns

Nature Communications(2019)10.1038/s41467-019-10461-0

N/A

2.8DataRank · unranked

151 citations

Gökçen Eraslan, Christian M. Page, Jari Lahti, Marius Lahti-Pulkkinen, Esa Hämäläinen +233 more

fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy

Bioinformatics(2017)10.1093/bioinformatics/btx107

N/A

2.8DataRank · unranked

79 citations

Michael Schwarzfischer, Dirk Loeffler, Sotiris Dimopoulos, Simon Hastreiter, Carsten Marr +2 more

Hypothalamic miR-103 Protects from Hyperphagic Obesity in Mice

Journal of Neuroscience(2014)10.1523/jneurosci.4251-13.2014

N/A

2.8DataRank · unranked

82 citations

K. Hajdukiewicz, J. Reymann, J. Beneke, R. Czajkowski, L. C. Roth +23 more

An integrated cell atlas of the human lung in health and disease

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.10.483747

Top 8%

2.8DataRank

Top 8%97 citations

Daniel Strobl, Luke Zappia, Nikolay S. Markov, Laure-Emmanuelle Zaragosi, Marie-Jeanne Arguel +77 more

SpatialData: an open and universal data framework for spatial omics

Nature Methods(2024)10.1038/s41592-024-02212-x

N/A

2.7DataRank · unranked

173 citations

Giovanni Palla, Kevin A. Yamauchi, Valeh Valiollah Pour Amiri, Elyas Heidari, Tim Treis +17 more

Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts

Aging(2014)10.18632/aging.100698

N/A

2.7DataRank · unranked

77 citations

Faiza Kalfalah, Ana-Maria Florea, Steffen Sass, Fabian Kruse, Vera Rieder +13 more

A novel molecular disease classifier for psoriasis and eczema

Experimental Dermatology(2016)10.1111/exd.13077

N/A

2.7DataRank · unranked

76 citations

Linda Krause, Felix Lauffer, Anne Atenhan, Jenny Thomas, Sebastian P. Stark +11 more

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

BMC Public Health(2020)10.1186/s12889-020-09164-9

N/A

2.6DataRank · unranked

65 citations

Elmar Saathoff, Michael Pritsch, Jessica Michelle Guggenbühl Noller, Inge Kroidl, Laura Olbrich +31 more

MicroRNAs coordinately regulate protein complexes

BMC Systems Biology(2011)10.1186/1752-0509-5-136

N/A

2.6DataRank · unranked

59 citations

Sabine Dietmann, Ulrike C Burk, Simone Brabletz, Dominik Lutter, Andreas Kowarsch +8 more

Soft Dimension Reduction for ICA by Joint Diagonalization on the Stiefel Manifold

Lecture Notes in Computer Science(2009)10.1007/978-3-642-00599-2_45

N/A

2.6DataRank · unranked

53 citations

Thomas P. Cason, P. -A. Absil, Thomas Cason, Pierre-Antoine Absil, Fabian Joachim Theis

Clinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group

Leukemia(2016)10.1038/leu.2016.185

N/A

2.6DataRank · unranked

40 citations

A Corbacioglu, V I Gaidzik, P Paschka, D Weber, M Heuser +42 more

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

Bioinformatics(2012)10.1093/bioinformatics/bts385

N/A

2.6DataRank · unranked

67 citations

Fabian Joachim Theis, Florian Buettner

Epithelial cell plasticity drives endoderm formation during gastrulation

Nature Cell Biology(2021)10.1038/s41556-021-00694-x

N/A

2.5DataRank · unranked

111 citations

Silvia Schirge, Ingo Burtscher, Maren Büttner, Michael Sterr, Dapeng Yang +10 more

Spatial transcriptomics landscape of lesions from non-communicable inflammatory skin diseases

Nature Communications(2022)10.1038/s41467-022-35319-w

Top 9%

2.5DataRank

Top 9%89 citations

M. Mubarak, A. Farnoud, E. Scala, Nils Kurzen, A. C. Pilz +18 more

Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/208819

N/A

2.5DataRank · unranked

48 citations

Fiona Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens +4 more

Multimodal single cell data integration challenge: results and lessons learned

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.11.487796

N/A

2.5DataRank · unranked

79 citations

Malte D. Luecken, Daniel B. Burkhardt, Robrecht Cannoodt, Pia Rautenstrauch, Anna Laddach +13 more

Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

Nature Cell Biology(2021)10.1038/s41556-020-00617-2

N/A

2.4DataRank · unranked

79 citations

Maren Büttner, Sophie Tritschler, Michael Sterr, Alexandra Aliluev, Lena Oppenländer +13 more

Toll-like receptor 7/8 agonists stimulate plasmacytoid dendritic cells to initiate TH17-deviated acute contact dermatitis in human subjects

Journal of Allergy and Clinical Immunology(2018)10.1016/j.jaci.2017.07.045

N/A

2.4DataRank · unranked

57 citations

Felix Lauffer, Linda Krause, Jenny Thomas, Anne Atenhan, Regina Franz +16 more

Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression

Biophysical Journal(2012)10.1016/j.bpj.2011.11.4000

N/A

2.4DataRank · unranked

74 citations

Fabian Joachim Theis, Carsten Marr, Michael Strasser

Metabolomics screening identifies reducedL-carnitine to be associated with progressive emphysema

Clinical Science(2016)10.1042/cs20150438

N/A

2.4DataRank · unranked

42 citations

Jörg Bartel, Korbinian Ballweg, Stefanie Günter, Cornelia Prehn, Jan Krumsiek +6 more

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Nature Methods(2023)10.1038/s41592-023-01994-w

N/A

2.3DataRank · unranked

123 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

Spatial proteomics in three-dimensional intact specimens

Cell(2022)10.1016/j.cell.2022.11.021

N/A

2.3DataRank · unranked

124 citations

Andreas-David Brunner, Furkan Ozturk, Saketh Kapoor, Zhouyi Rong, Hongcheng Mai +27 more

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

PLOS Computational Biology(2020)10.1371/journal.pcbi.1007616

N/A

2.3DataRank · unranked

88 citations

Till F. M. Andlauer, Jade Martins, Stella Iurato, Brigitte Kühnel, Melanie Waldenberger +26 more

scvi-tools: a library for deep probabilistic analysis of single-cell omics data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.28.441833

N/A

2.3DataRank · unranked

72 citations

Romain Lopez, Galen Xing, Pierre Boyeau, Katherine Wu, Michael Jayasuriya +20 more

CellRank 2: unified fate mapping in multiview single-cell data

Nature Methods(2024)10.1038/s41592-024-02303-9

N/A

2.2DataRank · unranked

190 citations

Marius Lange, Michal Klein, Paul A. Reyfman, Fabian Joachim Theis, Herbert B. Schiller

Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More

Lecture Notes in Computer Science(2014)10.1007/978-3-319-12982-2_5

N/A

2.2DataRank · unranked

61 citations

Fabian Joachim Theis, Christiane Fuchs, Fabian Fröhlich

IL‐17C amplifies epithelial inflammation in human psoriasis and atopic eczema

Journal of the European Academy of Dermatology and Venereology(2020)10.1111/jdv.16126

N/A

2.1DataRank · unranked

51 citations

V. Baghin, W. Kempf, M. Absmaier‐Kijak, M. Morelli, S. Madonna +20 more

Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts

European Respiratory Journal(2024)10.1183/13993003.01326-2023

N/A

2.1DataRank · unranked

105 citations

Arunima Sengupta, Sara Asgharpour, Meshal Ansari, Jeanine C. Pestoni, Paulina Ogar +30 more

Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

Molecular Cancer Research(2018)10.1158/1541-7786.mcr-17-0334

N/A

2.1DataRank · unranked

42 citations

Manuel Rodríguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst +20 more

Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia

Pain(2013)10.1016/j.pain.2013.07.005

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2.1DataRank · unranked

48 citations

Christiane Fuchs, Hye-Sook Ahn, Elizabeth K. Joseph, Jörg Isensee, Fabian Joachim Theis +9 more

Integration and querying of multimodal single-cell data with PoE-VAE

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.16.484643

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2.1DataRank · unranked

64 citations

Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi +2 more

An integrated transcriptomic cell atlas of human neural organoids

Nature(2024)10.1038/s41586-024-08172-8

Top 10%

2.1DataRank

Top 10%127 citations

Leander Dony, Jonas Simon Fleck, Artur Szalata, Katelyn X. Li, Irena Slišković +21 more

Diffusion pseudotime robustly reconstructs lineage branching

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/041384

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2.0DataRank · unranked

55 citations

Maren Büttner, Francesca Finotello, Florian Buettner, Fabian Joachim Theis, Florian Wolf +1 more

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Nature Communications(2021)10.1038/s41467-021-24467-0

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2.0DataRank · unranked

43 citations

Nichelle I. Winters, Mei-i Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann +67 more

Population-level integration of single-cell datasets enables multi-scale analysis across samples

Nature Methods(2023)10.1038/s41592-023-02035-2

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2.0DataRank · unranked

108 citations

Soroor Hediyeh-zadeh, Amir Ali Moinfar, Marco Wagenstetter, Luke Zappia, Mohammad Lotfollahi +2 more

On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms

Signal Processing(2006)10.1016/j.sigpro.2005.05.032

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2.0DataRank · unranked

25 citations

Gonzalo A. García, Fabian Joachim Theis

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

BMC Systems Biology(2017)10.1186/s12918-017-0433-1

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2.0DataRank · unranked

56 citations

Sabine Hug, Kathrin Hatz, Linus Görlitz, Christiane Fuchs, Fabian Joachim Theis +1 more

Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation

Science Advances(2021)10.1126/sciadv.abe4497

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1.9DataRank · unranked

92 citations

Elena Brivio, Alice Santambrogio, Carlo De Donno, Aron Kos, Miriam Peters +27 more

Metabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality

Psychoneuroendocrinology(2013)10.1016/j.psyneuen.2012.11.014

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1.9DataRank · unranked

49 citations

Rebecca T. Emeny, Jan Krumsiek, Maria E. Lacruz, Karoline Lukaschek, Sibylle Häfner +15 more

Learning interpretable cellular responses to complex perturbations in high-throughput screens

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.14.439903

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1.9DataRank · unranked

52 citations

Anna Klimovskaia Susmelj, Carlo De Donno, Yuge Ji, Ignacio Ibarra Del Río, Francesca Finotello +5 more

The Sox17‐mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development

genesis(2011)10.1002/dvg.20829

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1.8DataRank · unranked

44 citations

Wenke Barkey, Michael Schwarzfischer, Fabian Joachim Theis, Heiko Lickert, Ingo Burtscher

High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling

Mathematical Biosciences(2013)10.1016/j.mbs.2013.04.002

N/A

1.8DataRank · unranked

71 citations

J. Bachmann, Sabine Hug, Andreas Raue, Christiane Fuchs, Jasmin Bachmann +3 more

Opposing effects of allogrooming on disease transmission in ant societies

Philosophical Transactions of the Royal Society B: Biological Sciences(2015)10.1098/rstb.2014.0108

N/A

1.8DataRank · unranked

59 citations

Line V. Ugelvig, Carsten Marr, Sylvia Cremer, Fabian Joachim Theis

CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

PLOS ONE(2016)10.1371/journal.pone.0146732

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1.8DataRank · unranked

44 citations

Fabian Fröhlich, Andreas Raue, Fabian Joachim Theis, Christiane Fuchs, Atefeh Kazeroonian

Graph representation learning for single-cell biology

Current Opinion in Systems Biology(2021)10.1016/j.coisb.2021.05.008

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1.7DataRank · unranked

53 citations

David S. Fischer, Stephan Günnemann, Fabian Joachim Theis, Leon Hetzel

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics

PLoS Computational Biology(2014)10.1371/journal.pcbi.1003686

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1.7DataRank · unranked

58 citations

Christine Hasenauer, Tim Hucho, Fabian Joachim Theis, Christiane Fuchs

Deep learning does not outperform classical machine learning for cell-type annotation

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/653907

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1.7DataRank · unranked

36 citations

Maren Büttner, Niry Andriamanga, Fabian Joachim Theis, Niklas D. Köhler

Toward modeling metabolic state from single-cell transcriptomics

Molecular Metabolism(2022)10.1016/j.molmet.2021.101396

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1.7DataRank · unranked

66 citations

David S. Fischer, Fabian Joachim Theis, Karin Hrovatin

Lactation is associated with altered metabolomic signatures in women with gestational diabetes

Diabetologia(2016)10.1007/s00125-016-4055-8

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1.7DataRank · unranked

24 citations

Andreas Beyerlein, Alida Kindt, Jan Krumsiek, Ferdinand Stückler, Michaela Rossbauer +15 more

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Nature Methods(2025)10.1038/s41592-025-02617-2

Top 13%

1.7DataRank

Top 13%97 citations

Louis Benedikt Kuemmerle, Christoffer Mattsson-Langseth, Sebastian Tismeyer, Christophe Avenel, Kuan-lin Huang +16 more

The future of rapid and automated single-cell data analysis using reference mapping

Cell(2024)10.1016/j.cell.2024.03.009

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1.7DataRank · unranked

71 citations

Yuhan Hao, Fabian Joachim Theis, Rahul Satija, Mohammad Lotfollahi

Primary cilia and SHH signaling impairments in human and mouse models of Parkinson’s disease

Nature Communications(2022)10.1038/s41467-022-32229-9

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1.7DataRank · unranked

69 citations

Malte D. Luecken, Dietrich Trümbach, Sina Hembach, Kristina M. Niedermeier, Nicole Wenck +19 more

Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease

Cell Reports(2023)10.1016/j.celrep.2023.112525

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1.7DataRank · unranked

74 citations

Kevin Baßler, Wataru Fujii, Christina Nalkurthi, Anna Christina Schaar, Lorenzo Bonaguro +50 more

Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva

Journal of Proteome Research(2014)10.1021/pr501130a

N/A

1.6DataRank · unranked

44 citations

Gabi Kastenmüller, Dennis O. Mook-Kanamori, Noha A. Yousri, Fabian Joachim Theis, Karsten Suhre +4 more

CellRank for directed single-cell fate mapping

Research Square(2020)10.21203/rs.3.rs-94819/v1

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1.6DataRank · unranked

35 citations

Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti +7 more

Artificial Neural Networks and Machine Learning – ICANN 2019: Text and Time Series

Lecture Notes in Computer Science(2019)10.1007/978-3-030-30490-4

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1.6DataRank · unranked

37 citations

Věra Kůrková, Pavel Karpov, Fabian Joachim Theis, Theis, Fabian, Igor V. Tetko

Assessment of batch-correction methods for scRNA-seq data with a new test metric

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/200345

N/A

1.6DataRank · unranked

23 citations

Zhichao Miao, Francesca Finotello, Sarah A. Teichmann, Fabian Joachim Theis, Florian Wolf +1 more

Spatiotemporal Blind Source Separation Using Double-Sided Approximate Joint Diagonalization

University of Regensburg Publication Server (University of Regensburg)(2005)10.5281/zenodo.39285

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1.6DataRank · unranked

26 citations

Peter J. Gruber, Ingo R. Keck, Anke Meyer‐Baese, Elmar W. Lang, Fabian Joachim Theis

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

Nature Metabolism(2023)10.1038/s42255-023-00876-x

Top 13%

1.6DataRank

Top 13%85 citations

Aimée Bastidas-Ponce, Mostafa Bakhti, Luke Zappia, Maren Büttner, Ciro Salinno +6 more

Transformers and genome language models

Nature Machine Intelligence(2025)10.1038/s42256-025-01007-9

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1.6DataRank · unranked

79 citations

Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi +4 more

Synthetic enforcement of STING signaling in cancer cells appropriates the immune microenvironment for checkpoint inhibitor therapy

Science Advances(2023)10.1126/sciadv.add8564

N/A

1.6DataRank · unranked

48 citations

Sophie E. Isay, Zsuzsanna Kurgyis, Patricia Loll, Mohammed H. Mosa, Malte D. Luecken +9 more

Nicheformer: a foundation model for single-cell and spatial omics

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.15.589472

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1.6DataRank · unranked

40 citations

Alejandro Tejada-Lapuerta, Giovanni Palla, Robert M. Gutgesell, Lennard Halle, Mariia Minaeva +6 more

Increasing Neural Stem Cell Division Asymmetry and Quiescence Are Predicted to Contribute to the Age-Related Decline in Neurogenesis

Cell Reports(2018)10.1016/j.celrep.2018.11.088

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1.6DataRank · unranked

50 citations

Filippo Calzolari, Christiane Fuchs, Fabian Joachim Theis, Jovica Ninkovic, Carsten Marr +2 more

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary

PLoS Computational Biology(2009)10.1371/journal.pcbi.1000569

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1.6DataRank · unranked

40 citations

Florian Blöchl, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian Joachim Theis +1 more

EpiScanpy: integrated single-cell epigenomic analysis

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/648097

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1.6DataRank · unranked

30 citations

David S. Fischer, Fabian Joachim Theis, Maria Colomé‐Tatché, Maria Lucia Richter, Anna Danese

Median-based clustering for underdetermined blind signal processing

IEEE Signal Processing Letters(2006)10.1109/lsp.2005.861590

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1.6DataRank · unranked

29 citations

Fabian Joachim Theis, Carlos G. Puntonet, Elmar W. Lang

MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

Nature Computational Science(2024)10.1038/s43588-024-00627-2

Top 13%

1.5DataRank

Top 13%68 citations

Filipe Menezes, Sabrina Benassou, Kieran Didi, André Santos Dias Mourão, Radosław Kitel +10 more

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

arXiv (Cornell University)(2022)10.48550/arxiv.2204.13545

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1.5DataRank · unranked

43 citations

Simon Böhm, Niki Kilbertus, Stephan Günnemann, Mohammad Nader Lotfollahi, Fabian Joachim Theis +1 more

Peptide serum markers in islet autoantibody-positive children

Diabetologia(2016)10.1007/s00125-016-4150-x

N/A

1.5DataRank · unranked

37 citations

Michael Laimighofer, Peter Achenbach, Andreas Beyerlein, Tonia de las Heras Gala, Jan Krumsiek +4 more

TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury

Nature Neuroscience(2022)10.1038/s41593-022-01199-y

N/A

1.5DataRank · unranked

59 citations

Klara Tereza Novoselc, Saskia Hutten, Sofia Kalpazidou, Christina Koupourtidou, Rico Schieweck +22 more

The global gene expression profile of the secondary transition during pancreatic development

Mechanisms of Development(2016)10.1016/j.mod.2015.11.004

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1.5DataRank · unranked

37 citations

Nikola S. Mueller, Silvia Engert, Michael Sterr, Ingo Burtscher, Aurelia Raducanu +6 more

ICA over Finite Fields

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_80

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1.5DataRank · unranked

16 citations

Fabian Joachim Theis, Peter J. Gruber, Harold W. Gutch

A Vine-copula Based Adaptive MCMC Sampler for Efficient Inference of Dynamical Systems

Bayesian Analysis(2013)10.1214/13-ba801

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1.5DataRank · unranked

31 citations

Claudia Czado, Sabine Hug, Fabian Joachim Theis, Daniel Schmidl

Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/705244

N/A

1.5DataRank · unranked

34 citations

Lukas M. Simon, Meshal Ansari, Laura F. Mattner, Ilias Angelidis, Christoph H. Mayr +22 more

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.12.503709

N/A

1.4DataRank · unranked

33 citations

Herbert B. Schiller, Mohammad Lotfollahi, Dominik Klein, Michal Klein, Aaron Streets +3 more

Parameter estimation for dynamical systems with discrete events and logical operations

Bioinformatics(2016)10.1093/bioinformatics/btw764

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1.4DataRank · unranked

42 citations

Fabian Joachim Theis, J. O. Rädler, Christiane Fuchs, Fabian Fröhlich

Asc-1 regulates white versus beige adipocyte fate in a subcutaneous stromal cell population

Nature Communications(2021)10.1038/s41467-021-21826-9

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1.4DataRank · unranked

35 citations

Irem Altun, Ruth Karlina, Viktorian Miok, Tobias Wiedemann, David S. Fischer +16 more

A modular framework for gene set analysis integrating multilevel omics data

Nucleic Acids Research(2013)10.1093/nar/gkt752

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1.4DataRank · unranked

31 citations

Florian Buettner, Nikola S. Mueller, Fabian Joachim Theis, Steffen Sass

The Heckscher–Ohlin model and the network structure of international trade

International Review of Economics & Finance(2011)10.1016/j.iref.2010.11.003

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1.4DataRank · unranked

52 citations

Florian Blöchl, Tilman Brück, Fabian Joachim Theis, Thushyanthan Baskaran

Scanpy for analysis of large-scale single-cell gene expression data

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/174029

N/A

1.4DataRank · unranked

21 citations

Philipp Angerer, Fabian Joachim Theis, Francesca Finotello

Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data

Bioinformatics(2014)10.1093/bioinformatics/btu134

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1.4DataRank · unranked

25 citations

Victoria Moignard, Berthold Göttgens, Fabian Joachim Theis, Florian Buettner

Knowledge-based gene expression classification via matrix factorization

Bioinformatics(2008)10.1093/bioinformatics/btn245

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1.3DataRank · unranked

39 citations

P. Knollmüller, M. Stetter, Dominik Lutter, Ana Maria Tomé, Fabian Joachim Theis +4 more

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis

Genome Biology(2019)10.1186/s13059-019-1748-6

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1.3DataRank · unranked

28 citations

Florian Opperer, Can Sönmezer, Dmitry Shaposhnikov, Steffen Sass, Christian Krendl +5 more

Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells

Cell Systems(2016)10.1016/j.cels.2016.11.001

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1.3DataRank · unranked

34 citations

Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam Filipczyk, Oliver Hilsenbeck +4 more

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.21.940650

N/A

1.3DataRank · unranked

24 citations

Fabian Joachim Theis, Meshal Ansari

miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm

Development(2014)10.1242/dev.104232

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1.3DataRank · unranked

24 citations

Dominik Lutter, Ingo Burtscher, Lena Uetzmann, Fabian Joachim Theis, Heiko Lickert +1 more

A field guide to cultivating computational biology

PLOS Biology(2021)10.1371/journal.pbio.3001419

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1.3DataRank · unranked

22 citations

Casey S. Greene, Piero Carninci, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +11 more

Separation of Uncorrelated Stationary time series using Autocovariance Matrices

Journal of Time Series Analysis(2015)10.1111/jtsa.12159

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1.3DataRank · unranked

55 citations

Katrin Illner, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Fabian Joachim Theis +2 more

SpatialData: an open and universal data framework for spatial omics

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.05.539647

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1.3DataRank · unranked

32 citations

Giovanni Palla, Kevin A. Yamauchi, Valeh Valiollah Pour Amiri, Elyas Heidari, Tim Treis +9 more

Early Identification of Bronchopulmonary Dysplasia Using Novel Biomarkers by Proteomic Screening

American Journal of Respiratory and Critical Care Medicine(2018)10.1164/rccm.201706-1218le

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1.3DataRank · unranked

29 citations

Steffen Sass, Harald Ehrhardt, Daphne S. Mous, Robbert J. Rottier, Prajakta Oak +9 more

To Transformers and Beyond: Large Language Models for the Genome

arXiv (Cornell University)(2023)10.48550/arxiv.2311.07621

N/A

1.2DataRank · unranked

32 citations

Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi +4 more

Sharpening of expression domains induced by transcription and microRNA regulationwithin a spatio-temporal model of mid-hindbrain boundary formation

BMC Systems Biology(2013)10.1186/1752-0509-7-48

N/A

1.2DataRank · unranked

22 citations

Yen-Kar Ng, Christiane Fuchs, Dominik Lutter, Dietrich Trümbach, Wolfgang Wurst +4 more

Learning interpretable latent autoencoder representations with annotations of feature sets

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.02.401182

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1.2DataRank · unranked

24 citations

Mohammad Lotfollahi, Fabian Joachim Theis, Francesca Finotello, Sergei Rybakov

Towards multimodal foundation models in molecular cell biology

Nature(2025)10.1038/s41586-025-08710-y

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1.2DataRank · unranked

88 citations

Alejandro Tejada-Lapuerta, Maria Brbić, Julio Saez-Rodriguez, Simona Cristea, Hani Goodarzi +4 more

Generalizing RNA velocity to transient cell states through dynamical modeling

Nature Biotechnology(2020)10.1038/s41587-020-0591-3

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1.2DataRank · unranked

3016 citations

Marius Lange, Stefan Peidli, Francesca Finotello, Fabian Joachim Theis, Volker Bergen

Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

npj Systems Biology and Applications(2018)10.1038/s41540-018-0079-7

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1.2DataRank · unranked

33 citations

Anita Reiser, Laura Fink, Daniel Woschée, Thomas Ligon, Fabian Joachim Theis +3 more

Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage

Nature Communications(2022)10.1038/s41467-022-31054-4

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1.1DataRank · unranked

30 citations

Andrea Musumeci, Christopher Sie, Ezgi Dursun, Elena Winheim, Johannes Bagnoli +11 more

Nicheformer: A Foundation Model for Single-Cell and Spatial Omics

SSRN Electronic Journal(2024)10.2139/ssrn.4803291

N/A

1.1DataRank · unranked

31 citations

Alejandro Tejada-Lapuerta, Giovanni Palla, Lennard Halle, Mariia Minaeva, Larsen Vornholz +6 more

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs

BMC Bioinformatics(2010)10.1186/1471-2105-11-522

N/A

1.1DataRank · unranked

24 citations

Florian Blöchl, Volker Stümpflen, Fabian Joachim Theis, Mara L. Hartsperger

Independent Subspace Analysis Is Unique, Given Irreducibility

Lecture notes in computer science(2007)10.1007/978-3-540-74494-8_7

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1.1DataRank · unranked

14 citations

Fabian Joachim Theis, Harold W. Gutch

Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation

Frontiers in Immunology(2022)10.3389/fimmu.2022.917232

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1.1DataRank · unranked

50 citations

Wataru Fujii, Theodore S. Kapellos, Erika Dudkin, Nico Reusch, Ari Horne +44 more

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus

RNA Biology(2012)10.4161/rna.22081

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1.1DataRank · unranked

22 citations

Sebastian J. Kopetzky, Ignaty Leshchiner, Ivan Kondofersky, Fabian Joachim Theis, Dmitrij Frishman +2 more

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells

Genome Biology(2019)10.1186/s13059-019-1663-x

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1.1DataRank · unranked

1780 citations

Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky +4 more

Deep Learning-based Propensity Scores for Confounding Control in Comparative Effectiveness Research

Epidemiology(2021)10.1097/ede.0000000000001338

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1.1DataRank · unranked

35 citations

Tim Becker, Jessica Davies, Fabian Schmich, Dominik Rüttinger, Fabian Joachim Theis +3 more

ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data

Engineering Applications of Artificial Intelligence(2009)10.1016/j.engappai.2008.11.010

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1.1DataRank · unranked

13 citations

Simon Foo, Fabian Joachim Theis, Peter J. Gruber, Anke Meyer‐Baese, Simon Y. Foo

Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

Nature Communications(2021)10.1038/s41467-021-24730-4

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1.1DataRank · unranked

40 citations

Meshal Ansari, Karolin I. Wagner, Sebastian Jarosch, Yiqi Huang, Christoph H. Mayr +28 more

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

Proceedings of the National Academy of Sciences(2014)10.1073/pnas.1311647111

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1.1DataRank · unranked

57 citations

Christiane Fuchs, Andreas Roller, Fabian Joachim Theis, Kevin A. Janes, Sameer S. Bajikar

Eleven grand challenges in single-cell data science

Genome Biology(2020)10.1186/s13059-020-1926-6

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1.1DataRank · unranked

1396 citations

Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson +49 more

A computational model to predict severity of atopic eczema from 30 serum proteins

Journal of Allergy and Clinical Immunology(2016)10.1016/j.jaci.2016.04.018

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1.1DataRank · unranked

15 citations

Vagkan Mourantchanian, Knut Brockow, Fabian Joachim Theis, Bettina Knapp, Nikola S. Mueller +4 more

MISATO - Machine learning dataset of protein-ligand complexes for structure-based drug discovery

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.24.542082

Top 19%

1.1DataRank

Top 19%23 citations

Filipe Menezes, Sabrina Benassou, Stefan Kesselheim, Marie Piraud, Fabian Joachim Theis +4 more

From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study

PubMed(2010)10.2390/biecoll-jib-2010-151

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1.1DataRank · unranked

14 citations

Fabian Joachim Theis, Steffen Klamt, Raimo Franke

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Nature Biotechnology(2015)10.1038/nbt.3102

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1.1DataRank · unranked

1296 citations

Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian Joachim Theis +6 more

Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1

PLOS ONE(2015)10.1371/journal.pone.0135284

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1.1DataRank · unranked

24 citations

Steffen Sass, Nikola S. Mueller, Stefan Krebs, Stefan Bauersachs, Sebastian Kaiser +6 more

Deep learning: new computational modelling techniques for genomics

Nature Reviews Genetics(2019)10.1038/s41576-019-0122-6

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1.1DataRank · unranked

1199 citations

Žiga Avsec, Julia-Stefanie Frick, Fabian Joachim Theis, Gökçen Eraslan

Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses

Human Molecular Genetics(2014)10.1093/hmg/ddu301

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1.1DataRank · unranked

28 citations

So-Youn Shin, Jan Krumsiek, Thomas Illig, Fabian Joachim Theis, Matti Uusitupa +9 more

Single-cell RNA-seq denoising using a deep count autoencoder

Nature Communications(2019)10.1038/s41467-018-07931-2

N/A

1.1DataRank · unranked

1140 citations

Lukas M. Simon, Maria Mircea, Nikola S. Mueller, Fabian Joachim Theis, Gökçen Eraslan

Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data

Lecture Notes in Computer Science(2008)10.1007/978-3-540-69384-0_79

N/A

1.1DataRank · unranked

39 citations

J. M. Górriz, M. Gómez-Río, A. Romero, R. Chaves, A. Lassl +9 more

Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning

Nucleic Acids Research(2020)10.1093/nar/gkaa926

N/A

1.1DataRank · unranked

27 citations

Lisa Rausch, Thomas Brocker, Jan Kranich, Fabian Joachim Theis, Nikolaos‐Kosmas Chlis

Sfaira accelerates data and model reuse in single cell genomics

Genome Biology(2021)10.1186/s13059-021-02452-6

N/A

1.1DataRank · unranked

34 citations

Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos +5 more

Considerations for building and using integrated single-cell atlases

Nature Methods(2024)10.1038/s41592-024-02532-y

N/A

1.0DataRank · unranked

52 citations

Avi Srivastava, Vladimir A. Shitov, Graham Heimberg, Maiia Schulman, Amanda J. Oliver +10 more

scCODA: A Bayesian model for compositional single-cell data analysis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.14.422688

N/A

1.0DataRank · unranked

16 citations

Johannes Ostner, Christian L. Müller, Fabian Joachim Theis, Benjamin Schubert, Maren Büttner

Establishment of a high-resolution 3D modeling system for studying pancreatic epithelial cell biology in vitro

Molecular Metabolism(2019)10.1016/j.molmet.2019.09.005

N/A

1.0DataRank · unranked

28 citations

Katharina Scheibner, Sophie Tritschler, Aimée Bastidas-Ponce, Marta Tarquis-Medina, Fabian Joachim Theis +2 more

Best practices for single-cell analysis across modalities

Nature Reviews Genetics(2023)10.1038/s41576-023-00586-w

N/A

1.0DataRank · unranked

1013 citations

Anna Christina Schaar, Christopher Lance, Anastasia Litinetskaya, Felix Drost, Luke Zappia +34 more

Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis

BMC Bioinformatics(2008)10.1186/1471-2105-9-100

N/A

1.0DataRank · unranked

23 citations

Peter Ugocsai, Margot Grandl, Evelyn Orso, Elmar W. Lang, Gerd Schmitz +4 more

Second-Order Source Separation Based on Prior Knowledge Realized in a Graph Model

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_54

N/A

1.0DataRank · unranked

17 citations

Andreas Kowarsch, Fabian Joachim Theis, Florian Blöchl

A cellular census of human lungs identifies novel cell states in health and in asthma

Nature Medicine(2019)10.1038/s41591-019-0468-5

N/A

1.0DataRank · unranked

956 citations

Gozde Kar, Marijn Berg, Orestes A. Carpaij, Krzysztof Polanski, Lukas M. Simon +31 more

Model-based branching point detection in single-cell data by K-branches clustering

Bioinformatics(2017)10.1093/bioinformatics/btx325

N/A

1.0DataRank · unranked

17 citations

Francesca Finotello, Fabian Joachim Theis, Florian Wolf, Nikolaos K. Chlis

GIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice

Nature Metabolism(2025)10.1038/s42255-025-01294-x

N/A

1.0DataRank · unranked

38 citations

Ahmed Khalil, Arkadiusz Liskiewicz, Gandhari Maity-Kumar, Aaron Novikoff, Gerald Grandl +20 more

Single-cell reference mapping to construct and extend cell-type hierarchies

NAR Genomics and Bioinformatics(2023)10.1093/nargab/lqad070

Top 20%

1.0DataRank

Top 20%38 citations

Mohammad Lotfollahi, Daniel Strobl, Avi Srivastava, Marcel J.T. Reinders, Fabian Joachim Theis +2 more

Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap

Neuro-Oncology(2025)10.1093/neuonc/noaf113

Top 20%

1.0DataRank

Top 20%55 citations

Sergio Marco Salas, Erik Samuelsson, Mariia Minaeva, Ignacio Ibarra, Marco Grillo +9 more

Swarm Learning for decentralized and confidential clinical machine learning

Nature(2021)10.1038/s41586-021-03583-3

N/A

1.0DataRank · unranked

821 citations

Hartmut Schultze, Krishnaprasad Lingadahalli Shastry, Sathyanarayanan Manamohan, Saikat Mukherjee, Vishesh Garg +183 more

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

Nature Communications(2020)10.1038/s41467-020-17358-3

N/A

0.988DataRank · unranked

725 citations

Lukas M. Simon, Meshal Ansari, Jaymin J. Kathiriya, Ilias Angelidis, Christoph H. Mayr +25 more

Diffusion maps for high-dimensional single-cell analysis of differentiation data

Bioinformatics(2015)10.1093/bioinformatics/btv325

N/A

0.985DataRank · unranked

709 citations

Florian Buettner, Fabian Joachim Theis, Laleh Haghverdi

Design and power analysis for multi-sample single cell genomics experiments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.01.019851

N/A

0.984DataRank · unranked

15 citations

Cristiana Cruceanu, Anika Böttcher, Heiko Lickert, Elisabeth B. Binder, Fabian Joachim Theis +2 more

destiny : diffusion maps for large-scale single-cell data in R

Bioinformatics(2015)10.1093/bioinformatics/btv715

N/A

0.981DataRank · unranked

689 citations

Laleh Haghverdi, Maren Büttner, Fabian Joachim Theis, Carsten Marr, Florian Buettner +1 more

scGen predicts single-cell perturbation responses

Nature Methods(2019)10.1038/s41592-019-0494-8

N/A

0.975DataRank · unranked

666 citations

Francesca Finotello, Fabian Joachim Theis, Mohammad Lotfollahi

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

Nature Communications(2019)10.1038/s41467-019-08831-9

N/A

0.975DataRank · unranked

664 citations

Lukas M. Simon, Isis E. Fernandez, Maximilian Strunz, Christoph H. Mayr, Flavia R. Greiffo +11 more

Mapping single-cell data to reference atlases by transfer learning

Nature Biotechnology(2021)10.1038/s41587-021-01001-7

N/A

0.962DataRank · unranked

610 citations

Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter +9 more

Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex

Nature Communications(2024)10.1038/s41467-024-46625-w

N/A

0.955DataRank · unranked

42 citations

Veronika Schwarz, Meshal Ansari, Simon Frerich, Judith Fischer-Sternjak, Riccardo Bocchi +11 more

Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints

BMC Systems Biology(2016)10.1186/s12918-016-0319-7

N/A

0.954DataRank · unranked

31 citations

Sebastian Raeth, Fabian Joachim Theis, Angelika Hausser, Christiane Fuchs, Angelika Haußer +1 more

Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib

Frontiers in Physiology(2017)10.3389/fphys.2017.00775

N/A

0.954DataRank · unranked

31 citations

Andreas Raue, Xiaoyun Huang, Joep Vanlier, Anja Jünger, Sebastian Bohl +26 more

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Cell(2021)10.1016/j.cell.2021.11.033

N/A

0.943DataRank · unranked

538 citations

Oliver Dietrich, Tommaso Mari, Saskia von Stillfried, Ignacio Ibarra Del Río, Mirja Mittermaier +61 more

A test metric for assessing single-cell RNA-seq batch correction

Nature Methods(2018)10.1038/s41592-018-0254-1

N/A

0.940DataRank · unranked

527 citations

Zhichao Miao, Francesca Finotello, Sarah A. Teichmann, Fabian Joachim Theis, Maren Büttner

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

Science(2018)10.1126/science.aaq1723

N/A

0.938DataRank · unranked

518 citations

Jordi Solana, Francesca Finotello, Salah Ayoub, Aristotelis Misios, Petar Glažar +5 more

Defining and benchmarking open problems in single-cell analysis

Nature Biotechnology(2025)10.1038/s41587-025-02694-w

N/A

0.937DataRank · unranked

29 citations

Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt, Nikolay S. Markov, Luke Zappia +48 more

Population-level integration of single-cell datasets enables multi-scale analysis across samples

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.28.517803

Top 22%

0.932DataRank

Top 22%27 citations

Soroor Hediyeh-zadeh, Marco Wagenstetter, Amir Ali Moinfar, Luke Zappia, Mohammad Lotfollahi +2 more

Hypergraphs and Cellular Networks

PLoS Computational Biology(2009)10.1371/journal.pcbi.1000385

N/A

0.926DataRank · unranked

480 citations

Utz-Uwe Haus, Utz‐Uwe Haus, Fabian Joachim Theis, Steffen Klamt

Postnonlinear Overcomplete Blind Source Separation Using Sparse Sources

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_91

N/A

0.925DataRank · unranked

13 citations

Shun-ichi Amari, Шун-ичи Амари, Fabian Joachim Theis

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

Cell Stem Cell(2015)10.1016/j.stem.2015.04.004

N/A

0.924DataRank · unranked

474 citations

David G. Kent, Florian Buettner, Mona Shehata, Iain C. Macaulay, Fernando J. Calero-Nieto +14 more

Optimal distance metrics for single-cell RNA-seq populations

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.26.572833

N/A

0.908DataRank · unranked

19 citations

Tessa D. Green, Stefan Peidli, Mojtaba Bahrami, Meiqi Liu, Luke Zappia +4 more

Decoding the regulatory network of early blood development from single-cell gene expression measurements

Nature Biotechnology(2015)10.1038/nbt.3154

N/A

0.906DataRank · unranked

419 citations

Steven Woodhouse, Laleh Haghverdi, Andrew J. Lilly, Yosuke Tanaka, Adam C. Wilkinson +13 more

Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation

Nature Neuroscience(2013)10.1038/nn.3371

N/A

0.905DataRank · unranked

416 citations

Martin Krüger, Felix Buggenthin, Julia Schwausch, Jovica Ninkovic, Hans Clevers +9 more

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Immunity(2020)10.1016/j.immuni.2020.11.017

N/A

0.901DataRank · unranked

405 citations

Neha Mishra, Florian Tran, Thomas Bahmer, Lena Best, Johanna I. Blase +169 more

Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers

PLoS Genetics(2011)10.1371/journal.pgen.1002215

N/A

0.899DataRank · unranked

400 citations

Janina S. Ried, Zhonghao Yu, Jan Krumsiek, Christian Gieger, Cornelia Prehn +16 more

A BaSiC tool for background and shading correction of optical microscopy images

Nature Communications(2017)10.1038/ncomms14836

N/A

0.898DataRank · unranked

396 citations

Kurt Thorn, Oliver Hilsenbeck, Lichao Wang, Fabian Joachim Theis, Carsten Marr +3 more

Robust Sparse Component Analysis Based on a Generalized Hough Transform

EURASIP Journal on Advances in Signal Processing(2006)10.1155/2007/52105

N/A

0.893DataRank · unranked

10 citations

Pando G. Georgiev, Andrzej Cichocki, Fabian Joachim Theis

Probe set selection for targeted spatial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.16.504115

N/A

0.890DataRank · unranked

24 citations

Malte D. Luecken, Alexandra B. Firsova, Lisa Barros de Andrade e Sousa, Lena Straßer, Lukas Heumos +14 more

Epigenetic germline inheritance of diet-induced obesity and insulin resistance

Nature Genetics(2016)10.1038/ng.3527

N/A

0.886DataRank · unranked

366 citations

Steffen Sass, Moya Wu, Daniela Dyckhoff, Matthias Tschöp, Fabian Joachim Theis +5 more

scCODA is a Bayesian model for compositional single-cell data analysis

Nature Communications(2021)10.1038/s41467-021-27150-6

N/A

0.882DataRank · unranked

356 citations

Johannes Ostner, Christian L. Müller, Fabian Joachim Theis, Benjamin Schubert, Maren Büttner

Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_58

N/A

0.881DataRank · unranked

10 citations

Nikola S. Mueller, Claudia Plant, Christian Böhm, Fabian Joachim Theis

Sparse Component Analysis and Blind Source Separation of Underdetermined Mixtures

IEEE Transactions on Neural Networks(2005)10.1109/tnn.2005.849840

N/A

0.880DataRank · unranked

352 citations

Pando G. Georgiev, Fabian Joachim Theis, Andrzej Cichocki

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

BMC Systems Biology(2011)10.1186/1752-0509-5-21

N/A

0.873DataRank · unranked

337 citations

Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian Joachim Theis, Jan Krumsiek

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

Cytometry Part A(2019)10.1002/cyto.a.23863

N/A

0.870DataRank · unranked

330 citations

Jonathan Roth, James W. Fairman, Tim Becker, Kyle W. Karhohs, Matthieu Broisin +7 more

Reconstructing cell cycle and disease progression using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/081364

N/A

0.869DataRank · unranked

21 citations

Niklas D. Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees +4 more

Is the humoral immunity dispensable for the pathogenesis of psoriasis?

Journal of the European Academy of Dermatology and Venereology(2018)10.1111/jdv.15101

N/A

0.867DataRank · unranked

15 citations

M. Küpper, V. Baghin, Jenny Thomas, Richa Batra, Manja Jargosch +8 more

Label-free cell cycle analysis for high-throughput imaging flow cytometry

Nature Communications(2016)10.1038/ncomms10256

N/A

0.863DataRank · unranked

315 citations

Holger Hennig, Huw D. Summers, Fabian Joachim Theis, Joana Cerveira, James O. Patterson +5 more

Early life adversity shapes social subordination and cell type–specific transcriptomic patterning in the ventral hippocampus

Science Advances(2023)10.1126/sciadv.adj3793

N/A

0.863DataRank · unranked

38 citations

Juan Pablo López, Joeri Bordes, Carlo De Donno, Julien Dine, Elena Brivio +14 more

How to build the virtual cell with artificial intelligence: Priorities and opportunities

Cell(2024)10.1016/j.cell.2024.11.015

N/A

0.861DataRank · unranked

310 citations

Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed +37 more

anndata: Annotated data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.16.473007

N/A

0.859DataRank · unranked

306 citations

Sergei Rybakov, Fabian Joachim Theis, Philipp Angerer, Francesca Finotello, Valeh Valiollah Pour Amiri

SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins

RNA Biology(2015)10.1080/15476286.2015.1068496

N/A

0.859DataRank · unranked

15 citations

Carsten Marr, Sita Saunders, Daniel Maticzka, Heiko Lickert, Rolf Backofen +3 more

MicroRNA Loss Enhances Learning and Memory in Mice

The Journal of Neuroscience(2010)10.1523/jneurosci.3030-10.2010

N/A

0.858DataRank · unranked

304 citations

Anna Kiryk, Martin Novak, Marina Herwerth, Jan Rodriguez Parkitna, Marcin Wawrzyniak +13 more

Reconstructing cell cycle and disease progression using deep learning

Nature Communications(2017)10.1038/s41467-017-00623-3

N/A

0.858DataRank · unranked

304 citations

Niklas D. Köhler, Thomas Blasi, Andrew Filby, Anne E. Carpenter, Paul Rees +3 more

Gender-specific pathway differences in the human serum metabolome

Metabolomics(2015)10.1007/s11306-015-0829-0

N/A

0.857DataRank · unranked

301 citations

Kirstin Mittelstrass, Kieu Trinh Do, Ferdinand Stückler, Cameron D. Palmer, Jerzy Adamski +17 more

RNA velocity—current challenges and future perspectives

Molecular Systems Biology(2021)10.15252/msb.202110282

N/A

0.857DataRank · unranked

301 citations

Ruslan A Soldatov, Peter V. Kharchenko, Fabian Joachim Theis, Ruslan Soldatov, Volker Bergen

Multi‐scale modeling of GMP differentiation based on single‐cell genealogies

The FEBS Journal(2012)10.1111/j.1742-4658.2012.08664.x

N/A

0.854DataRank · unranked

21 citations

Michael Strasser, Michael Schwarzfischer, Oliver Hilsenbeck, Fabian Joachim Theis, Carsten Marr

FedNorm: Modality-Based Normalization in Federated Learning for Multi-Modal Liver Segmentation

arXiv (Cornell University)(2022)10.48550/arxiv.2205.11096

N/A

0.852DataRank · unranked

16 citations

Annette Peters, Christopher L. Schlett, Fabian Bamberg, Fabian Joachim Theis, Daniel Rueckert +3 more

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

Nature Cell Biology(2013)10.1038/ncb2709

N/A

0.845DataRank · unranked

279 citations

Iain C. Macaulay, Gemma Swiers, Florian Buettner, Judith Schütte, Fernando J. Calero-Nieto +10 more

Concepts and limitations for learning developmental trajectories from single cell genomics

Development(2019)10.1242/dev.170506

N/A

0.839DataRank · unranked

268 citations

Maren Büttner, David S. Fischer, Marius Lange, Volker Bergen, Heiko Lickert +2 more

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

Bioinformatics(2015)10.1093/bioinformatics/btv405

N/A

0.836DataRank · unranked

263 citations

B. Steiert, T. Maiwald, H. Hass, C. Tönsing, L. Adlung +26 more

Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies

PLoS Biology(2012)10.1371/journal.pbio.1001300

N/A

0.834DataRank · unranked

258 citations

Meghan L. Vyleta, Fabian Joachim Theis, Miriam Stock, Simon Tragust, Martina Klatt +5 more

Single cells make big data: New challenges and opportunities in transcriptomics

Current Opinion in Systems Biology(2017)10.1016/j.coisb.2017.07.004

N/A

0.833DataRank · unranked

257 citations

Sophie Tritschler, Francesca Finotello, Fabian Joachim Theis, Lukas M. Simon, Florian Wolf +2 more

Predicting cellular responses to complex perturbations in high‐throughput screens

Molecular Systems Biology(2023)10.15252/msb.202211517

N/A

0.832DataRank · unranked

256 citations

Anna Klimovskaia Susmelj, Carlo De Donno, Leon Hetzel, Yuge Ji, Ignacio Ibarra Del Río +16 more

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

BMC Systems Biology(2009)10.1186/1752-0509-3-98

N/A

0.831DataRank · unranked

254 citations

Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian Joachim Theis +1 more

scSLAM-seq reveals core features of transcription dynamics in single cells

Nature(2019)10.1038/s41586-019-1369-y

N/A

0.825DataRank · unranked

244 citations

Marisa A. P. Baptista, Tobias Krammer, Thomas Hennig, Marius Lange, Panagiota Arampatzi +7 more

Second-Order Blind Source Separation Based on Multi-dimensional Autocovariances

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_92

N/A

0.822DataRank · unranked

17 citations

Elmar W. Lang, Anke Meyer‐Baese, Fabian Joachim Theis

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies

Science(2022)10.1126/science.abo1984

N/A

0.818DataRank · unranked

233 citations

Eric L. Lindberg, Henrike Maatz, Antonio M. A. Miranda, Anissa Viveiros, Nikolay Shvetsov +50 more

IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling

Nature Communications(2019)10.1038/s41467-018-08152-3

N/A

0.817DataRank · unranked

231 citations

Hatice Zeynep Nenseth, Su Qu, Omer F. Kuzu, Turid Frahnow, Lukas M. Simon +12 more

Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma

Nature Biomedical Engineering(2024)10.1038/s41551-024-01273-9

N/A

0.807DataRank · unranked

35 citations

Mulham Najajreh, David P. Cook, Carlo H. Maurer, Stefanie Bärthel, Hendrik A. Messal +44 more

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

Nature(2016)10.1038/nature18320

N/A

0.805DataRank · unranked

213 citations

Michael Schwarzfischer, Dirk Loeffler, Konstantinos D. Kokkaliaris, Oliver Hilsenbeck, Nadine Moritz +18 more

Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

PLoS Genetics(2012)10.1371/journal.pgen.1003005

N/A

0.803DataRank · unranked

211 citations

Karsten Suhre, Anne M. Evans, Matthew W. Mitchell, Robert P. Mohney, Michael V. Milburn +10 more

Prospective identification of hematopoietic lineage choice by deep learning

Nature Methods(2017)10.1038/nmeth.4182

N/A

0.802DataRank · unranked

209 citations

Florian Buettner, Philipp S. Hoppe, Max Endele, Manuel Kroiss, Michael Strasser +8 more

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

Metabolomics(2018)10.1007/s11306-018-1420-2

N/A

0.798DataRank · unranked

203 citations

Simone Wahl, Johannes Raffler, Sophie Molnos, Michael Laimighofer, Jerzy Adamski +12 more

The discovAIR project: a roadmap towards the Human Lung Cell Atlas

European Respiratory Journal(2022)10.1183/13993003.02057-2021

Top 25%

0.797DataRank

Top 25%26 citations

Laure-Emmanuelle Zaragosi, Elo Madissoon, Avi Srivastava, Alexandra B. Firsova, Elena De Domenico +36 more

Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes

Cell Stem Cell(2015)10.1016/j.stem.2015.05.014

N/A

0.793DataRank · unranked

197 citations

Sébastien Gillotin, Bernd Sutor, Daniela Drechsel, Martin Irmler, Helle F. Jørgensen +7 more

Modeling intercellular communication in tissues using spatial graphs of cells

Nature Biotechnology(2022)10.1038/s41587-022-01467-z

N/A

0.792DataRank · unranked

196 citations

Anna Christina Schaar, Fabian Joachim Theis, David S. Fischer

Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation

IFAC Proceedings Volumes(2014)10.3182/20140824-6-za-1003.02298

N/A

0.791DataRank · unranked

13 citations

Fabian Joachim Theis, Christiane Fuchs, Atefeh Kazeroonian

Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone

Nature Neuroscience(2015)10.1038/nn.3963

N/A

0.785DataRank · unranked

187 citations

Julia Michel, Emily Violette Baumgart, Fabian Joachim Theis, Magdalena Götz, Jovica Ninkovic +1 more

Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain

Science(2015)10.1126/science.aaa2729

N/A

0.785DataRank · unranked

186 citations

Rosario Sanchez-Gonzalez, Rossella Di Giaimo, Emily Violette Baumgart, Fabian Joachim Theis, Magdalena Götz +3 more

Mature neutrophils and a NF-κB-to-IFN transition determine the unifying disease recovery dynamics in COVID-19

Cell Reports Medicine(2022)10.1016/j.xcrm.2022.100652

N/A

0.782DataRank · unranked

24 citations

Emma Kooistra, Melanie Nuesch-Germano, Tal Pecht, Neta Milman, Nico Reusch +22 more

Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation

Cell Reports(2015)10.1016/j.celrep.2014.12.032

N/A

0.779DataRank · unranked

179 citations

Elena Panzilius, Harald S. Bartsch, Martin Irmler, Johannes Beckers, Vijayalakshmi Kari +15 more

Mapping lineage-traced cells across time points with moslin

Genome Biology(2024)10.1186/s13059-024-03422-4

N/A

0.761DataRank · unranked

24 citations

Zoe Piran, Michal Klein, Bastiaan Spanjaard, Dominik Klein, Jan Philipp Junker +3 more

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.19.613754

N/A

0.758DataRank · unranked

20 citations

Laura D. Martens, Alexander Karollus, Trevor Manz, Jason D. Buenrostro, Fabian Joachim Theis +2 more

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice

Life Science Alliance(2020)10.26508/lsa.202000924

N/A

0.750DataRank · unranked

22 citations

Dominik Lutter, Viktorian Miok, David S. Fischer, Irem Altun, Theresa Schöttl +20 more

Quantification of regenerative potential in primary human mammary epithelial cells

Development(2015)10.1242/dev.123554

N/A

0.749DataRank · unranked

146 citations

Haruko Miura, Lisa K. Meixner, Martin Irmler, Uwe J. Kloos, Benjamin Hirschi +11 more

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis

BMC Bioinformatics(2013)10.1186/1471-2105-14-s10-s7

N/A

0.747DataRank · unranked

15 citations

Christiane Fuchs, Fabian Joachim Theis, Sabrina Hock

LifeTime and improving European healthcare through cell-based interceptive medicine

Nature(2020)10.1038/s41586-020-2715-9

N/A

0.747DataRank · unranked

144 citations

Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela G. Bertero +178 more

Machine learning integrative approaches to advance computational immunology

Genome Medicine(2024)10.1186/s13073-024-01350-3

N/A

0.745DataRank · unranked

28 citations

Fabian Joachim Theis, Fabiola Curion

Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation

Cell Death & Disease(2023)10.1038/s41419-023-05855-4

N/A

0.741DataRank · unranked

25 citations

Christoph Ogris, Amnah Othman, Pia Erdoesi, Wolfgang Schmidt-Heck, Ina Biermayer +18 more

Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study

Brain(2022)10.1093/brain/awac224

N/A

0.737DataRank · unranked

135 citations

Mathilde Ripart, Kirstie Whitaker, Felice D’Arco, Kshitij Mankad, Andrew A. Chen +72 more

netReg: network-regularized linear models for biological association studies

Bioinformatics(2017)10.1093/bioinformatics/btx677

N/A

0.724DataRank · unranked

26 citations

Christiane Fuchs, Nikola S. Mueller, Fabian Joachim Theis, Simon Dirmeier

Blind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images

Biophysical Journal(2009)10.1016/j.bpj.2008.10.068

N/A

0.723DataRank · unranked

123 citations

Mišo Mitkovski, Frank Kirchhoff, Erwin Neher, Fabian Joachim Theis, André Zeug +1 more

Predicting antigen specificity of single T cells based on TCR CDR 3 regions

Molecular Systems Biology(2020)10.15252/msb.20199416

N/A

0.722DataRank · unranked

122 citations

Yihan Wu, Benjamin Schubert, Fabian Joachim Theis, David S. Fischer

Complex Principal Component and Correlation Structure of 16 Yeast Genomic Variables

Molecular Biology and Evolution(2011)10.1093/molbev/msr077

N/A

0.721DataRank · unranked

10 citations

N. Latif, P. Wong, D Frishman, Fabian Joachim Theis

Vertex centralities in input-output networks reveal the structure of modern economies

Physical Review E(2011)10.1103/physreve.83.046127

N/A

0.721DataRank · unranked

121 citations

Fabian Joachim Theis, Fernando Vega-Redondo, Eric O’N. Fisher, Fernando Vega‐Redondo, Eric O'n. Fisher +1 more

Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images

Lecture Notes in Computer Science(2022)10.1007/978-3-031-16434-7_67

N/A

0.718DataRank · unranked

16 citations

Olle G. Holmberg, Hannah Spitzer, Johannes B Schiefelbein, Ben Asani, Michael Hafner +3 more

The quinone‐reactive Ni/Fe‐hydrogenase of Wolinella succinogenes

European Journal of Biochemistry(1992)10.1111/j.1432-1033.1992.tb16905.x

N/A

0.717DataRank · unranked

118 citations

Viktor GEISLER, Ruth LENGER, Torsten Krafft, Falk FAHRENHOLZ, Elzbieta KOJRO +10 more

Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study

BMC Medicine(2013)10.1186/1741-7015-11-60

N/A

0.717DataRank · unranked

118 citations

Christina Holzapfel, Xiao Dong, Erik Bader, Zhonghao Yu, Cornelia Prehn +19 more

Synaptotagmin-13 orchestrates pancreatic endocrine cell egression and islet morphogenesis

Nature Communications(2022)10.1038/s41467-022-31862-8

N/A

0.708DataRank · unranked

25 citations

Aimée Bastidas-Ponce, Sophie Tritschler, Oliver Czarnecki, Marta Tarquis-Medina, Eva Nedvedova +14 more

AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients

International Journal of Oncology(2017)10.3892/ijo.2017.3834

N/A

0.704DataRank · unranked

108 citations

Petros Christopoulos, Thomas Muley, Arne Warth, Ursula Klingmueller, Michael Thomas +7 more

Author response: The Human Cell Atlas

(2017)10.7554/elife.27041.011

Top 29%

0.700DataRank

Top 29%14 citations

Sarah A. Teichmann, Matthew E. Hurles, Ido Amit, Kerstin Lindblad‐Toh, Bernd Bodenmiller +60 more

MIPS: curated databases and comprehensive secondary data resources in 2010

Nucleic Acids Research(2010)10.1093/nar/gkq1157

Top 29%

0.697DataRank

Top 29%103 citations

Andreas Ruepp, Thomas Rattei, Mathias Walter, Dmitrij Frishman, Karsten Suhre +11 more

Causal machine learning for single-cell genomics

Nature Genetics(2025)10.1038/s41588-025-02124-2

N/A

0.696DataRank · unranked

27 citations

Stefan Bauer, Meshal Ansari, Yoshua Bengio, Fabian Joachim Theis, Paul A. Bertin +1 more

Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways

Mucosal Immunology(2016)10.1038/mi.2015.110

N/A

0.695DataRank · unranked

102 citations

A M Chaker, R Effner, M Ulrich, F Guerth, G Piontek +19 more

Second Order Subspace Analysis and Simple Decompositions

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_46

N/A

0.691DataRank · unranked

7 citations

Takanori Maehara, Fabian Joachim Theis, Harold W. Gutch

Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01806-0

N/A

0.691DataRank · unranked

29 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

Nature Communications(2023)10.1038/s41467-023-43429-2

N/A

0.689DataRank · unranked

21 citations

Katharina Essig, Sylvia Herter, Marina Bacac, Fabian Joachim Theis, Elke Glasmacher +4 more

From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study

Journal of Integrative Bioinformatics(2010)10.1515/jib-2010-151

N/A

0.680DataRank · unranked

8 citations

Fabian Joachim Theis, Steffen Klamt, Raimo Franke

Data-Driven Modelling of Biological Multi-Scale Processes

Journal of Coupled Systems and Multiscale Dynamics(2015)10.1166/jcsmd.2015.1069

N/A

0.680DataRank · unranked

40 citations

Nick Jagiella, Sabrina Hross, Fabian Joachim Theis, Christiane Fuchs

Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma

Allergy(2013)10.1111/all.12110

N/A

0.673DataRank · unranked

88 citations

H. Baurecht, Nita G. Forouhi, J. J. Heinrich, Maja Jagodic, Albertine J. Oldehinkel +25 more

RAMONA: a Web application for gene set analysis on multilevel omics data

Bioinformatics(2014)10.1093/bioinformatics/btu610

N/A

0.668DataRank · unranked

8 citations

Florian Buettner, Nikola S. Mueller, Fabian Joachim Theis, Steffen Sass

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data

Bioinformatics(2020)10.1093/bioinformatics/btaa198

N/A

0.667DataRank · unranked

14 citations

David S. Fischer, Fabian Joachim Theis, Antonio Scialdone, Carsten Marr, Philipp Angerer

Statistical single cell multi-omics integration

Current Opinion in Systems Biology(2018)10.1016/j.coisb.2018.01.003

N/A

0.666DataRank · unranked

84 citations

Maria Colomé‐Tatché, Fabian Joachim Theis

An integrated transcriptomic cell atlas of human neural organoids

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.05.561097

N/A

0.665DataRank · unranked

23 citations

Leander Dony, Jonas Simon Fleck, Artur Szalata, Katelyn X. Li, Irena Slišković +10 more

A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease

Nature Communications(2023)10.1038/s41467-023-42862-7

N/A

0.662DataRank · unranked

22 citations

Constantin Stautner, Duc Tung Vu, Alexander Heinz, Martin Regensburger, Ozge Karayel +20 more

Modeling fragment counts improves single-cell ATAC-seq analysis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.04.490536

N/A

0.661DataRank · unranked

14 citations

David S. Fischer, Vicente A. Yépez, Fabian Joachim Theis, Julia-Stefanie Frick, Laura D. Martens

Ketamine exerts its sustained antidepressant effects via cell-type-specific regulation of Kcnq2

Neuron(2022)10.1016/j.neuron.2022.05.001

N/A

0.659DataRank · unranked

80 citations

Malte D. Luecken, Elena Brivio, Stoyo Karamihalev, Aron Kos, Carlo De Donno +29 more

Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

Cancer Research(2011)10.1158/0008-5472.can-10-2987

N/A

0.657DataRank · unranked

79 citations

Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue +13 more

Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway

Nature Communications(2017)10.1038/s41467-017-01525-0

N/A

0.654DataRank · unranked

77 citations

Toma Keser, Annika Wahl, Antti Hassinen, Lin Liu, Genadij Razdorov +26 more

CellFlow enables generative single-cell phenotype modeling with flow matching

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.11.648220

N/A

0.653DataRank · unranked

28 citations

Jonas Simon Fleck, Daniil Bobrovskiy, Lea Zimmermann, Sören Becker, Alessandro Palma +14 more

Quantitative characterization of cell niches in spatial atlases

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.21.581428

N/A

0.653DataRank · unranked

18 citations

Irene Bonafonte-Pardàs, Adib Miraki Feriz, Adam Boxall, Eneritz Agirre, Fani Memi +8 more

Hierarchical Extraction of Independent Subspaces of Unknown Dimensions

Lecture Notes in Computer Science(2009)10.1007/978-3-642-00599-2_33

N/A

0.650DataRank · unranked

11 citations

Harold W. Gutch, Fabian Joachim Theis, Peter J. Gruber

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Nature Genetics(2025)10.1038/s41588-025-02182-6

Top 31%

0.649DataRank

Top 31%30 citations

Lennard Halle, Soroor Hediyeh-zadeh, Merel Kuijs, Rya Riedweg, Umut Kilik +29 more

Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology

Frontiers in Immunology(2019)10.3389/fimmu.2019.01515

N/A

0.641DataRank · unranked

71 citations

Christoph Heuser, Gustavo P. de Almeida, Fabian Joachim Theis, Christina E. Zielinski, Subarna Palit

Uniqueness of linear factorizations into independent subspaces

Journal of Multivariate Analysis(2012)10.1016/j.jmva.2012.05.019

N/A

0.641DataRank · unranked

8 citations

Fabian Joachim Theis, Harold W. Gutch

Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine

Genome Biology(2009)10.1186/gb-2009-10-7-r81

N/A

0.639DataRank · unranked

70 citations

William HJ Norton, Dietrich Trümbach, Annemarie H. Meijer, Jovica Ninkovic, Stefanie Topp +10 more

A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes

Genes & Immunity(2012)10.1038/gene.2012.36

N/A

0.635DataRank · unranked

68 citations

J Lempainen, Melissa E. Garcia, M Bunk, Daniela Bezdan, Anette-Gabriele Ziegler +10 more

Aldh1b1 expression defines progenitor cells in the adult pancreas and is required for Kras-induced pancreatic cancer

Proceedings of the National Academy of Sciences(2019)10.1073/pnas.1901075116

N/A

0.635DataRank · unranked

68 citations

Ioannis Serafimidis, Sara Iwaszkiewicz, Mathias Lesche, Susanne Reinhardt, Nora Bölicke +10 more

The Nature and Perception of Fluctuations in Human Musical Rhythms

PLoS ONE(2011)10.1371/journal.pone.0026457

N/A

0.635DataRank · unranked

68 citations

Ragnar Fleischmann, Anneke Fredebohm, York Hagmayer, Jan Nagler, Annette Witt +4 more

Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis

Science Translational Medicine(2023)10.1126/scitranslmed.adh0908

N/A

0.624DataRank · unranked

63 citations

Janine Gote-Schniering, Diana Porras-Gonzalez, Lin Yang, Laurens J. De Sadeleer, R. Christoph Jentzsch +27 more

Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models

Cell Systems(2017)10.1016/j.cels.2016.12.002

N/A

0.624DataRank · unranked

63 citations

Dennis Rickert, Fabian Joachim Theis, Christiane Fuchs, Nick Jagiella

miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging

Journal of Investigative Dermatology(2015)10.1038/jid.2014.422

N/A

0.624DataRank · unranked

63 citations

Julia Tigges, Steffen Sass, Alexandra Schütze, Ana-Maria Florea, Anke C. Fender +8 more

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.13.456196

Top 32%

0.622DataRank

Top 32%10 citations

Fabian Joachim Theis, Luke Zappia

Integrated multi-omics single cell atlas of the human retina

Research Square(2023)10.21203/rs.3.rs-3471275/v1

Top 32%

0.619DataRank

Top 32%19 citations

Jin Li, Jun Wang, Ignacio Ibarra, Xuesen Cheng, Malte D. Luecken +19 more

Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

Respiratory Research(2022)10.1186/s12931-022-02150-2

N/A

0.617DataRank · unranked

20 citations

Rashad M. Mahbub, Dennis K. Ninaber, Senani N. H. Rathnayake, Wim Timens, Maarten van den Berge +6 more

Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy

Gut(2016)10.1136/gutjnl-2015-310913

N/A

0.617DataRank · unranked

60 citations

Philipp Bruns, Nora A Behler, Ligong Chang, Anna Melissa Schlitter, Jing Cao +21 more

A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling

Gut(2015)10.1136/gutjnl-2014-307616

N/A

0.617DataRank · unranked

60 citations

Weiwei Wu, Tao Cheng, Anna Melissa Schlitter, Chengjia Qian, Philipp Bruns +18 more

First Results On Uniqueness Of Sparse Non-Negative Matrix Factorization

University of Regensburg Publication Server (University of Regensburg)(2005)10.5281/zenodo.39217

N/A

0.606DataRank · unranked

56 citations

Kurt Stadlthanner, Toshihisa Tanaka, Fabian Joachim Theis

Blind source separation and sparse component analysis of overcomplete mixtures

(2004)10.1109/icassp.2004.1327155

N/A

0.606DataRank · unranked

56 citations

Fabian Joachim Theis, Andrzej Cichocki, F. Georgiev

Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics

Science(2025)10.1126/science.adr8785

Top 33%

0.605DataRank

Top 33%29 citations

Nil Üresin, Sabrina Richter, Mikkel Bruhn Schuster, Despoina Barmpouri, Henrietta Holze +7 more

Defining and benchmarking open problems in single-cell analysis

Research Square(2024)10.21203/rs.3.rs-4181617/v1

N/A

0.603DataRank · unranked

17 citations

Scott Gigante, Daniel B. Burkhardt, Robrecht Cannoodt, Daniel Strobl, Nikolay S. Markov +45 more

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

PLOS Computational Biology(2020)10.1371/journal.pcbi.1007147

N/A

0.599DataRank · unranked

12 citations

Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian Joachim Theis +4 more

Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics

Lecture Notes in Computer Science(2015)10.1007/978-3-319-23401-4_6

N/A

0.599DataRank · unranked

10 citations

Carsten Marr, Fabian Joachim Theis, Christiane Fuchs, Carolin Loos

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin

Scientific Reports(2018)10.1038/s41598-018-19200-9

N/A

0.598DataRank · unranked

53 citations

Peter Huypens, Steffen Sass, Richa Batra, Louise Fritsche, Sara Brucker +11 more

Computational approaches for systems metabolomics

Current Opinion in Biotechnology(2016)10.1016/j.copbio.2016.04.009

N/A

0.596DataRank · unranked

52 citations

Jörg Bartel, Fabian Joachim Theis, Jan Krumsiek

Delineating the effective use of self-supervised learning in single-cell genomics

Nature Machine Intelligence(2024)10.1038/s42256-024-00934-3

N/A

0.595DataRank · unranked

21 citations

Mojtaba Bahrami, Yufan Xia, David S. Fischer, Fabian Joachim Theis, Till Richter

Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli

PLoS Computational Biology(2010)10.1371/journal.pcbi.1000836

N/A

0.595DataRank · unranked

15 citations

Fabian Joachim Theis, Larry S. Liebovitch, Marc-Thorsten Hütt, Marc‐Thorsten Hütt, Carsten Marr

Two membrane anchors of Wolinella succinogenes hydrogenase and their function in fumarate and polysulfide respiration

Archives of Microbiology(1998)10.1007/s002030050614

N/A

0.593DataRank · unranked

51 citations

Jörg Simon, Roland Groß, Fabian Joachim Theis, Achim Kröger, Roland Gross

CellRank for directed single-cell fate mapping

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.19.345983

N/A

0.593DataRank · unranked

51 citations

Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti +7 more

Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach

Allergy(2017)10.1111/all.13205

N/A

0.581DataRank · unranked

47 citations

J. Götschke, P. Nathan, F. Alessandrini, A. Tufman, R. Fischer +17 more

T cells modulate the microglial response to brain ischemia

eLife(2022)10.7554/elife.82031

N/A

0.578DataRank · unranked

46 citations

Alba Simats, Sophie Tritschler, Steffanie Heindl, Simon Besson-Girard, Gemma Llovera +9 more

Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2

Current Biology(2020)10.1016/j.cub.2020.01.027

N/A

0.561DataRank · unranked

41 citations

Subarna Palit, Jerónimo R. Miranda-Rodríguez, Aleksandar Janjic, Anika Böttcher, Heiko Lickert +5 more

Feature selection methods affect the performance of scRNA-seq data integration and querying

Nature Methods(2025)10.1038/s41592-025-02624-3

N/A

0.560DataRank · unranked

18 citations

Sabrina Richter, Ciro Ramírez-Suástegui, Raphael Kfuri-Rubens, Larsen Vornholz, Weixu Wang +5 more

Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk

Radiation and Environmental Biophysics(2018)10.1007/s00411-017-0728-z

N/A

0.557DataRank · unranked

40 citations

Frauke Neff, Savneet Kaur Bains, Scott Bright, Deborah Lord, Peter Reitmeir +29 more

Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks

Journal of Theoretical Biology(2010)10.1016/j.jtbi.2010.07.007

N/A

0.556DataRank · unranked

9 citations

Carsten Marr, Fabian Joachim Theis, Dominik M. Wittmann

Denoising using local projective subspace methods

Neurocomputing(2006)10.1016/j.neucom.2005.12.025

N/A

0.553DataRank · unranked

39 citations

Kurt Stadlthanner, Peter J. Gruber, Matthias Böhm, Fabian Joachim Theis, Elmar W. Lang +4 more

Impulse model-based differential expression analysis of time course sequencing data

Nucleic Acids Research(2018)10.1093/nar/gky675

N/A

0.553DataRank · unranked

39 citations

Fabian Joachim Theis, Nir Yosef, David S. Fischer

The neglected twin: Nummular eczema is a variant of atopic dermatitis with codominant TH2/TH17 immune response

Journal of Allergy and Clinical Immunology(2023)10.1016/j.jaci.2023.04.009

N/A

0.553DataRank · unranked

39 citations

Manja Jargosch, Nikola S. Mueller, Natalie Garzorz-Stark, Caroline Pilz, Felix Lauffer +9 more

A foundation model to predict and capture human cognition

Nature(2025)10.1038/s41586-025-09215-4

N/A

0.553DataRank · unranked

39 citations

Elif Akata, Matthias Bethge, Franziska Brändle, Fred Callaway, Julian Coda-Forno +36 more

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids

medRxiv(2020)10.1101/2020.01.21.20018358

N/A

0.552DataRank · unranked

9 citations

Lukas M. Simon, Gabriela Leuschner, Meshal Ansari, Philipp E. Geyer, Ilias Angelidis +16 more

On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation

IEEE Transactions on Biomedical Engineering(2006)10.1109/tbme.2005.863968

N/A

0.551DataRank · unranked

5 citations

Kurt Stadlthanner, H.-R. Kalbitzer, Matthias Böhm, Peter J. Gruber, Fabian Joachim Theis +6 more

Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data

(2021)10.1101/2021.09.01.458535

N/A

0.550DataRank · unranked

9 citations

Leander Dony, Harshita Agarwala, Fabian Joachim Theis, Mohammad Lotfollahi

Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells

Stem Cell Reports(2014)10.1016/j.stemcr.2014.05.010

N/A

0.550DataRank · unranked

38 citations

Susanne Wingert, Pangrazio De Giacomo, Nadine Haetscher, Maike Rehage, Boris Brill +5 more

Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer’s Disease

medRxiv(2023)10.1101/2023.10.25.23297558

N/A

0.548DataRank · unranked

17 citations

James M. Vicari, Christian Porras, Collin Spencer, Milos Pjanic, Xinyi Wang +30 more

Correction: Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

PLoS ONE(2013)10.1371/annotation/ea0193d8-1f7f-492a-b0b7-d877629fdcee

N/A

0.542DataRank · unranked

36 citations

Marcel Schilling, Julie Bachmann, Andrew Matteson, Max Schelker, Daniel Kaschek +8 more

Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies

Frontiers in Public Health(2021)10.3389/fpubh.2021.583377

N/A

0.538DataRank · unranked

35 citations

Tim Fuchs, Pavol Harar, Dennis Elbrächter, David S. Fischer, Julius Berner +6 more

Design and power analysis for multi-sample single cell genomics experiments

Research Square(2021)10.21203/rs.3.rs-331370/v1

N/A

0.535DataRank · unranked

6 citations

Cristiana Cruceanu, Anika Böttcher, Heiko Lickert, Elisabeth B. Binder, Fabian Joachim Theis +2 more

Polyploidisation pleiotropically buffers ageing in hepatocytes

Journal of Hepatology(2024)10.1016/j.jhep.2024.03.043

N/A

0.527DataRank · unranked

11 citations

Maren Büttner, Ioannis K. Deligiannis, Mateusz Strzelecki, Liwei Zhang, Fabian Joachim Theis +5 more

Scalable and universal prediction of cellular phenotypes enables in silico experiments

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.12.607533

N/A

0.527DataRank · unranked

12 citations

Alejandro Tejada-Lapuerta, Niklas A. Schmacke, Zihe Zheng, Xinyue Zhang, Simrah Khan +6 more

Exposure to naphthalene and β-pinene-derived secondary organic aerosol induced divergent changes in transcript levels of BEAS-2B cells

Environment International(2022)10.1016/j.envint.2022.107366

N/A

0.524DataRank · unranked

32 citations

Svenja Offer, Elena Hartner, Sebastiano Di Bucchianico, Christoph Bisig, Stefanie Bauer +48 more

Reporting electricity consumption is essential for sustainable AI

Nature Machine Intelligence(2023)10.1038/s42256-023-00750-1

N/A

0.524DataRank · unranked

32 citations

Marie Piraud, Achim Streit, Fabian Joachim Theis, Markus Götz, Charlotte Debus

Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells

Stem Cell Reports(2018)10.1016/j.stemcr.2018.04.019

N/A

0.524DataRank · unranked

32 citations

Stavroula Skylaki, Dirk Loeffler, Andreas Reimann, Oliver Hilsenbeck, Philipp S. Hoppe +6 more

hadge: a comprehensive pipeline for donor deconvolution in single-cell studies

Genome Biology(2024)10.1186/s13059-024-03249-z

N/A

0.523DataRank · unranked

9 citations

Xichen Wu, Lukas Heumos, Mylene Mariana Gonzales André, Lennard Halle, Matiss Ozols +9 more

Sfaira accelerates data and model reuse in single cell genomics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.16.419036

N/A

0.522DataRank · unranked

10 citations

Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Sophie Tritschler +4 more

A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion

Acta Diabetologica(2013)10.1007/s00592-013-0526-2

N/A

0.520DataRank · unranked

31 citations

Jan Krumsiek, Christiane Winkler, Fabian Joachim Theis, Anette-Gabriele Ziegler, Anette‐Gabriele Ziegler +1 more

Denoising using local ICA and kernel-PCA

University of Regensburg Publication Server (University of Regensburg)(2005)10.1109/ijcnn.2004.1380936

N/A

0.520DataRank · unranked

4 citations

Fabian Joachim Theis, Kurt Stadlthanner, Elmar W. Lang, Ana Maria Tomé, Ana Rita Teixeira +1 more

Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice

International Journal of Radiation Biology(2021)10.1080/09553002.2021.1876951

N/A

0.518DataRank · unranked

8 citations

Alexander Cecil, Cornelia Prehn, Gabriele Möller, Andreas Ohlmann, Gerhild Wildner +14 more

A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography

Photoacoustics(2020)10.1016/j.pacs.2020.100203

N/A

0.515DataRank · unranked

30 citations

Angelos Karlas, Nikolina-Alexia Fasoula, Michael Kallmayer, Hans-Henning Eckstein, Fabian Joachim Theis +5 more

Learning cell communication from spatial graphs of cells

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.11.451750

N/A

0.515DataRank · unranked

30 citations

Anna Christina Schaar, Fabian Joachim Theis, David S. Fischer

Model selection using limiting distributions of second-order blind source separation algorithms

Signal Processing(2015)10.1016/j.sigpro.2015.01.017

N/A

0.515DataRank · unranked

30 citations

Jari Miettinen, Christiane Fuchs, Sara Taskinen, Klaus Nordhausen, Hannu Oja +3 more

Determinants of expression of SARS‐CoV‐2 entry‐related genes in upper and lower airways

Allergy(2021)10.1111/all.15152

N/A

0.510DataRank · unranked

29 citations

Florian Massip, Cancan Qi, Maria Stella de Biase, Jos van Nijnatten, Elin T. G. Kersten +31 more

Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution

Nature Methods(2024)10.1038/s41592-024-02555-5

N/A

0.510DataRank · unranked

29 citations

Davide Castaldi, Marco Tullio Rigoli, Cristina Cheroni, Alessia Valenti, Sarah Stucchi +15 more

On the use of joint diagonalization in blind signal processing

University of Regensburg Publication Server (University of Regensburg)(2006)10.1109/iscas.2006.1693402

N/A

0.505DataRank · unranked

28 citations

Yasushi Inouye, Fabian Joachim Theis

Episode-Specific Differential Gene Expression of Peripheral Blood Mononuclear Cells in Rapid Cycling Supports Novel Treatment Approaches

Molecular Medicine(2008)10.2119/2008-00053.begemann

N/A

0.505DataRank · unranked

28 citations

Derya Sargin, Moritz J. Rossner, Claudia Bartels, Sven P. Wickert, Nike Stender +10 more

Small data methods in omics: the power of one

Nature Methods(2024)10.1038/s41592-024-02390-8

N/A

0.503DataRank · unranked

10 citations

Steven F. Grieco, Qing Nie, Fabian Joachim Theis, Xiangmin Xu, Kevin G. Johnston

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data

GigaScience(2018)10.1093/gigascience/giy070

N/A

0.500DataRank · unranked

27 citations

S Karg, A J Westermann, M Engel, A H A Elbehery, B Hense +10 more

Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression

Journal of Computational Biology(2016)10.1089/cmb.2015.0192

N/A

0.500DataRank · unranked

27 citations

Jan Krumsiek, Florian Buettner, Fabian Joachim Theis, Michael Laimighofer

Bayesian Independent Component Analysis Recovers Pathway Signatures from Blood Metabolomics Data

Journal of Proteome Research(2012)10.1021/pr300231n

N/A

0.500DataRank · unranked

27 citations

Karsten Suhre, Thomas Illig, Jerzy Adamski, Fabian Joachim Theis, Jan Krumsiek

Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns

Metabolomics(2016)10.1007/s11306-016-0983-z

N/A

0.500DataRank · unranked

27 citations

Jan Krumsiek, Wolfgang Otto, Stefan W. Röder, Tibor Kohajda, Michael Borte +7 more

Altered relaxation times in MRI indicate bronchopulmonary dysplasia

Thorax(2019)10.1136/thoraxjnl-2018-212384

N/A

0.500DataRank · unranked

27 citations

Birgit Ertl-Wagner, Harald Ehrhardt, Hannah Busen, Steffen Sass, Andreas Pomschar +10 more

Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma

Oncotarget(2017)10.18632/oncotarget.15283

N/A

0.500DataRank · unranked

27 citations

Elizabeth Varghese, Jennifer E. McCallum, Safa Mahgoub, Irfan Helmy, Sharon Varghese +6 more

Grassmann Clustering

University of Regensburg Publication Server (University of Regensburg)(2006)10.5281/zenodo.40099

N/A

0.500DataRank · unranked

27 citations

Fabian Joachim Theis, Peter J. Gruber

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps

Nature Methods(2023)10.1038/s41592-023-01894-z

N/A

0.494DataRank · unranked

26 citations

Scott M. Berry, Mark W. Donoghoe, Lucas Pelkmans, Fabian Joachim Theis, Hannah Spitzer

Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes

Science(2025)10.1126/science.adi8577

N/A

0.490DataRank · unranked

22 citations

Charlotte Nesbitt, Samuel A. Miller, Daniel B. Burkhardt, Inna Lipchina, Doris Fu +18 more

Vertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes

Molecular Metabolism(2021)10.1016/j.molmet.2021.101330

N/A

0.489DataRank · unranked

25 citations

Subarna Palit, Kerstin Stemmer, Tobias Greisle, Michael Sterr, Ciro Salinno +8 more

2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.13.632601

N/A

0.486DataRank · unranked

7 citations

Niklas Müller-Bötticher, Alexander Malt, Leyao Ma, Paul Kiessling, Paul Horn +14 more

FASTGenomics: An analytical ecosystem for single-cell RNA sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/272476

N/A

0.483DataRank · unranked

12 citations

Paweł Biernat, Matthias Becker, Kevin Baßler, Patrick Günther, Jenny Balfer +21 more

Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression

Cancer Cell(2025)10.1016/j.ccell.2025.06.004

N/A

0.474DataRank · unranked

16 citations

Hilary A. Kenny, Rahul Krishnan, Lucy Kelliher, Janna Heide, Leonhard Donle +23 more

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/335216

N/A

0.470DataRank · unranked

22 citations

Jonathan Roth, James W. Fairman, Tim Becker, Kyle W. Karhohs, Matthieu Broisin +7 more

Scaling cross-tissue single-cell annotation models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.07.561331

N/A

0.469DataRank · unranked

7 citations

David S. Fischer, Evan Biederstedt, Fabian Joachim Theis, Alexandra–Chloé Villani, Felix H. Fischer

cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics

Physical Biology(2017)10.1088/1478-3975/aa609a

N/A

0.464DataRank · unranked

21 citations

Florian Buettner, Carsten Marr, Fabian Joachim Theis, Michael Strasser, Thomas Blasi

Generative modeling and latent space arithmetics predict single-cell perturbation response across cell types, studies and species

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/478503

N/A

0.464DataRank · unranked

21 citations

Francesca Finotello, Fabian Joachim Theis, Mohammad Lotfollahi, Florian Wolf

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation

Scientific Reports(2019)10.1038/s41598-019-42750-5

N/A

0.464DataRank · unranked

21 citations

R. Lickert, R. Fuerst, Fabian Joachim Theis, Daniela Bezdan, Anette-Gabriele Ziegler +6 more

Single‐cell biology: what does the future hold?

Molecular Systems Biology(2023)10.15252/msb.202311799

N/A

0.464DataRank · unranked

21 citations

Jingyi Hou, M. Madan Babu, Prisca Liberali, Ido Amit, Bart Deplancke +7 more

Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression

Science Advances(2025)10.1126/sciadv.ady0080

N/A

0.459DataRank · unranked

19 citations

Sara Jiménez, Weston Elison, Luca Tucciarone, Abigail Howell, Gaowei Wang +18 more

Reconstructing disease dynamics for mechanistic insights and clinical benefit

Nature Communications(2023)10.1038/s41467-023-42354-8

N/A

0.458DataRank · unranked

6 citations

Neta Milman, Ayelet Alpert, Hannah Spitzer, Ben Asani, Evgeny Bakin +7 more

Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways

medRxiv(2020)10.1101/2020.08.31.20169946

N/A

0.457DataRank · unranked

20 citations

J. van Nijnatten, Elin T. G. Kersten, Nazanin Z. Kermani, Diana van Heemst, U-BIOPRED study group +42 more

Predicting cell morphological responses to perturbations using generative modeling

Nature Communications(2025)10.1038/s41467-024-55707-8

N/A

0.457DataRank · unranked

20 citations

Fabian Joachim Theis, Mohammad Lotfollahi, Alessandro Palma

MEMO: multi-experiment mixture model analysis of censored data

Bioinformatics(2016)10.1093/bioinformatics/btw190

N/A

0.456DataRank · unranked

7 citations

Christiane Fuchs, Stephanie Heinrich, Silke Hauf, Fabian Joachim Theis, Eva‐Maria Geissen +2 more

12 Grand Challenges in Single-Cell Data Science

(2019)10.7287/peerj.preprints.27885v3

N/A

0.449DataRank · unranked

7 citations

Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson +50 more

Unified fate mapping in multiview single-cell data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.19.549685

N/A

0.449DataRank · unranked

19 citations

Marius Lange, Michal Klein, Paul A. Reyfman, Fabian Joachim Theis, Herbert B. Schiller

Bayesian model selection validates a biokinetic model for zirconium processing in humans

BMC Systems Biology(2012)10.1186/1752-0509-6-95

N/A

0.449DataRank · unranked

19 citations

Sabine Hug, Wei Bo Li, Fabian Joachim Theis, Doreen Schmidl, Matthias Greiter +1 more

Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma

American Journal of Respiratory Cell and Molecular Biology(2021)10.1165/rcmb.2020-0553oc

N/A

0.449DataRank · unranked

19 citations

Andy Lan, Ilse M. Boudewijn, Senani N. H. Rathnayake, Gerard H. Koppelman, Meshal Ansari +5 more

Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young

Pediatric Diabetes(2017)10.1111/pedi.12543

N/A

0.449DataRank · unranked

19 citations

Michael Laimighofer, Jan Krumsiek, Fabian Joachim Theis, Christiane Winkler, Jill M. Norris +6 more

Biases in machine-learning models of human single-cell data

Nature Cell Biology(2025)10.1038/s41556-025-01619-8

N/A

0.448DataRank · unranked

7 citations

Vladimir A. Shitov, Malte D. Luecken, Niki Kilbertus, Stefan Bauer, Marie Piraud +3 more

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids

Science Advances(2025)10.1126/sciadv.adn8631

N/A

0.447DataRank · unranked

13 citations

Anthi C. Krontira, Lea Kaspar, Ruhel Ahmad, Ilknur Safak Demirel, Małgorzata Grochowicz +11 more

Disentangling cellular heterogeneity into interpretable biological factors through structured latent representations

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.06.622266

N/A

0.444DataRank · unranked

14 citations

Fabian Joachim Theis, Amir Ali Moinfar

Asthma in farm children is more determined by genetic polymorphisms and in non‐farm children by environmental factors

Pediatric Allergy and Immunology(2020)10.1111/pai.13385

N/A

0.442DataRank · unranked

18 citations

Michael Kabesch, Elisabeth Horak, Charlotte Braun‐Fahrländer, Jon Genuneit, Andrzej Boznanski +7 more

Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways

PLoS ONE(2010)10.1371/journal.pone.0011154

N/A

0.442DataRank · unranked

18 citations

Carsten Marr, Daniel Schmidl, Andreas Ruepp, Fabian Joachim Theis, Andreas Kowarsch

On model identifiability in analytic postnonlinear ICA

Neurocomputing(2005)10.1016/j.neucom.2004.11.015

N/A

0.439DataRank · unranked

7 citations

Fabian Joachim Theis, Peter J. Gruber

Hybridizing sparse component analysis with genetic algorithms for microarray analysis

Neurocomputing(2008)10.1016/j.neucom.2007.09.017

N/A

0.434DataRank · unranked

17 citations

Elmar W. Lang, Fabian Joachim Theis, Elke Lang, Ana Maria Tomé, Carlos G. Puntonet +2 more

Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.02.518917

N/A

0.434DataRank · unranked

17 citations

Corazon Ericka Mae Itang, Constantin Ammar, Florian A. Rosenberger, Isabell Bludau, Patricia Skowronek +11 more

OmniPath: integrated knowledgebase for multi-omics analysis

Nucleic Acids Research(2025)10.1093/nar/gkaf1126

Top 43%

0.433DataRank

Top 43%15 citations

Jonathan Schaul, Nicolàs Palacio‐Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli +27 more

A robust model for spatiotemporal dependencies

Neurocomputing(2008)10.1016/j.neucom.2007.06.012

N/A

0.433DataRank · unranked

10 citations

Ingo R. Keck, Elmar W. Lang, Peter J. Gruber, Fabian Joachim Theis

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.22.521557

Top 43%

0.432DataRank

Top 43%7 citations

Aimée Bastidas-Ponce, Mostafa Bakhti, Luke Zappia, Maren Büttner, Ciro Sallino +6 more

Copy number aberrations from Affymetrix SNP 6.0 genotyping data—how accurate are commonly used prediction approaches?

Briefings in Bioinformatics(2018)10.1093/bib/bby096

N/A

0.427DataRank · unranked

5 citations

Ivan Kondofersky, Steffen Sass, Fabian Joachim Theis, Nikola S. Mueller, Kristian Unger +1 more

Single-cell reference mapping to construct and extend cell-type hierarchies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.07.499109

Top 44%

0.423DataRank

Top 44%7 citations

Mohammad Lotfollahi, Daniel Strobl, Avi Srivastava, Marcel J.T. Reinders, Fabian Joachim Theis +2 more

Bayesian Blind Source Separation for Data with Network Structure

Journal of Computational Biology(2014)10.1089/cmb.2014.0117

N/A

0.419DataRank · unranked

5 citations

Christiane Fuchs, Fabian Joachim Theis, Katrin Illner

Uncertainty Quantification for Atlas-Level Cell Type Transfer

arXiv (Cornell University)(2022)10.48550/arxiv.2211.03793

N/A

0.417DataRank · unranked

5 citations

Leon Hetzel, Giovanni Palla, Avi Srivastava, Malte D. Luecken, Fabian Joachim Theis +1 more

GraphCompass: Spatial metrics for differential analyses of cell organization across conditions

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.02.578605

Top 44%

0.417DataRank

Top 44%8 citations

Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis, Karin Hrovatin, Giovanni Palla +3 more

scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution

Nature Methods(2025)10.1038/s41592-025-02854-5

N/A

0.416DataRank · unranked

14 citations

Laura D. Martens, Alexander Karollus, Trevor Manz, Jason D. Buenrostro, Fabian Joachim Theis +2 more

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma

International Journal of Molecular Sciences(2015)10.3390/ijms161226230

N/A

0.416DataRank · unranked

15 citations

Adriana Pitea, Kristian Unger, Julia Hess, Julia Heß, Nikola S. Mueller +2 more

Graph neural networks learn emergent tissue properties from spatial molecular profiles

Nature Communications(2025)10.1038/s41467-025-63758-8

N/A

0.415DataRank · unranked

12 citations

Sabrina Richter, Ali Ertürk, David S. Fischer, Fabian Joachim Theis, Mayar Ali

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.19.101592

N/A

0.408DataRank · unranked

6 citations

Ashis Saha, Mélanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller‐Nurasyid +11 more

Identification and Quantification of 1-Hydroxybutene-2-yl Mercapturic Acid in Human Urine by UPLC- HILIC-MS/MS as a Novel Biomarker for 1,3-Butadiene Exposure

Chemical Research in Toxicology(2012)10.1021/tx3002862

N/A

0.406DataRank · unranked

14 citations

Gerhard Scherer, Jan Krumsiek, Fabian Joachim Theis, Josef Ecker, Katharina Sterz

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation

BMC Bioinformatics(2010)10.1186/1471-2105-11-585

N/A

0.406DataRank · unranked

14 citations

Florian Blöchl, Sebastian Bohl, Maria Saile, Norbert Gretz, Ursula Klingmüller +3 more

Cell-type specific impact of glucocorticoid receptor activation on the developing brain

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.09.897868

N/A

0.404DataRank · unranked

8 citations

Leander Dony, Anthi C. Krontira, David S. Fischer, Simone Roeh, Rossella Di Giaimo +14 more

Integrated Single Cell Analysis of Human Lung Fibrosis Resolves Cellular Origins of Predictive Protein Signatures in Body Fluids

SSRN Electronic Journal(2020)10.2139/ssrn.3538700

N/A

0.404DataRank · unranked

6 citations

Lukas M. Simon, Gabriela Leuschner, Meshal Ansari, Philipp E. Geyer, Ilias Angelidis +17 more

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

medRxiv(2020)10.1101/2020.04.30.20085290

N/A

0.396DataRank · unranked

13 citations

Tim Fuchs, Pavol Harar, Dennis Elbrächter, David S. Fischer, Julius Berner +6 more

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)

medRxiv(2020)10.1101/2020.04.28.20082743

N/A

0.396DataRank · unranked

13 citations

Elmar Saathoff, Michael Pritsch, Jessica Michelle Guggenbühl Noller, Inge Kroidl, Laura Olbrich +11 more

Sparse Nonnegative Matrix Factorization with Genetic Algorithms for Microarray Analysis

2007 International Joint Conference on Neural Networks(2007)10.1109/ijcnn.2007.4370971

N/A

0.396DataRank · unranked

13 citations

P. Georgieva, Dominik Lutter, Fabian Joachim Theis, Elmar W. Lang, Ana Maria Tomé +3 more

ProCyon: A multimodal foundation model for protein phenotypes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.10.627665

N/A

0.391DataRank · unranked

8 citations

Yepeng Huang, Robert Calef, Valentina Giunchiglia, Tianlong Chen, George Dasoulas +19 more

An integrated transcriptomic cell atlas of human endoderm-derived organoids

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.20.567825

N/A

0.390DataRank · unranked

9 citations

Lennard Halle, Soroor Hediyeh-zadeh, Merel Kuijs, Umut Kilik, Qianhui Yu +24 more

Information-Theoretic Model Selection for Independent Components

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_32

N/A

0.390DataRank · unranked

2 citations

Fabian Joachim Theis, Christian Böhm, Anke Meyer‐Baese, Claudia Plant

Joint low-rank approximation for extracting non-Gaussian subspaces

Signal Processing(2007)10.1016/j.sigpro.2007.01.033

N/A

0.385DataRank · unranked

12 citations

Fabian Joachim Theis, Motoaki Kawanabe

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.28.121541

N/A

0.385DataRank · unranked

12 citations

Wataru Fujii, Theodore S. Kapellos, Arik Horne, Benedikt Reiz, Erika Dudkin +41 more

Autocrine Sfrp1 inhibits lung fibroblast invasion during transition to injury induced myofibroblasts

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.11.499594

N/A

0.385DataRank · unranked

12 citations

Arunima Sengupta, Meshal Ansari, Jeanine C. Pestoni, Paulina Ogar, Ilias Angelidis +27 more

Cellular connectomes as arbiters of local circuit models in the cerebral cortex

Nature Communications(2021)10.1038/s41467-021-22856-z

N/A

0.385DataRank · unranked

12 citations

Alessandro Motta, Carsten Marr, Fabian Joachim Theis, Moritz Helmstaedter, Emmanuel Klinger

Characterization of missing values in untargeted MS-based metabolomics data and evaluation of missing data handling strategies

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/260281

N/A

0.385DataRank · unranked

12 citations

Simone Wahl, Johannes Raffler, Sophie Molnos, Michael Laimighofer, Jerzy Adamski +12 more

Mobile decision support for transplantation patient data

International Journal of Medical Informatics(2004)10.1016/j.ijmedinf.2004.04.003

N/A

0.385DataRank · unranked

12 citations

Dominik Hartl, Manfred Stangl, Klaus E Gerauer, Alexander T. Mehlhorn, Fabian Joachim Theis +1 more

Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases

Klinische Monatsblätter für Augenheilkunde(2023)10.1055/a-2227-3742

N/A

0.381DataRank · unranked

8 citations

Robin Mittas, Nastassya Horlava, Johannes B Schiefelbein, Ben Asani, Stylianos Michalakis +9 more

Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis

Lecture Notes in Computer Science(2014)10.1007/978-3-319-12982-2_6

N/A

0.375DataRank · unranked

6 citations

Sabrina Hross, Fabian Joachim Theis, Christiane Fuchs, Fabian Fröhlich

Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis

Mechanisms of lung injury and repair(2023)10.1183/13993003.congress-2023.oa1569

N/A

0.373DataRank · unranked

6 citations

Janine Gote-Schniering, Diana Porras-Gonzalez, Lin Yang, Laurens J. De Sadeleer, R. Christoph Jentzsch +25 more

Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/174094

N/A

0.373DataRank · unranked

11 citations

Thomas Kessler, Daniel Weindl, Alexey Shadrin, Leonard Schmiester, Hendrik Hache +11 more

TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus

Nucleic Acids Research(2016)10.1093/nar/gkw805

N/A

0.373DataRank · unranked

11 citations

Stefan Mockenhaupt, Daniel Rupp, Tobias Bauer, Nagarajan Paramasivam, Bettina Knapp +13 more

Multi-Experiment Nonlinear Mixed Effect Modeling of Single-Cell Translation Kinetics after Transfection

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/285478

N/A

0.373DataRank · unranked

11 citations

L. Fink, Thomas Ligon, Fabian Joachim Theis, J. O. Rädler, Christiane Fuchs +3 more

Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.11.532085

N/A

0.369DataRank · unranked

8 citations

Charlotte Rich‐Griffin, Devika Agarwal, Sarah Ouologuem, Tom Thomas, Fabian Joachim Theis +2 more

A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

(2019)10.1101/527408

N/A

0.366DataRank · unranked

7 citations

G. Kar, Krzysztof Polanski, T. Gomes, Corry-Anke Brandsma, Irene H. Heijink +32 more

Learning Tn5 Sequence Bias from ATAC-seq on Naked Chromatin

Lecture Notes in Computer Science(2020)10.1007/978-3-030-61609-0_9

N/A

0.364DataRank · unranked

3 citations

David S. Fischer, Fabian Joachim Theis, Meshal Ansari

Publisher Correction: Multi-experiment nonlinear mixed effect modeling of single-cell translation kinetics after transfection

npj Systems Biology and Applications(2019)10.1038/s41540-019-0083-6

N/A

0.363DataRank · unranked

4 citations

Anita Reiser, Laura Fink, Daniel Woschée, Thomas Ligon, Fabian Joachim Theis +3 more

iVUN: interactive Visualization of Uncertain biochemical reaction Networks

BMC Bioinformatics(2013)10.1186/1471-2105-14-s19-s2

N/A

0.360DataRank · unranked

10 citations

Christiane Fuchs, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer +4 more

Multi-omics regulatory network inference in the presence of missing data

Briefings in Bioinformatics(2023)10.1093/bib/bbad309

N/A

0.360DataRank · unranked

10 citations

Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Markus List, Christoph Ogris +3 more

destiny – diffusion maps for large-scale single-cell data in R

bioRxiv (Cold Spring Harbor Laboratory)(2015)10.1101/023309

N/A

0.360DataRank · unranked

10 citations

Laleh Haghverdi, Maren Büttner, Fabian Joachim Theis, Carsten Marr, Florian Buettner +1 more

Beyond Predictions in Neural ODEs: Identification and Interventions

arXiv (Cornell University)(2021)10.4230/dagrep.12.9.150

N/A

0.349DataRank · unranked

5 citations

Fabian Joachim Theis, Niki Kilbertus, von Luxburg, Ulrike, Montgomery, Jessica, Meshal Ansari

Graph neural networks learn emergent tissue properties from spatial molecular profiles

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.08.519537

N/A

0.348DataRank · unranked

7 citations

Mayar Ali, Sabrina Richter, Ali Ertürk, Fabian Joachim Theis, David S. Fischer

Bayesian Model Selection Methods and Their Application to Biological ODE Systems

Studies in Mechanobiology, Tissue Engineering and Biomaterials(2015)10.1007/978-3-319-21296-8_10

N/A

0.345DataRank · unranked

9 citations

Daniel Schmidl, Wei Bo Li, Fabian Joachim Theis, Matthias Greiter, Sabine Hug

Gene regulatory networks simplified by nonlinear balanced truncation

SPIE Proceedings(2008)10.1117/12.777292

N/A

0.345DataRank · unranked

9 citations

Anke Meyer‐Baese, Fabian Joachim Theis

Uniqueness of Non-Gaussianity-Based Dimension Reduction

IEEE Transactions on Signal Processing(2011)10.1109/tsp.2011.2159600

N/A

0.345DataRank · unranked

9 citations

Motoaki Kawanabe, Klaus-Robert Müller, Klaus‐Robert Müller, Fabian Joachim Theis

Spatial single-cell atlas reveals regional variations in healthy and diseased human lung

Nature Communications(2025)10.1038/s41467-025-65704-0

N/A

0.345DataRank · unranked

9 citations

Sergio Marco Salas, Louis Benedikt Kuemmerle, Xesús M. Abalo, Alexandros Sountoulidis, Ludvig Larsson +24 more

Separation of water artifacts in 2D NOESY protein spectra using congruent matrix pencils

Neurocomputing(2006)10.1016/j.neucom.2005.02.008

N/A

0.345DataRank · unranked

9 citations

H.-R. Kalbitzer, Ana Maria Tomé, Fabian Joachim Theis, Elmar W. Lang, Wolfram Gronwald +2 more

A map of β-cell differentiation pathways supports cell therapies for diabetes

Nature(2019)10.1038/d41586-019-01211-9

N/A

0.345DataRank · unranked

9 citations

Heiko Lickert, Fabian Joachim Theis

Huge Splicing Frequency in Human Y Chromosomal UTY Gene

OMICS: A Journal of Integrative Biology(2011)10.1089/omi.2010.0107

N/A

0.345DataRank · unranked

9 citations

Fabian Joachim Theis, Martin Hrabé de Angelis, Hans-Jochem Kolb, Jerzy Adamski, Hans‐Jochem Kolb +1 more

A single-cell cytokine dictionary of human peripheral blood

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.12.693897

Top 52%

0.335DataRank

Top 52%8 citations

Sören Becker, Larsen Vornholz, Efthymia Papalexi, Joey Pangallo, Amir Ali Moinfar +25 more

12 Grand challenges in single-cell data science

(2019)10.7287/peerj.preprints.27885v2

N/A

0.330DataRank · unranked

5 citations

Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson +50 more

RegVelo: gene-regulatory-informed dynamics of single cells

(2024)10.1101/2024.12.11.627935

N/A

0.330DataRank · unranked

8 citations

Zhiyuan Hu, Herbert B. Schiller, Sarah Mayes, Marius Lange, Jingye Wang +4 more

Artificial intelligence in tuberculosis: a new ally in disease control

Breathe(2024)10.1183/20734735.0056-2024

N/A

0.330DataRank · unranked

8 citations

Traian Constantin Panciu, Christoph Lange, Raquel Duarte, M. McClean, Fabian Joachim Theis +1 more

Exploratory Matrix Factorization Techniques for Large Scale Biomedical Data Sets

Recent Advances in Biomedical Signal Processing(2012)10.2174/978160805218911101010026

N/A

0.330DataRank · unranked

8 citations

Reinhard Schachtner, Dominik Lutter, David A. Herold, Andreas Kodewitz, Florian Blöchl +6 more

A bilinear algorithm for sparse representations

Computational Optimization and Applications(2007)10.1007/s10589-007-9043-y

N/A

0.330DataRank · unranked

8 citations

Panos Pardalos, Pãnos M. Pardalos, Fabian Joachim Theis, Pando G. Georgiev

Heterogeneous Development of β-Cell Populations in Diabetes-Resistant and -Susceptible Mice

Diabetes(2022)10.2337/db21-1030

N/A

0.330DataRank · unranked

8 citations

Thilo Speckmann, Mandy Stadion, Erika Zuljan, Heja Aga, Michael Sterr +8 more

A Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring

PLOS ONE(2015)10.1371/journal.pone.0123643

N/A

0.330DataRank · unranked

8 citations

Heidi Soellner, Maria A. Castiblanco-Urbina, Stefan Winzeck, Julia Sundermeier, Fabian Joachim Theis +3 more

Bayesian Fuzzy Clustering of Colored Graphs

Lecture Notes in Computer Science(2012)10.1007/978-3-642-28551-6_65

N/A

0.326DataRank · unranked

2 citations

Fabian Joachim Theis

Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.16.524219

N/A

0.326DataRank · unranked

4 citations

Janine Gote-Schniering, Diana Porras-Gonzalez, Lin Yang, Laurens J. De Sadeleer, R. Christoph Jentzsch +24 more

Deep learning the collisional cross sections of the peptide universe from a million training samples

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.19.102285

Top 53%

0.325DataRank

Top 53%5 citations

Niklas D. Köhler, Andreas-David Brunner, Jean-Marc H. Wanka, Eugenia Voytik, Maximilian T. Strauss +3 more

A multimodal cross-species comparison of pancreas development

Research Square(2024)10.21203/rs.3.rs-4151759/v1

N/A

0.324DataRank · unranked

6 citations

Kaiyuan Yang, Hannah Spitzer, Michael Sterr, Karin Hrovatin, Sean de la O +17 more

An Ensemble Approach for Inferring Semi-quantitative Regulatory Dynamics for the Differentiation of Mouse Embryonic Stem Cells Using Prior Knowledge

Advances in Experimental Medicine and Biology(2011)10.1007/978-1-4419-7210-1_14

N/A

0.322DataRank · unranked

4 citations

Philipp Bruns, Fabian Joachim Theis, Dominik Lutter

Comparison of maximum entropy and minimal mutual information in a nonlinear setting

Signal Processing(2002)10.1016/s0165-1684(02)00200-1

N/A

0.319DataRank · unranked

4 citations

Christoph Bauer, Elmar W. Lang, C. Bauer, Fabian Joachim Theis

Blind Source Separation of Linear Mixtures with Singular Matrices

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_16

N/A

0.316DataRank · unranked

5 citations

Fabian Joachim Theis, Pando G. Georgiev

Large-scale modeling of cancer signaling: Mechanistic modeling meets Big Data

European Journal of Cancer(2016)10.1016/s0959-8049(16)32716-2

N/A

0.316DataRank · unranked

2 citations

T. Kessler, Anja Thormann, Fabian Fröhlich, Alexey Shadrin, Torsten Keßler +6 more

Socioeconomic and risk-related drivers of compliance with measures to prevent SARS-CoV-2 infection: evidence from the Munich-based KoCo19 study

BMC Public Health(2023)10.1186/s12889-023-15759-9

N/A

0.315DataRank · unranked

6 citations

Michael Laxy, Katja Radon, Ronan Le Gleut, Noemi Castelletti, Jessica Michelle Guggenbüehl Noller +33 more

Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions

Lecture Notes in Computer Science(2019)10.1007/978-3-030-30493-5

N/A

0.312DataRank · unranked

7 citations

Věra Kůrková, Pavel Karpov, Fabian Joachim Theis, Theis, Fabian, Igor V. Tetko

Optimization Algorithms for Sparse Representations and Applications

Kluwer Academic Publishers eBooks(2006)10.1007/0-387-29550-x_3

N/A

0.312DataRank · unranked

7 citations

Fabian Joachim Theis, Andrzej Cichocki, Pando G. Georgiev

Overcomplete ICA with a Geometric Algorithm

Lecture Notes in Computer Science(2002)10.1007/3-540-46084-5_170

N/A

0.312DataRank · unranked

7 citations

Elmar W. Lang, Tobias Westenhuber, Carlos G. Puntonet, Fabian Joachim Theis

3D Spatial Analysis of fMRI Data on a Word Perception Task

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_123

N/A

0.312DataRank · unranked

7 citations

Fabian Joachim Theis, Elmar W. Lang, Karsten Specht, Carlos G. Puntonet, Peter J. Gruber +1 more

Extended Sparse Nonnegative Matrix Factorization

Lecture Notes in Computer Science(2005)10.1007/11494669_31

N/A

0.312DataRank · unranked

7 citations

Fabian Joachim Theis, Carlos G. Puntonet, Elmar W. Lang, Kurt Stadlthanner

Publisher Correction: Inhibition of LTβR signalling activates WNT-induced regeneration in lung

Nature(2020)10.1038/s41586-020-03087-6

N/A

0.312DataRank · unranked

7 citations

Gerrit John-Schuster, Danijela Heide, Dominik Pfister, Mareike Lehmann, Yan Hu +47 more

Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure

IEEE Transactions on Circuits and Systems I: Regular Papers(2010)10.1109/tcsi.2010.2052485

N/A

0.312DataRank · unranked

7 citations

Fabian Joachim Theis

Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS

iScience(2023)10.1016/j.isci.2023.107328

N/A

0.311DataRank · unranked

5 citations

Lisa Bast, Judith S. Hecker, Jennifer Rivière, Maja Rothenberg-Thurley, Luisa Vogel +10 more

Pattern Repulsion Revisited

Lecture Notes in Computer Science(2001)10.1007/3-540-45723-2_94

N/A

0.304DataRank · unranked

4 citations

Elmar W. Lang, Christoph Bauer, Carlos G. Puntonet, Elmar Wolfgang Lang, Fabian Joachim Theis

Joint Diagonalization of Several Scatter Matrices for ICA

Lecture Notes in Computer Science(2012)10.1007/978-3-642-28551-6_22

N/A

0.302DataRank · unranked

5 citations

Harold W. Gutch, Hannu Oja, Fabian Joachim Theis, Klaus Nordhausen

inVAE: Conditionally invariant representation learning for generating multivariate single-cell reference maps

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.06.627196

N/A

0.302DataRank · unranked

6 citations

Ferdinand Kapl, Duy Pham, Batuhan Cakir, Takahiro Jimba, James Cranley +7 more

Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.04.510766

N/A

0.301DataRank · unranked

5 citations

Dominik Klein, Giovanni Palla, Soeren Becker, Herbert B. Schiller, Niki Kilbertus +2 more

Identifiability Conditions and Subspace Clustering in Sparse BSS

Lecture notes in computer science(2007)10.1007/978-3-540-74494-8_45

N/A

0.294DataRank · unranked

4 citations

Fabian Joachim Theis, Anca Ralescu, Pando G. Georgiev

Integrating single-cell RNA-seq datasets with substantial batch effects

BMC Genomics(2025)10.1186/s12864-025-12126-3

N/A

0.294DataRank · unranked

5 citations

Amir Ali Moinfar, Luke Zappia, Shrey Parikh, Alejandro Tejada-Lapuerta, Benjamin J. Lengerich +3 more

longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types

Bioinformatics(2024)10.1093/bioinformatics/btae137

N/A

0.292DataRank · unranked

6 citations

Monika Budde, Teodora Pandeva, Ivan Kondofersky, Sabrina K. Schaupp, Fabian Joachim Theis +6 more

How to extract marker genes from microarray data sets

2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society(2007)10.1109/iembs.2007.4353266

N/A

0.292DataRank · unranked

6 citations

Dominik Lutter, Fabian Joachim Theis, Elmar W. Lang, Gerd Schmitz, Ana Maria Tomé +2 more

A Foundation Model for Spatial Proteomics

arXiv (Cornell University)(2025)10.48550/arxiv.2506.03373

N/A

0.292DataRank · unranked

6 citations

Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Guillaume Jaume, Yuchen Wang +55 more

Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment

Stem Cell Reports(2023)10.1016/j.stemcr.2023.08.008

N/A

0.292DataRank · unranked

6 citations

Caroline Remmert, Maren Marder, Misao Akishiba, Judith Bushe, Annette Feuchtinger +6 more

Proteomics of spatially identified tissues in whole organs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.02.466753

N/A

0.292DataRank · unranked

6 citations

Andreas-David Brunner, Zhouyi Rong, Hongcheng Mai, Marvin Thielert, Rami Al-Maskari +14 more

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/269092

N/A

0.292DataRank · unranked

6 citations

S Karg, AJ Westermann, M Engel, AHA Elbehery, B Hense +8 more

Tree-Dependent and Topographic Independent Component Analysis for fMRI Analysis

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_99

N/A

0.292DataRank · unranked

6 citations

Fabian Joachim Theis, Oliver Lange, Carlos G. Puntonet, Anke Meyer‐Baese

Statistical Analysis of Sample-Size Effects in ICA

Lecture notes in computer science(2007)10.1007/978-3-540-77226-2_43

N/A

0.292DataRank · unranked

6 citations

Fabian Joachim Theis, J. Michael Herrmann

Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data

Bioinformatics(2025)10.1093/bioinformatics/btaf268

N/A

0.292DataRank · unranked

5 citations

Laura D. Martens, Anna Christina Schaar, Maiia Schulman, Julia-Stefanie Frick, Fabian Joachim Theis +1 more

Single cell decomposition of multicellular aging programs associated with impaired lung regeneration

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.24.666371

N/A

0.279DataRank · unranked

5 citations

M. Camila Melo-Narváez, Gowtham Boosarpu, David Lauer, Sai Rama Sridatta Prakki, Huijuan Wang +24 more

A multimodal cross-species comparison of pancreas development

Nature Communications(2025)10.1038/s41467-025-64774-4

Top 58%

0.273DataRank

Top 58%5 citations

Hannah Spitzer, Michael Sterr, Karin Hrovatin, Sean de la O, Xinghao Zhang +16 more

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/351353

N/A

0.269DataRank · unranked

5 citations

Lukas M. Simon, Isis E. Fernandez, Maximilian Strunz, Christoph H. Mayr, Flavia R. Greiffo +8 more

Dependent component analysis

EURASIP Journal on Advances in Signal Processing(2013)10.1186/1687-6180-2013-185

N/A

0.269DataRank · unranked

5 citations

Fabian Joachim Theis, Erçan E. Kuruoğlu, Ercan E Kuruoglu

Sparse Nonnegative Matrix Factorization Applied to Microarray Data Sets

Lecture Notes in Computer Science(2006)10.1007/11679363_32

N/A

0.269DataRank · unranked

5 citations

T. Langmann, Fabian Joachim Theis, Elmar W. Lang, Ana Maria Tomé, Carlos G. Puntonet +4 more

Delineating the Effective Use of Self-Supervised Learning in Single-Cell Genomics

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.16.580624

N/A

0.269DataRank · unranked

5 citations

Mojtaba Bahrami, Yufan Xia, David S. Fischer, Fabian Joachim Theis, Till Richter

Steady‐state robustness of qualitative gene regulation networks

International Journal of Robust and Nonlinear Control(2011)10.1002/rnc.1786

N/A

0.269DataRank · unranked

5 citations

S. Waldherr, Christian Breindl, Steffen Waldherr, Dominik M. Wittmann, Fabian Joachim Theis +2 more

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Genome Medicine(2022)10.1186/s13073-022-01124-9

N/A

0.269DataRank · unranked

5 citations

Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid +14 more

Uniqueness Of Real And Complex Linear Independent Component Analysis Revisited

University of Regensburg Publication Server (University of Regensburg)(2004)10.5281/zenodo.38622

N/A

0.269DataRank · unranked

5 citations

Fabian Joachim Theis

Centaur: a foundation model of human cognition

arXiv (Cornell University)(2024)10.48550/arxiv.2410.20268

N/A

0.269DataRank · unranked

5 citations

Elif Akata, Matthias Bethge, Franziska Brändle, Fred Callaway, Julian Coda-Forno +35 more

Essstörungen im Internet: Eine experimentelle Studie zu den Auswirkungen von Pro-Essstörungs- und Selbsthilfewebsites

PPmP - Psychotherapie · Psychosomatik · Medizinische Psychologie(2012)10.1055/s-0031-1301336

N/A

0.269DataRank · unranked

5 citations

Markus Wolf, Peter Fiedler, Matthias Backenstrass, Hans Kordy, Fabian Joachim Theis +1 more

Toward a ToxAtlas of Carbon-Based Nanomaterials: Single-Cell RNA Sequencing Reveals Initiating Cell Circuits in Pulmonary Inflammation

ACS Nano(2025)10.1021/acsnano.5c12054

N/A

0.269DataRank · unranked

5 citations

Lianyong Han, Meshal Ansari, Maximilian Strunz, Verena Haefner, Ilias Angelidis +13 more

Predicting antigen-specificity of single T-cells based on TCR CDR3 regions

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/734053

N/A

0.269DataRank · unranked

5 citations

Yihan Wu, Benjamin Schubert, Fabian Joachim Theis, David S. Fischer

The a d coefficient as a descriptive measure of the within‐group agreement of ratings

British Journal of Mathematical and Statistical Psychology(2010)10.1348/000711009x465647

N/A

0.269DataRank · unranked

5 citations

Patricia Simon, Fabian Joachim Theis, Ludwig Kreuzpointner

Reconstruction of graphs based on random walks

Theoretical Computer Science(2009)10.1016/j.tcs.2009.05.026

N/A

0.269DataRank · unranked

5 citations

Daniel Schmidl, Florian Blöchl, Fabian Joachim Theis, Dominik M. Wittmann

Network-based metabolite ratios for an improved functional characterization of genome-wide association study results

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/048512

N/A

0.269DataRank · unranked

5 citations

Ferdinand Stückler, Karsten Suhre, Christian Gieger, Matti Uusitupa, Nicole Soranzo +3 more

The 2010 Signal Separation Evaluation Campaign (SiSEC2010): Biomedical Source Separation

Lecture Notes in Computer Science(2010)10.1007/978-3-642-15995-4_16

N/A

0.267DataRank · unranked

2 citations

Guido Nolte, Dominik Lutter, Alexey Ozerov, Vikrham Gowreesunker, Hiroshi Sawada +3 more

Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm

medRxiv(2022)10.1101/2022.06.16.22276342

N/A

0.264DataRank · unranked

4 citations

Olle G. Holmberg, Johannes B Schiefelbein, Michael Hafner, Tina Herold, Hannah Spitzer +8 more

Centroid Clustering of Cellular Lineage Trees

Lecture Notes in Computer Science(2014)10.1007/978-3-319-10265-8_2

N/A

0.260DataRank · unranked

3 citations

Michael Schwarzfischer, Nina Hubig, Claudia Plant, Carsten Marr, Michael A. Rieger +3 more

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

BMC Systems Biology(2015)10.1186/s12918-015-0208-5

N/A

0.259DataRank · unranked

3 citations

Justin Feigelman, Fabian Joachim Theis, Carsten Marr, Michael Strasser

Variant-risk-exon interplay impacts circadian rhythm and dopamine signaling pathway in severe psychiatric disorders

medRxiv(2022)10.1101/2022.08.09.22278128

N/A

0.249DataRank · unranked

4 citations

Natalie Matosin, Nathalie Gerstner, Anna S. Fröhlich, Anna C. Koller, Franziska Degenhardt +9 more

Author response: The single-cell eQTLGen consortium

(2020)10.7554/elife.52155.sa2

N/A

0.241DataRank · unranked

4 citations

DH de Vries, Hilde E. Groot, Gosia Trynka, CC Hon, Marc Jan Bonder +12 more

New Riemannian metrics for speeding-up the convergence of over- and underdetermined ICA

University of Regensburg Publication Server (University of Regensburg)(2006)10.1109/iscas.2006.1693643

N/A

0.241DataRank · unranked

4 citations

Francesco Piazza, Fabian Joachim Theis, Stefano Squartini

Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors

iScience(2023)10.1016/j.isci.2023.108205

N/A

0.241DataRank · unranked

4 citations

Meshal Ansari, Ilias Angelidis, Ruth Olmer, Ulrich Martin, Fabian Joachim Theis +3 more

Cellular drivers of injury response and regeneration in the adult zebrafish heart

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.07.425670

N/A

0.241DataRank · unranked

4 citations

Sara Lelek, Bastiaan Spanjaard, Mariana Guedes Simões, Meshal Ansari, Ronny Schäfer +4 more

scARE: Attribution Regularization for Single Cell Representation Learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.05.547784

N/A

0.241DataRank · unranked

4 citations

Fabian Joachim Theis, Kemal Inecik

Theoretical Analysis of Time-to-Peak Responses in Biological Reaction Networks

Bulletin of Mathematical Biology(2010)10.1007/s11538-010-9548-x

N/A

0.241DataRank · unranked

4 citations

Sebastian Bohl, Ursula Klingmüller, Sebastian Böhl, Fabian Joachim Theis

Mathematics in independent component analysis

Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings.(2003)10.1109/isspa.2003.1224952

N/A

0.241DataRank · unranked

4 citations

Fabian Joachim Theis

Publisher Correction: Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway

Nature Communications(2018)10.1038/s41467-017-02379-2

N/A

0.241DataRank · unranked

4 citations

Toma Keser, Annika Wahl, Antti Hassinen, Lin Liu, Genadij Razdorov +26 more

Which Sectors of a Modern Economy are Most Central?

SSRN Electronic Journal(2010)10.2139/ssrn.1681277

N/A

0.241DataRank · unranked

4 citations

Fabian Joachim Theis, Fernando Vega-Redondo, Eric O'Neill Fisher, Fernando Vega‐Redondo, Florian Bloechl

An Isa Algorithm With Unknown Group Sizes Identifies Meaningful Clusters In Metabolomics Data

Max Planck Institute for Plasma Physics(2011)10.5281/zenodo.42701

N/A

0.241DataRank · unranked

4 citations

Jan Krumsiek, Fabian Joachim Theis, Harold W. Gutch

Trevor Hastie, Robert Tibshirani, and Martin Wainwright. Statistical Learning with Sparsity: The Lasso and Generalizations. Boca Raton: CRC Press

Biometrics(2018)10.1111/biom.12895

N/A

0.241DataRank · unranked

4 citations

Fabian Joachim Theis, Ivan Kondofersky

Interpretable surface-based detection of focal cortical dysplasias: a MELD study

medRxiv(2021)10.1101/2021.12.13.21267721

N/A

0.241DataRank · unranked

4 citations

Mathilde Ripart, Kirstie Whitaker, Antonio Napolitano, Luca De Palma, Alessandro De Benedictis +89 more

Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome

CHEST(2023)10.1016/j.chest.2022.12.050

N/A

0.232DataRank · unranked

3 citations

Benedikt Ditz, Brigitte W.M. Willemse, Meshal Ansari, Fabian Joachim Theis, Wim Timens +6 more

12 Grand Challenges in Single-Cell Data Science

(2019)10.7287/peerj.preprints.27885

N/A

0.228DataRank · unranked

2 citations

Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson +50 more

Author Correction: Targeted pharmacological therapy restores β-cell function for diabetes remission

Nature Metabolism(2020)10.1038/s42255-020-0201-1

N/A

0.228DataRank · unranked

3 citations

Aimée Bastidas-Ponce, Sophie Tritschler, Mostafa Bakhti, Anika Böttcher, Miguel A. Sánchez-Garrido +24 more

Identification of cell types, states and programs by learning gene set representations

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.08.556842

N/A

0.219DataRank · unranked

3 citations

Holly J. Whitfield, Malvika Kharbanda, Fabiola Curion, Dharmesh D. Bhuva, Fabian Joachim Theis +2 more

HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Cancer Research(2024)10.1158/0008-5472.can-24-0456

N/A

0.218DataRank · unranked

3 citations

Adriana Pitea, Gwendolyn M. Jang, Zhong Xu, Huat Chye Lim, Alex L. Choi +22 more

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.21.576532

N/A

0.216DataRank · unranked

3 citations

Anthi C. Krontira, Lea Kaspar, Ruhel Ahmad, Ilknur Safak Demirel, Tim Schaefer +11 more

Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.23.432413

N/A

0.213DataRank · unranked

2 citations

Meshal Ansari, Ilias Angelidis, Fabian Joachim Theis, Herbert B. Schiller, Micha Drukker +1 more

Self-supervised retinal thickness prediction enables deep learning from unlabeled data to boost classification of diabetic retinopathy

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/861757

N/A

0.208DataRank · unranked

3 citations

Niklas D. Köhler, Thiago Gonçalves dos Santos Martins, Jakob Siedlecki, Tina Herold, Leonie Keidel +6 more

Local features in biomedical image clusters extracted with independent component analysis

University of Regensburg Publication Server (University of Regensburg)(2004)10.1109/ijcnn.2003.1223300

N/A

0.208DataRank · unranked

3 citations

Fabian Joachim Theis, Wolfgang Bäumler, Elmar W. Lang, Christoph Bauer

Single-cell RNA sequencing reveals in vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

medRxiv(2020)10.1101/2020.12.07.20245274

N/A

0.208DataRank · unranked

3 citations

Meshal Ansari, Sebastian Jarosch, Yiqi Huang, Christoph H. Mayr, Maximilian Strunz +28 more

Automatic identification of relevant genes from low-dimensional embeddings of single cell RNAseq data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.21.000398

N/A

0.208DataRank · unranked

3 citations

David S. Fischer, Fabian Joachim Theis, Antonio Scialdone, Carsten Marr, Philipp Angerer

Denoising Using Local ICA and a Generalized Eigendecomposition with Time-Delayed Signals

Lecture Notes in Computer Science(2004)10.1007/978-3-540-30110-3_125

N/A

0.208DataRank · unranked

3 citations

Kurt Stadlthanner, Ana Maria Tomé, Fabian Joachim Theis, Carlos G. Puntonet, Elmar W. Lang +2 more

Modularity Maximization and Tree Clustering: Novel Ways to Determine Effective Geographic Borders

Springer Optimization and Its Applications(2011)10.1007/978-1-4614-0754-6_7

N/A

0.208DataRank · unranked

3 citations

Daniel Grady, Rafael Brune, Christian Thiemann, Fabian Joachim Theis, Dirk Brockmann

Impulse model-based differential expression analysis of time course sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/113548

N/A

0.208DataRank · unranked

3 citations

Fabian Joachim Theis, Nir Yosef, David S. Fischer

Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue

medRxiv(2022)10.1101/2022.05.18.22275097

N/A

0.208DataRank · unranked

3 citations

Sophie Roenneberg, Larissa Graner, Franziska Schlenker, Roland Zengerle, Fabian Joachim Theis +6 more

Artificial Neural Networks and Machine Learning – ICANN 2019: Deep Learning

Lecture Notes in Computer Science(2019)10.1007/978-3-030-30484-3

N/A

0.208DataRank · unranked

3 citations

Věra Kůrková, Pavel Karpov, Fabian Joachim Theis, Theis, Fabian, Igor V. Tetko

What do you most hope spatial molecular profiling will help us understand? Part 1

Cell Systems(2023)10.1016/j.cels.2023.05.009

N/A

0.208DataRank · unranked

3 citations

Daniel Dar, Sanja Vicković, Linghua Wang, Luciane T. Kagohara, André F. Rendeiro +3 more

Metabolism gene signatures and surgical site infections in abdominal surgery

International Journal of Surgery(2015)10.1016/j.ijsu.2015.01.009

N/A

0.208DataRank · unranked

3 citations

Philipp Bruns, Susanne Raulefs, Simon Rieder, Laura Paul, Olivia Prazeresda Costa +6 more

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.07.490900

N/A

0.208DataRank · unranked

3 citations

Scott M. Berry, Mark W. Donoghoe, Lucas Pelkmans, Fabian Joachim Theis, Hannah Spitzer

Effective Parameters Determining the Information Flow in Hierarchical Biological Systems

Bulletin of Mathematical Biology(2010)10.1007/s11538-010-9604-6

N/A

0.208DataRank · unranked

3 citations

Dominik M. Wittmann, Fabian Joachim Theis, Florian Blöchl

Publisher Correction: Epithelial cell plasticity drives endoderm formation during gastrulation

Nature Cell Biology(2021)10.1038/s41556-021-00735-5

Top 65%

0.208DataRank

Top 65%2 citations

Silvia Schirge, Ingo Burtscher, Maren Büttner, Michael Sterr, Dapeng Yang +9 more

12 Grand challenges in single-cell data science

(2019)10.7287/peerj.preprints.27885v1

N/A

0.193DataRank · unranked

2 citations

Johannes Köster, Ewa Szcureck, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos +50 more

Prolonged WNT/ß-catenin signaling induces cellular senescence in aging and pulmonary fibrosis

03.03 - Mechanisms of lung injury and repair(2020)10.1183/23120541.lsc-2020.81

N/A

0.191DataRank · unranked

2 citations

Y. Hu, R Costa, William Janssen, Mareike Lehmann, Qianjiang Hu +8 more

MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/425439

Top 66%

0.188DataRank

Top 66%1 citations

Fabian Joachim Theis, George Tsitsiridis, Philipp Angerer, Lukas M. Simon

Author Correction: Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

Nature Cell Biology(2021)10.1038/s41556-021-00667-0

N/A

0.187DataRank · unranked

2 citations

Maren Büttner, Sophie Tritschler, Michael Sterr, Alexandra Aliluev, Lena Oppenländer +13 more

CellForge: Agentic Design of Virtual Cell Models

arXiv (Cornell University)(2025)10.48550/arxiv.2508.02276

N/A

0.185DataRank · unranked

2 citations

Z. Q. Yu, Jiapeng Chen, Yan Cui, Dan Shao, W.M. Wang +9 more

Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer

medRxiv(2025)10.1101/2025.08.25.25333715

N/A

0.178DataRank · unranked

2 citations

Hilary A. Kenny, Aasa Shimizu, Lisa Schweizer, Shani Ben-Moshe, Agnes Julia Bilecz +19 more

Exploratory electronic health record analysis with ehrapy

medRxiv(2023)10.1101/2023.12.11.23299816

N/A

0.178DataRank · unranked

2 citations

Philipp Ehmele, Tim Treis, Julius Upmeier zu Belzen, Altana Namsaraeva, Nastassya Horlava +15 more

A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types

Advances in Neural Information Processing Systems 37(2024)10.52202/079017-0650

N/A

0.171DataRank · unranked

2 citations

Andrew Benz, Daniel Burkhardt, Robrecht Cannoodt, Mauricio Cortes, Jason Fong +18 more

Modulation of TCR stimulation and pifithrin-α improve the genomic safety profile of CRISPR-engineered human T cells

Cell Reports Medicine(2024)10.1016/j.xcrm.2024.101846

N/A

0.165DataRank · unranked

2 citations

Jule S. Müschen, Julia Ritter, Julia Klermund, Bettina E. Bernard, Saskia Kolb +10 more

SOMICA - an application of self-organizing maps to geometric independent component analysis

University of Regensburg Publication Server (University of Regensburg)(2004)10.1109/ijcnn.2003.1223886

N/A

0.165DataRank · unranked

2 citations

Carlos G. Puntonet, Elmar W. Lang, Fabian Joachim Theis

FedscGen: privacy-aware federated batch effect correction of single-cell RNA sequencing data

Research Square(2024)10.21203/rs.3.rs-4807285/v1

N/A

0.165DataRank · unranked

2 citations

Stefan Bonn, Olga Zolotareva, Jan Baumbach, Fabian Joachim Theis, Mohammad Bakhtiari

Kernel-PCA denoising of artifact-free protein NMR spectra

Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)(2005)10.1109/ijcnn.2004.1380913

N/A

0.165DataRank · unranked

2 citations

Elmar W. Lang, Peter J. Gruber, Fabian Joachim Theis, Ana Maria Tomé, Ana Rita Teixeira +2 more

Model-based branching point detection in single-cell data by K-Branches clustering

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/094532

N/A

0.165DataRank · unranked

2 citations

Francesca Finotello, Fabian Joachim Theis, Florian Wolf, Nikolaos K. Chlis

Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast * *The authors acknowledge financial support from the Postdoctoral Fellowship Program (PFP) of the Helmholtz Zentrum Munchen.

IFAC-PapersOnLine(2016)10.1016/j.ifacol.2016.12.136

N/A

0.165DataRank · unranked

2 citations

Anna K. Fiedler, Fabian Joachim Theis, Christiane Fuchs, Sabrina Hross

Beyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.23.661141

N/A

0.165DataRank · unranked

2 citations

Antony Rose, Muzlifah Haniffa, Malte D. Luecken, Fabian Joachim Theis, Kemal Inecik

Learning sequence-based regulatory dynamics in single-cell genomics

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.07.605876

N/A

0.165DataRank · unranked

2 citations

Johanna Schneeberger, Ege Erdogan, Lennart Redl, Laura Martens, Dominik Klein +3 more

Kalkulationsbeispiele

Leitfaden des Baubetriebs und der Bauwirtschaft(2018)10.1007/978-3-658-18109-3_3

N/A

0.165DataRank · unranked

2 citations

Constanze Stuhr, Christoph Winter, Clemens Müller, Markus Passeck, Ahmed Belkaied +10 more

Integration and Querying of Multimodal Single-Cell Data with PoE-VAE

Lecture Notes in Computer Science(2025)10.1007/978-3-031-90252-9_36

N/A

0.165DataRank · unranked

2 citations

Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi +2 more

Dynamic modelling of an ACADS genotype in fatty acid oxidation – Application of cellular models for the analysis of common genetic variants

PLOS ONE(2019)10.1371/journal.pone.0216110

N/A

0.165DataRank · unranked

2 citations

Ferdinand Stückler, Michael Salomon, Regina Ensenauer, Eva Reischl, Lena Hoerburger +9 more

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain

Database(2014)10.1093/database/bau083

Top 70%

0.165DataRank

Top 70%2 citations

J. Zhang, J. Schechter, B. Lentes, Martin Preusse, Jian Zhang +8 more

Deciphering brain organoid heterogeneity by identifying key quality determinants

Communications Biology(2025)10.1038/s42003-025-08855-6

N/A

0.165DataRank · unranked

2 citations

Elizaveta Gerasimova, Naime Zagha, Federica Furlanetto, Negar Nayebzade, Luke Zappia +15 more

Sparseness by Iterative Projections Onto Spheres

University of Regensburg Publication Server (University of Regensburg)(2006)10.1109/icassp.2006.1661374

N/A

0.165DataRank · unranked

2 citations

Toshihisa Tanaka, Fabian Joachim Theis

flowVI: Flow Cytometry Variational Inference

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.10.566661

N/A

0.165DataRank · unranked

2 citations

Adil Meric, Lars M. König, Fabian Joachim Theis, Kemal Inecik

Heterogeneous development of β-cell populations in diabetes-resistant and susceptible mice

Figshare(2022)10.2337/figshare.20080700.v1

N/A

0.165DataRank · unranked

2 citations

Thilo Speckmann, Mandy Stadion, Erika Zuljan, Heja Aga, Michael Sterr +8 more

Single-cell multiome and spatial profiling reveals pancreas cell type-specific gene regulatory programs driving type 1 diabetes progression

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.13.637721

N/A

0.165DataRank · unranked

2 citations

Sara Jimenez, Weston Elison, Luca Tucciarone, Abigail Howell, Gaowei Wang +20 more

Generalizing Geometric ICA to Nonlinear Settings

Lecture Notes in Computer Science(2003)10.1007/3-540-44869-1_87

N/A

0.165DataRank · unranked

2 citations

Carlos G. Puntonet, Elmar W. Lang, Fabian Joachim Theis

Estimating Hidden Influences in Metabolic and Gene Regulatory Networks

Lecture Notes in Computer Science(2009)10.1007/978-3-642-00599-2_49

N/A

0.165DataRank · unranked

2 citations

Fabian Joachim Theis, Florian Blöchl

Blind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images

Biophysical Journal(2009)10.1016/j.bpj.2008.12.056

N/A

0.165DataRank · unranked

2 citations

Mišo Mitkovski, Frank Kirchhoff, Erwin Neher, Fabian Joachim Theis, André Zeug +1 more

Postnonlinear blind source separation via linearization identification

University of Regensburg Publication Server (University of Regensburg)(2005)10.1109/ijcnn.2004.1380961

N/A

0.165DataRank · unranked

2 citations

Elmar W. Lang, Fabian Joachim Theis

Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

SPIE Proceedings(2011)10.1117/12.884196

N/A

0.165DataRank · unranked

2 citations

Jan Krumsiek, Fabian Joachim Theis, Christian Böhm, Anke Meyer‐Baese, Nikola S. Mueller

Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/167676

N/A

0.165DataRank · unranked

2 citations

R. Lickert, R. Fürst, Daniela Bezdan, Anette-Gabriele Ziegler, Michael Laimighofer +7 more

scPortrait integrates single-cell images into multimodal modeling

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.22.677590

N/A

0.165DataRank · unranked

2 citations

Niklas A. Schmacke, Alessandro Palma, Altana Namsaraeva, Ali Oğuz Can, Varvara Varlamova +7 more

TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates

(2024)10.1101/2024.06.20.599903

N/A

0.165DataRank · unranked

2 citations

Aleyna Kara, Antony Rose, Muzlifah Haniffa, Fabian Joachim Theis, Kemal Inecik

Variably methylated regions in the newborn epigenome: environmental, genetic and combined influences

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/436113

N/A

0.165DataRank · unranked

2 citations

Gökçen Eraslan, Jari Lahti, Christian M. Page, Marius Lahti-Pulkkinen, Esa Hämäläinen +30 more

Mapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.05.602277

N/A

0.165DataRank · unranked

2 citations

Nil Üresin, Sabrina Richter, Mikkel Bruhn Schuster, Despoina Barmpouri, Henrietta Holze +7 more

An integrated cell atlas of the human lung in health and disease

Research Square(2022)10.21203/rs.3.rs-1438584/v1

Top 71%

0.127DataRank

Top 71%1 citations

Avi Srivastava, Daniel Strobl, Luke Zappia, Elo Madissoon, Nikolay S. Markov +80 more

LNA++: Linear Noise Approximation with First and Second Order Sensitivities

Lecture Notes in Computer Science(2018)10.1007/978-3-319-99429-1_19

N/A

0.126DataRank · unranked

1 citations

Daniel Weindl, Fabian Joachim Theis, Carsten Marr, Christiane Fuchs, Justin Feigelman

Publisher Correction: An integrated transcriptomic cell atlas of human neural organoids

Nature(2024)10.1038/s41586-024-08482-x

Top 71%

0.120DataRank

Top 71%1 citations

Leander Dony, Jonas Simon Fleck, Artur Szalata, Katelyn X. Li, Irena Slišković +21 more

Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Nature Neuroscience(2024)10.1038/s41593-024-01858-2

N/A

0.118DataRank · unranked

1 citations

Gonçalo Castelo-Branco, Fei Chen, Simone Codeluppi, M. Ryan Corces, Jean Fan +26 more

A spatially resolved extracellular matrix proteome atlas of the distal human lung

Mechanisms of lung injury and repair(2023)10.1183/13993003.congress-2023.oa2626

Top 72%

0.111DataRank

Top 72%1 citations

Janine Gote-Schniering, Michaela Müller, Pascal Albanese, Andris Jankevics, R. Christoph Jentzsch +22 more

Label Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry

Journal of Allergy and Clinical Immunology(2017)10.1016/j.jaci.2016.12.537

N/A

0.104DataRank · unranked

1 citations

Holger Hennig, Fabian Joachim Theis, Paul Rees, Huw D. Summers, Catherine A. Thornton +1 more

A field guide to cultivating computational biology

arXiv (Cornell University)(2021)10.48550/arxiv.2104.11364

N/A

0.104DataRank · unranked

1 citations

Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley +9 more

scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.24.513494

N/A

0.104DataRank · unranked

1 citations

Katharina Essig, Nikolaos‐Kosmas Chlis, Sylvia Herter, Marina Bacac, Fabian Joachim Theis +4 more

Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine

Frontiers in Microbiology(2019)10.3389/fmicb.2018.03338

N/A

0.104DataRank · unranked

1 citations

Vitaly V. Ganusov, Stanca M. Ciupe, Ramit Mehr, Ruy M. Ribeiro, Esteban A. Hernandez-Vargas +3 more

Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Mechanistic Discovery

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.10.657924

N/A

0.104DataRank · unranked

1 citations

Julius Upmeier zu Belzen, Luis Herrmann, Khue Nguyen, Fabian Joachim Theis, Benjamin Wild +3 more

Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.24.529840

N/A

0.104DataRank · unranked

1 citations

Veronika Schwarz, Meshal Ansari, Simon Frerich, Judith Fischer-Sternjak, Riccardo Bocchi +8 more

CD23 Levels on B Cells Determine Long-Term Therapeutic Response in Patients with Atopic Eczema Treated with Selective IgE Immune Apheresis

Journal of Investigative Dermatology(2021)10.1016/j.jid.2020.05.122

N/A

0.104DataRank · unranked

1 citations

Rosi Wang, Richa Batra, Alexander Böhner, Natalie Garzorz-Stark, Bernadette Eberlein +7 more

SOMICA and geometric ICA

Sixth International Conference of Information Fusion, 2003. Proceedings of the(2003)10.1109/icif.2003.177411

N/A

0.104DataRank · unranked

1 citations

Fabian Joachim Theis, Carlos G. Puntonet, Elmar W. Lang

Deciphering Brain Organoids Heterogeneity by Identifying Key Quality Determinants

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.13.632763

N/A

0.104DataRank · unranked

1 citations

Naime Zagha, Tom Boerstler, Federica Furlanetto, Negar Nayebzade, Luke Zappia +14 more

AutoAssign – An Automatic Assignment Tool for Independent Components

Lecture Notes in Computer Science(2005)10.1007/11492542_10

N/A

0.104DataRank · unranked

1 citations

Kurt Stadlthanner, Fabian Joachim Theis, Carlos G. Puntonet, Elmar W. Lang, Ana Maria Tomé +3 more

Low numbers of cytokine transcripts drive inflammatory skin diseases by initiating amplification cascades in localized epidermal clusters

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.10.447894

N/A

0.104DataRank · unranked

1 citations

A. Farnoud, E. Scala, A. C. Pilz, M. Mubarak, M. Stahle +17 more

SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching

arXiv (Cornell University)(2022)10.48550/arxiv.2205.07110

N/A

0.104DataRank · unranked

1 citations

Varsha G. Raghavan, Amanda M. Robinson, Robert A. Barton, Adeeb Rahman, Drausin Wulsin +5 more

Author Correction: IRE1α-XBP1s pathway promotes prostate cancer by activating c-MYC signaling

Nature Communications(2024)10.1038/s41467-024-50645-x

N/A

0.104DataRank · unranked

1 citations

Hatice Zeynep Nenseth, Su Qu, Omer F. Kuzu, Turid Frahnow, Lukas M. Simon +12 more

ArchMap: A web-based platform for reference-based analysis of single-cell datasets

Research Square(2024)10.21203/rs.3.rs-5110946/v1

N/A

0.104DataRank · unranked

1 citations

Mohammad Lotfollahi, Fabian Joachim Theis, Ronald Skorobogat, Xavier George, Simon Richter +4 more

Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells

Experimental Hematology(2014)10.1016/j.exphem.2014.07.215

N/A

0.104DataRank · unranked

1 citations

Susanne Wingert, Pangrazio De Giacomo, Nadine Haetscher, Boris Brill, Lothar Hennighausen +4 more

Mapping cells to gene programs

Research Square(2023)10.21203/rs.3.pex-2092/v1

N/A

0.104DataRank · unranked

1 citations

Sergei Rybakov, Karin Hrovatin, Soroor Hediyeh-zadeh, Alexander V. Misharin, Fabian Joachim Theis +2 more

ConvexGating infers gating strategies from clusters in single cell cytometry data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.11.623019

N/A

0.104DataRank · unranked

1 citations

Karola Mai, Thomas P. Hofer, Elfriede Nößner, Lorenzo Bonaguro, Celia L. Hartmann +11 more

394 Gene expression based molecular test proves clinical validity as diagnostic aid for the differential diagnosis of psoriasis and eczema in formalin fixed and paraffin embedded tissue

British Journal of Dermatology(2023)10.1093/bjd/ljad162.019

N/A

0.104DataRank · unranked

1 citations

Anais Doll, Deniz Uereyener, Sophie Roenneberg, Christina Hillig, Lucca Weber +18 more

Preprocessed IgG Fc glycomics data in four Croatian cohorts (LC-ESI-MS)

Figshare(2017)10.6084/m9.figshare.5335861

Top 78%

0.104DataRank

Top 78%1 citations

Maja Pučić‐Baković, Toma Keser, Annika Wahl, Antti Hassinen, Jeong‐Yeh Yang +26 more

A new ica method based on a lattice of the observation space

Sixth International Conference of Information Fusion, 2003. Proceedings of the(2003)10.1109/icif.2003.177405

N/A

0.104DataRank · unranked

1 citations

F. Rojas, M. Álvarez, Fernando Rojas, Carlos G. Puntonet, Fabian Joachim Theis +2 more

Dynamic regimes of random fuzzy logic networks

New Journal of Physics(2011)10.1088/1367-2630/13/1/013041

N/A

0.104DataRank · unranked

1 citations

Fabian Joachim Theis, Dominik M. Wittmann

Scalable parameter estimation for genome-scale biochemical reaction networks

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/089086

N/A

0.104DataRank · unranked

1 citations

Barbara Kaltenbacher, Fabian Joachim Theis, Christiane Fuchs, Fabian Fröhlich

Centaur: a foundation model of human cognition

PsyArXiv (OSF Preprints)(2024)10.31234/osf.io/d6jeb

N/A

0.104DataRank · unranked

1 citations

Elif Akata, Matthias Bethge, Franziska Brändle, Fred Callaway, Julian Coda-Forno +38 more

Topological Constructions in the o–Graph Calculus

Mathematische Nachrichten(2002)10.1002/1522-2616(200207)241:1<170::aid-mana170>3.0.co;2-3

N/A

0.104DataRank · unranked

1 citations

Fabian Joachim Theis

MAGNet: Motif-Agnostic Generation of Molecules from Shapes

arXiv (Cornell University)(2023)10.48550/arxiv.2305.19303

N/A

0.104DataRank · unranked

1 citations

Johanna Sommer, Angela Oliveira Pisco, Fabian Joachim Theis, Stephan Günnemann, Leon Hetzel

TNF- α disrupts the malate-aspartate shuttle, driving metabolic rewiring in iPSC-derived enteric neural lineages from Parkinson’s Disease patients

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.25.644826

N/A

0.104DataRank · unranked

1 citations

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4i dataset for "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps"

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.7299516

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Chronic WNT/ß-catenin signaling impairs mitochondrial function in lung epithelial cells

Mechanisms of lung injury and repair(2021)10.1183/13993003.congress-2021.oa2699

N/A

0.104DataRank · unranked

1 citations

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Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice

Experimental and Clinical Endocrinology & Diabetes(2018)10.1055/a-0735-9533

N/A

0.104DataRank · unranked

1 citations

Moya Wu, Christiane Fuchs, Ivan Kondofersky, Fabian Joachim Theis, Martin Hrabé de Angelis +4 more

Artificial Neural Networks and Machine Learning – ICANN 2019: Image Processing

Lecture Notes in Computer Science(2019)10.1007/978-3-030-30508-6

N/A

0.104DataRank · unranked

1 citations

Věra Kůrková, Pavel Karpov, Fabian Joachim Theis, Theis, Fabian, Igor V. Tetko

Inferring catalysis in biological systems

IET Systems Biology(2016)10.1049/iet-syb.2015.0087

N/A

0.104DataRank · unranked

1 citations

Fabian Joachim Theis, Christiane Fuchs, Ivan Kondofersky

MISATO - Machine learning dataset for structure-based drug discovery

Zenodo (CERN European Organization for Nuclear Research)(2023)10.5281/zenodo.7711953

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Creating bottom-up RNA transfer vehicles from synthetic protein assemblies

Research Square(2024)10.21203/rs.3.rs-5123765/v1

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0.104DataRank · unranked

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Removing water artefacts from 2D protein NMR spectra using GEVD with congruent matrix pencils

Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings.(2003)10.1109/isspa.2003.1224821

N/A

0.104DataRank · unranked

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Image-based profiling: a powerful and challenging new data type

Biocomputing 2022(2021)10.1142/9789811250477_0038

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0.104DataRank · unranked

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T cells modulate the microglial response to brain ischemia

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.23.461546

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0.104DataRank · unranked

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Multi-omic Signatures Relate to the Severity of Pulmonary Outcome in Neonates Traced into Adult Disease

Network and Systems Medicine(2025)10.14293/nsm.25.1.0001

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0.104DataRank · unranked

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Künstliche Intelligenz und maschinelles Lernen in der Diabetesforschung

Der Diabetologe(2021)10.1007/s11428-021-00817-w

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0.104DataRank · unranked

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An algorithm for automatic assignment of artifact-related independent components in biomedical signal analysis

Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005.(2006)10.1109/ijcnn.2005.1556289

N/A

0.104DataRank · unranked

1 citations

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Endothelial regulatory circuits control cranial neural crest migration and plasticity

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.17.613303

N/A

0.104DataRank · unranked

1 citations

Sarah Mayes, Weixu Wang, José M. Santos-Pereira, Fabian Joachim Theis, Tatjana Sauka-Spengler +1 more

Source Data files for: Primary cilia and SHH signaling impairments in human and mouse models of Parkinson's disease

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.6677636

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Bayesian Inference of Latent Causes in Gene Regulatory Dynamics

Lecture Notes in Computer Science(2012)10.1007/978-3-642-28551-6_64

N/A

0.104DataRank · unranked

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Fabian Joachim Theis, Sabine Hug

Optimization Techniques for Date Representions with Biomedical Applications

Springer Optimization and Its Applications(2008)10.1007/978-0-387-09770-1_8

N/A

0.104DataRank · unranked

1 citations

Fabian Joachim Theis, Pando G. Georgiev

Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields

Lecture Notes in Computer Science(2016)10.1007/978-3-319-47157-0_35

N/A

0.104DataRank · unranked

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Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.07.692889

N/A

0.104DataRank · unranked

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Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons

Translational Psychiatry(2025)10.1038/s41398-025-03366-8

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0.104DataRank · unranked

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A Toolbox for Model-Free Analysis of fMRI Data

Lecture Notes in Computer Science(2007)10.1007/978-3-540-74494-8_27

N/A

0.104DataRank · unranked

1 citations

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TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates

Lecture Notes in Computer Science(2025)10.1007/978-3-031-90252-9_23

N/A

0.104DataRank · unranked

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Clustering of dependent components: a new paradigm for fMRI signal detection

(2005)10.1109/ijcnn.2004.1380910

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0.104DataRank · unranked

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Fabian Joachim Theis, O. Lange, Axel Wismüller, Anke Meyer‐Baese

Benchmarking atlas-level data integration in single-cell genomics - integration task datasets

Figshare(2020)10.6084/m9.figshare.12420968.v7

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Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.15.480506

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0.104DataRank · unranked

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In vivo identification of apoptotic and extracellular vesicle-bound live cells using image-based deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.14.040691

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0.104DataRank · unranked

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A Fast and Efficient Method for Compressing fMRI Data Sets

Lecture Notes in Computer Science(2005)10.1007/11550907_122

N/A

0.104DataRank · unranked

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Toshihisa Tanaka, Fabian Joachim Theis

Stability Analysis of an Unsupervised Competitive Neural Network

The 2006 IEEE International Joint Conference on Neural Network Proceedings(2006)10.1109/ijcnn.2006.246799

N/A

0.104DataRank · unranked

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V. Thummler, Anke Meyer‐Baese, Vera Thümmler, Fabian Joachim Theis

Community effort to unravel the complex human neuronal landscape exemplified for the striatum

Research Square(2024)10.21203/rs.3.rs-3960911/v1

N/A

0.104DataRank · unranked

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A scalable gene network model of regulatory dynamics in single cells

arXiv (Cornell University)(2025)10.48550/arxiv.2503.20027

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0.104DataRank · unranked

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Joseph D. Viviano, Alejandro Tejada-Lapuerta, Weixu Wang, Stefan Bauer, Fabian Joachim Theis +2 more

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms

BMC Bioinformatics(2017)10.1186/s12859-017-1838-y

N/A

0.104DataRank · unranked

1 citations

Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler +13 more

Meeting the challenges of high-dimensional data analysis in immunology

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/473215

N/A

0.104DataRank · unranked

1 citations

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FADVI: disentangled representation learning for robust integration of single-cell and spatial omics data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.03.683998

N/A

0.104DataRank · unranked

1 citations

Gang Qu, Lukas M. Simon, Fabian Joachim Theis, Zhongming Zhao, Wendao Liu

Anatomic-landmark detection using graphical context modelling

2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)(2015)10.1109/isbi.2015.7164114

N/A

0.104DataRank · unranked

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Vasileios Belagiannis, Carsten Marr, Guang-Zhong Yang, Nassir Navab, Fabian Joachim Theis +2 more

Systems Biology Meets Metabolism

Genetics Meets Metabolomics(2012)10.1007/978-1-4614-1689-0_17

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0.104DataRank · unranked

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Supplementary Figures S1-S8 from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

INDIGO (University of Illinois at Chicago)(2023)10.1158/1541-7786.22517488.v1

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0DataRank · unranked

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Polygenic Burden Analysis of Longitudinal Clusters of Psychopathological Features In A Cross-Diagnostic Group of Individuals with Severe Mental Illness

European Neuropsychopharmacology(2017)10.1016/j.euroneuro.2016.09.441

N/A

0DataRank · unranked

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Ivan Kondofersky, Monika Budde, Kristina Adorjan, Fanny Aldinger, Heike Anderson-Schmidt +15 more

Additional file 2 of Network reconstruction for trans acting genetic loci using multi-omics data and prior information

Open MIND(2022)10.6084/m9.figshare.21520295

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Spatial Association and Sympathetic Predominance in Tertiary Lymphoid Structure Innervation in Pancreatic Cancer

Pancreatology(2025)10.1016/j.pan.2025.07.155

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Carmen Mota Reyes, Maximilian Kiessler, Ina Dietsche, Luise Rupp, Leonard Halle +14 more

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

Zenodo (CERN European Organization for Nuclear Research)(2019)10.5281/zenodo.2908234

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siRNA-mediated perturbations in human precision-cut lung slices coupled to time-resolved single-nuclei RNA-seq

ILD/DPLD of known origin(2025)10.1183/23120541.lsc-2025.tp120

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Schwann Cell Dedifferentiation, Demyelination, and Nerve Remodeling Drive Neural Invasion in Pancreatic Cancer: The Concept of Neoplastic Gliopathy

Pancreatology(2025)10.1016/j.pan.2025.07.098

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mvTCR - trained models

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.8112246

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Supplementary Data - Materials and Methods from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

INDIGO (University of Illinois at Chicago)(2023)10.1158/1541-7786.22517494.v1

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Manuel Rodríguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst +20 more

Data from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

(2025)10.1158/0008-5472.c.7676185

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scConcept: Contrastive pretraining for technology-agnostic single-cell representations beyond reconstruction

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.14.682419

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Alejandro Tejada-Lapuerta, Sören Becker, Fatemeh S. Hashemi G., Fabian Joachim Theis, Mojtaba Bahrami

scifAI: Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

Research Square(2022)10.21203/rs.3.rs-2190942/v1

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Figure S1 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Figshare(2025)10.1158/0008-5472.28428331

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Additional file 2 of Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

Figshare(2017)10.6084/m9.figshare.c.3810316_d2

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The Role Of Micrornas In The Course Of Severe Mental Disorders

European Neuropsychopharmacology(2017)10.1016/j.euroneuro.2016.09.527

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Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.12.247585

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[DEPRECATED] Theislab sfaira Model Repository

Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.4304660

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Training Transitive and Commutative Multimodal Transformers with LoReTTa

arXiv (Cornell University)(2023)10.48550/arxiv.2305.14243

N/A

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Measuring Non-Gaussianity by Phi-Transformed and Fuzzy Histograms

Advances in Artificial Neural Systems(2012)10.1155/2012/962105

N/A

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Data from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

(2023)10.1158/0008-5472.c.6502887

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A Fast Predictive Lossless Coder for fMRI Data Sets

2006 International Conference on Image Processing(2006)10.1109/icip.2006.312956

N/A

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Modularity maximization and tree clustering: Novel ways to determine effective geographic borders

arXiv (Cornell University)(2011)10.48550/arxiv.1104.1200

N/A

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(2023)10.1158/0008-5472.22390284

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Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields

arXiv (Cornell University)(2016)10.48550/arxiv.1608.07616

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Michael Sterr, Lichao Wang, Fausto Milletarì, Nassir Navab, Anika Böttcher +4 more

LSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema

3.2 Airway Cell Biology and Immunopathology(2016)10.1183/13993003.congress-2016.oa463

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HBV rewires liver cancer signaling by altering PP2A complexes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.15.532845

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Figure S4 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Figshare(2025)10.1158/0008-5472.28428322

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Disentangled Representation Learning with the Gromov-Monge Gap

arXiv (Cornell University)(2024)10.48550/arxiv.2407.07829

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Data Driven Computational Modeling of Hematopoiesis in Myelodysplastic Syndromes Unveils Differences in Hematopoietic Stem Cell Kinetics Compared to Age-Matched Healthy Controls

Blood(2018)10.1182/blood-2018-99-115942

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Fully integrative data analysis of NMR metabolic fingerprints with comprehensive patient data: a case report based on the German Chronic Kidney Disease (GCKD) study

arXiv (Cornell University)(2018)10.48550/arxiv.1810.04281

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Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.11.30.691399

N/A

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Model-free Region Of Interest Based Analysis of fMRI Data

University of Regensburg Publication Server (University of Regensburg)(2006)10.1109/melcon.2006.1653142

N/A

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Publisher Correction: GIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice

Nature Metabolism(2025)10.1038/s42255-025-01308-8

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[DEPRECATED] Theislab sfaira Model Repository

Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.4304659

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QuiCAT: a scalable and flexible framework for mapping synthetic sequences

Bioinformatics(2025)10.1093/bioinformatics/btaf607

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Figshare(2019)10.6084/m9.figshare.9277604

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A BioID-derived proximity interactome for Protein Phosphatase PP2A

Molecular & Cellular Proteomics(2022)10.1016/j.mcpro.2022.100324

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Supplementary text from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

(2025)10.1158/0008-5472.28428316

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Zusammenfassung und Ausblick

Lebenszyklusorientierte Betriebskosten bei gebäudetechnischen Anlagen im deutschen Krankenhaussektor(2011)10.1007/978-3-8349-6870-8_7

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DISCO-seq: 3D single-cell transcriptomics of intact biological systems

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.10.693352

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LSC Abstract – Systemic and local metabolomics profiling reveals novel insights into the progression of emphysema

ERS Lung Science Conference 2016(2016)10.1183/13993003.congress-2016.op7

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Jörg Bartel, Cornelia Prehn, Jan Krumsiek, Jerzy Adamski, Oliver Eickelberg +3 more

Mode of actions of nanomaterial-induced respiratory toxicity

Occupational and environmental health(2024)10.1183/13993003.congress-2024.pa2217

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Supplementary Methods, Figures and References from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

INDIGO (University of Illinois at Chicago)(2023)10.1158/0008-5472.22390281.v1

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Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue +14 more

Adaptive signal analysis of immunological data

Sixth International Conference of Information Fusion, 2003. Proceedings of the(2003)10.1109/icif.2003.177356

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Fabian Joachim Theis

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Gabler eBooks(2011)10.1007/978-3-8349-6870-8

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Fabian Joachim Theis

Robust Stability Analysis and Design Under Consideration of Multiple Feedback Loops of the Tryptophan Regulatory Network of Escherichia coli

Advances in Experimental Medicine and Biology(2010)10.1007/978-1-4419-5913-3_22

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Figshare(2019)10.6084/m9.figshare.9277595

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Figshare(2025)10.1158/0008-5472.28431540

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arXiv (Cornell University)(2025)10.48550/arxiv.2507.11789

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Figshare(2025)10.1158/0008-5472.28428325

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Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.6677637

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Zeitschrift für Gastroenterologie(2023)10.1055/s-0042-1759925

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(2023)10.1158/1541-7786.c.6541735

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Lecture Notes in Computer Science(2003)10.1007/3-540-44869-1_34

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Informatik Spektrum(2019)10.1007/s00287-019-01220-y

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A Large-Scale Benchmark of Cross-Modal Learning for Histology and Gene Expression in Spatial Transcriptomics

arXiv (Cornell University)(2025)10.48550/arxiv.2508.01490

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Diabetologia(2014)10.1007/s00125-014-3435-1

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(2023)10.1158/0008-5472.22390287

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Zenodo (CERN European Organization for Nuclear Research)(2023)10.5281/zenodo.8307629

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Figshare(2020)10.6084/m9.figshare.12420968.v4

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Figshare(2019)10.6084/m9.figshare.9277580

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Supplementary Tables 1-8 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Figshare(2025)10.1158/0008-5472.28428319

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.17.468952

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Zenodo (CERN European Organization for Nuclear Research)(2021)10.5281/zenodo.4836517

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Suppl. Figure Legends from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

(2023)10.1158/1541-7786.22517497

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Figshare(2018)10.6084/m9.figshare.c.4324007.v1

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Myeloid lineage choice is not controlled by the PU.1 - Gata1 switch

Experimental Hematology(2013)10.1016/j.exphem.2013.05.270

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Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.3626854

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Experimental Hematology(2018)10.1016/j.exphem.2018.06.241

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.11.675512

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INDIGO (University of Illinois at Chicago)(2023)10.1158/0008-5472.22390287.v1

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Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature(2019)10.3410/f.734522090.793562309

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Figure S1 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Figshare(2025)10.1158/0008-5472.28431549

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Blind Sensor Characteristics Estimation in a Multi-Sensor Network Applied to fMRI Analysis

University of Regensburg Publication Server (University of Regensburg)(2005)10.1109/issnip.2004.1417466

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A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods

Research Square(2024)10.21203/rs.3.rs-5046381/v1

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Blind source recovery: algorithm comparison and fusion

AIP Conference Proceedings(2004)10.1063/1.1835229

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Fabian Joachim Theis

Bioinformatics in Psychiatric Genetics

Psychiatric Genetics(2018)10.1093/med/9780190221973.003.0009

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Figure S4 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

(2025)10.1158/0008-5472.28431537

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TGIF2 is a major regulator of neural stem cell fate and neurogenic priming

(2025)10.1101/2025.02.13.635953

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Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/284547

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SA125POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS

European Neuropsychopharmacology(2019)10.1016/j.euroneuro.2018.08.347

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Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings.(2003)10.1109/isspa.2003.1224857

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scCODA - benchmark data (Revision 2)

Zenodo (CERN European Organization for Nuclear Research)(2021)10.5281/zenodo.4305906

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Figshare(2019)10.6084/m9.figshare.9760592

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Additional file 6 of MPRAnalyze: statistical framework for massively parallel reporter assays

Figshare(2019)10.6084/m9.figshare.9760601

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Theoretische und konzeptionelle Grundlagen

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Supplementary Figures S1-S8 from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

(2023)10.1158/1541-7786.22517488

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File 2 MedB-1 Data from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

(2023)10.1158/0008-5472.22390293

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An Adaptive Approach to Blind Source Separation Using a Self-Organzing Map and a Neural Gas

Lecture Notes in Computer Science(2003)10.1007/3-540-44869-1_88

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Supplementary text from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

(2025)10.1158/0008-5472.28431528

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European Neuropsychopharmacology(2019)10.1016/j.euroneuro.2017.08.363

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File 3 L1236 Data from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

INDIGO (University of Illinois at Chicago)(2023)10.1158/0008-5472.22390290.v1

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Current Opinion in Biotechnology(2016)10.1016/j.copbio.2016.04.025

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INDIGO (University of Illinois at Chicago)(2023)10.1158/0008-5472.22390284.v1

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File 2 MedB-1 Data from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

INDIGO (University of Illinois at Chicago)(2023)10.1158/0008-5472.22390293.v1

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Qeios(2025)10.32388/dq3y3t

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Data from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

(2023)10.1158/1541-7786.c.6541735.v1

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scCODA - benchmark data

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(2024)10.1101/2024.11.11.622832

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European Neuropsychopharmacology(2017)10.1016/j.euroneuro.2016.09.450

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Lecture Notes in Computer Science(2005)10.1007/11550907_85

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Repository for Publications and Research Data (ETH Zurich)(2025)10.3929/ethz-c-000789679

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arXiv (Cornell University)(2023)10.48550/arxiv.2310.09254

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arXiv (Cornell University)(2025)10.48550/arxiv.2501.02526

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Kongreß der Deutschen Gesellschaft für Chirurgie München, 10.–13. April 1985(1985)10.1007/978-3-642-70325-6_60

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arXiv (Cornell University)(2023)10.48550/arxiv.2306.17246

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Lecture Notes in Computer Science(2007)10.1007/978-3-540-74695-9_9

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(2022)10.2337/figshare.20080700

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(2023)10.1158/0008-5472.22390290

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.07.687322

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pheno-seq – linking morphological features to gene expression in 3D cell culture systems

bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/311472

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Jeongbin Park, Friedrich Preußer, Lisa Amrhein, Zuguang Gu, Simon Steiger +14 more

POLYGENIC BURDEN ANALYSIS OF LONGITUDINAL CLUSTERS OF PSYCHOPATHOLOGICAL FEATURES IN A CROSS-DIAGNOSTIC GROUP OF INDIVIDUALS WITH SEVERE MENTAL ILLNESS

European Neuropsychopharmacology(2019)10.1016/j.euroneuro.2017.08.382

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Ivan Kondofersky, Monika Budde, Kristina Adorjan, Fanny Aldinger, Heike Anderson-Schmidt +14 more

4i dataset for "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps"

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.7299515

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Scott M. Berry, Lucas Pelkmans, Fabian Joachim Theis, Hannah Spitzer

Self-supervised retinal thickness prediction enables deep learning from unlabeled data to boost classification of diabetic retinopathy

Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.3626020

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Niklas D. Köhler, Thiago Gonçalves dos Santos Martins, Jakob Siedlecki, Tina Herold, Leonie Keidel +6 more

Vascular graft in infected aorto-bifemoral bypass

Gefässchirurgie(2001)10.1007/s007720000113

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T. Ferdinand, W. Hissen, Fabian Joachim Theis

Data from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

(2023)10.1158/0008-5472.c.6502887.v1

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Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue +14 more

Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/053231

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Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam Filipczyk, Oliver Hilsenbeck +4 more

Benchmarking atlas-level data integration in single-cell genomics - integration task datasets (Immune and pancreas)

Figshare(2020)10.6084/m9.figshare.12420968.v2

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Maren Büttner, Kridsadakorn Chaichoompu, Anna Danese, Marta Interlandi, Michaela Müller +6 more

EpiScanpy: integrated single-cell epigenomic analysis

Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.4292082

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Maria Lucia Richter, Kridsadakorn Chaichoompu, David S. Fischer, Fabian Joachim Theis, Maria Colomé‐Tatché +1 more

Supplementary Methods, Figures and References from Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets

(2023)10.1158/0008-5472.22390281

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Marcel Schilling, Martin Böhm, Bettina Hahn, Andreas Kowarsch, Andreas Raue +14 more

Clifti-GPT: Privacy-preserving federated fine-tuning and transferable inference of foundation models on clinical single-cell data

Research Square(2025)10.21203/rs.3.rs-7917089/v1

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Maria Louise Elkjaer, Ali Oğuz Can, Mhaned Oubounyt, Jan Baumbach, Maria L. Elkjaer +2 more

Benchmarking atlas-level data integration in single-cell genomics - integration task datasets

Figshare(2020)10.6084/m9.figshare.12420968.v5

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Supplementary Data - Materials and Methods from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

(2023)10.1158/1541-7786.22517494

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Manuel Rodríguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst +20 more

Spatiotemporal analysis of inflammaging and senescence programs in lung fibrosis using time-resolved single-cell transcriptomics and multiplexed immunofluorescence

Mechanisms of lung injury and repair(2023)10.1183/13993003.congress-2023.oa2624

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Mareike Lehmann, Meshal Ansari, Konstantin Wiedemann, M. Camila Melo-Narváez, Carina Steinchen +11 more

Additional file 5 of MPRAnalyze: statistical framework for massively parallel reporter assays

Figshare(2019)10.6084/m9.figshare.9760595

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David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian Joachim Theis, Nir Yosef +1 more

cgCorrect: A method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/057463

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Florian Buettner, Carsten Marr, Fabian Joachim Theis, Michael Strasser, Thomas Blasi

797: VERY EARLY ONSET INFLAMMATORY BOWEL DISEASE ATLAS REVEALS SIGNATURES OF POLYGENIC AND MONOGENIC DISEASE

Gastroenterology(2025)10.1016/s0016-5085(25)01381-2

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Christopher Lance, Jared Barends, Michael Field, Emma Anziano, Mia Sveen +19 more

Information Theoretic Concepts to Unravel Cell–Cell Communication

Lecture Notes in Bioengineering(2017)10.1007/978-3-319-54729-9_4

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Steffen Sass, Barbara Offermann, Amit Singh, Steffen Knauer, Andreas Schüttler +7 more

Repeated toxic injuries of murine liver are tolerated through microsteatosis and mild inflammation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.12.476054

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Christoph Ogris, Amnah Othman, Pia Erdoesi, Wolfgang Schmidt-Heck, Ina Biermayer +12 more

Supplementary Data - Tables from Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients

(2023)10.1158/1541-7786.22517491

N/A

0DataRank · unranked

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Manuel Rodríguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst +20 more

mvTCR - trained models

Zenodo (CERN European Organization for Nuclear Research)(2024)10.5281/zenodo.7215446

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Metering & Monitoring – Intelligente Gebäude

Aspekte der Baubetriebslehre in Forschung und Praxis(2015)10.1007/978-3-658-09359-4_36

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Frank Katzemich, Fabian Joachim Theis

Histological and molecular landscape of early pancreatic carcinogenesis

Pancreatology(2016)10.1016/j.pan.2016.05.113

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Philipp Bruns, Nora A Behler, Melissa Schlitter, Ivonne Regel, Susanne Raulefs +8 more

Rejoinder

Bayesian Analysis(2013)10.1214/13-ba801rej

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Claudia Czado, Sabine Hug, Fabian Joachim Theis, Doreen Schmidl, Daniel Schmidl

Predicting cell morphological responses to perturbations using generative modeling

Zenodo (CERN European Organization for Nuclear Research)(2024)10.5281/zenodo.8307628

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Fabian Joachim Theis, Mohammad Lotfollahi, Alessandro Palma

Additional file 2 of Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

Open MIND(2022)10.6084/m9.figshare.20882116

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Rashad M. Mahbub, Dennis K. Ninaber, Senani N. H. Rathnayake, Wim Timens, Maarten van den Berge +6 more

Integrating Polygenic Allele Burden Information And Phenomic Data To Characterize Complex Disease Trajectories In Severe Mental Illness

European Neuropsychopharmacology(2017)10.1016/j.euroneuro.2016.09.447

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Ivan Kondofersky, Kristina Adorjan, Fanny Aldinger, Heike Anderson-Schmidt, Till F.M. Andlauer +13 more

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/656967

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Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian Joachim Theis +4 more

Figure S2 from HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma

Figshare(2025)10.1158/0008-5472.28428328

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Adriana Pitea, Gwendolyn M. Jang, Zhong Xu, Huat Chye Lim, Alex L. Choi +22 more

Contributors

Genomic and Personalized Medicine(2009)10.1016/b978-0-12-369420-1.00122-0

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Matthew L. Anderson, Felicita Andreotti, Brian H. Annex, Anthony Antonellis, Dmitri Artemov +272 more

B-Cos Aligned Transformers Learn Human-Interpretable Features

arXiv (Cornell University)(2024)10.48550/arxiv.2401.08868

N/A

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Amal Lahiani, Yashin Dicente Cid, Melanie Boxberg, Peter Lienemann, Christian Matek +5 more

A single-cell cytokine dictionary of human peripheral blood

Research Square(2025)10.21203/rs.3.rs-8337240/v1

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Lukas Oesinghaus, Sören Becker, Larsen Vornholz, Efthymia Papalexi, Joey Pangallo +23 more

Transcriptional repression by TGIF2 coordinates neurogenic priming and neural stem cell maintenance

Science Advances(2026)10.1126/sciadv.aea9974

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Anthi C. Krontira, Franziska Vierl, Maria Lucia Richter, Weixu Wang, Juliane Merl-Pham +4 more

Fabian Joachim Theis

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