Prisca Liberali

Also affiliated with Board of the Swiss Federal Institutes of Technology, ETH Zurich, Friedrich Miescher Institute, Friedrich Miescher Institute

MedicineBiochemistry, Genetics and Molecular Biology

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

106Author DataRank

Indexed papers

61in 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 61 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.

The Human Cell Atlas

Zurich Open Repository and Archive (University of Zurich)(2017)10.5167/uzh-162597

Top 1%

9.7DataRank

Top 1%1600 citations

Sarah A. Teichmann, Matthew E. Hurles, Ido Amit, Christophe Benoıst, Kerstin Lindblad‐Toh +3 more

Papers

Driven by 644 papers — median percentile 72. Top paper: “The Human Cell Atlas”.

The Human Cell Atlas

Zurich Open Repository and Archive (University of Zurich)(2017)10.5167/uzh-162597

Top 1%

9.7DataRank

Top 1%1600 citations

Sarah A. Teichmann, Matthew E. Hurles, Ido Amit, Christophe Benoıst, Kerstin Lindblad‐Toh +3 more

IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment

Cell(2017)10.1016/j.cell.2017.06.016

N/A

8.4DataRank · unranked

191 citations

Mayte Suárez-Fariñas, Benjamin Izar, Ruth Dannenfelser, Itay Tirosh, Yong Liu +28 more

Dissecting Timing Variability in Yeast Meiosis

Cell(2007)10.1016/j.cell.2007.09.044

N/A

8.2DataRank · unranked

144 citations

Prisca Liberali, Sharad Ramanathan, Iftach Nachman

Automatic genome-wide reconstruction of phylogenetic gene trees

Bioinformatics(2007)10.1093/bioinformatics/btm193

N/A

7.0DataRank · unranked

139 citations

Avi Pfeffer, Nir Friedman, Prisca Liberali, Ilan Wapinski

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response

PLoS Biology(2012)10.1371/journal.pbio.1001369

N/A

6.3DataRank · unranked

178 citations

Hsiuyi V. Chen, Chih Long Liu, Ayelet Rahat, Avital Klien, Luis Soares +9 more

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Genome Biology(2016)10.1186/s13059-016-0880-9

N/A

5.9DataRank · unranked

189 citations

Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman +5 more

Single-cell transcriptomic profiling of the aging mouse brain

Nature Neuroscience(2019)10.1038/s41593-019-0491-3

Top 4%

5.6DataRank

Top 4%791 citations

Scott L. Lipnick, Brendan T. Innes, Sean K. Simmons, Xian Adiconis, Danielle Dionne +13 more

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

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

Nature Neuroscience(2018)10.1038/s41593-018-0154-9

Top 4%

5.2DataRank

Top 4%584 citations

Chris Gaiteri, Sarah E. Sullivan, Charles C. White, Shinya Tasaki, Jishu Xu +17 more

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

Cell Reports(2017)10.1016/j.celrep.2016.12.063

Top 4%

5.2DataRank

Top 4%1118 citations

Kimberly Johnson, Tia DiTommaso, Matthew Brian Couger, Duygu Payzin-Dogru, Tae J. Lee +21 more

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

Nature Communications(2020)10.1038/s41467-020-17440-w

N/A

5.2DataRank · unranked

186 citations

Brenton R. Paolella, Allison C. Warren, Kathryn Geiger-Schuller, Tsukasa Shibue, Michael Rothberg +18 more

Toward a Common Coordinate Framework for the Human Body

Cell(2019)10.1016/j.cell.2019.11.019

N/A

5.1DataRank · unranked

134 citations

Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler +8 more

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Neuron(2017)10.1016/j.neuron.2017.10.007

Top 4%

5.1DataRank

Top 4%301 citations

Daniel H. Geschwind, Arnold R. Kriegstein, John Ngai, Pavel Osten, Damon Polioudakis +5 more

Extracellular Vesicle Isolation and Analysis by Western Blotting

Methods in Molecular Biology(2017)10.1007/978-1-4939-7253-1_12

N/A

5.1DataRank · unranked

175 citations

Prisca Liberali, George M. Church, Dmitry Ter‐Ovanesyan, Emma J. K. Kowal

Transcriptional mediators of treatment resistance in lethal prostate cancer

Nature Medicine(2021)10.1038/s41591-021-01244-6

N/A

4.8DataRank · unranked

196 citations

Michael S. Cuoco, Jett Crowdis, Alice Bosma-Moody, Zhenwei Zhang, Kevin Bi +35 more

Chromatin potential identified by shared single cell profiling of RNA and chromatin

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.17.156943

N/A

4.7DataRank · unranked

125 citations

Bing Zhang, Zachary Chiang, Yan Hu, Jiarui Ding, Alison Brack +9 more

Efficient Generation of Transcriptomic Profiles by Random Composite Measurements

Cell(2017)10.1016/j.cell.2017.10.023

N/A

4.7DataRank · unranked

118 citations

Le Cong, Anthea Cheung, Matthew E. Hurles, Prisca Liberali, Brian Cleary

A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

Nature(2021)10.1038/s41586-021-03220-z

Top 5%

4.7DataRank

Top 5%392 citations

Caroline Martin, Stephanie Rudolph, Chong Guo, Charles R. Vanderburg, Naeem Nadaf +5 more

YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Genome Medicine(2014)10.1186/s13073-014-0100-8

N/A

4.5DataRank · unranked

151 citations

Jason Funt, Mor N. Lurie-Weinberger, Prisca Liberali, Chad L. Myers, Judith Berman +2 more

Transcriptomes of the B and T Lineages Compared by Multiplatform Microarray Profiling

The Journal of Immunology(2011)10.4049/jimmunol.1002695

N/A

4.5DataRank · unranked

106 citations

Scott Davis, Diane Mathis, the Immunological Genome Project Consortium, Yan Zhou, Natasha Asinovski +48 more

Impact of the Human Cell Atlas on medicine

Nature Medicine(2022)10.1038/s41591-022-02104-7

Top 5%

4.4DataRank

Top 5%229 citations

Aidan Maartens, Anna Hupalowska, Sarah A. Teichmann, Prisca Liberali, Jennifer E. Rood

Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis

Cell Stem Cell(2021)10.1016/j.stem.2021.08.007

N/A

4.3DataRank · unranked

142 citations

Charlie Chung, Haiwei Mou, Khristian E. Bauer-Rowe, Michael E. Xifaras, Ilgin Ergin +33 more

A multimodal cell census and atlas of the mammalian primary motor cortex

Nature(2021)10.1038/s41586-021-03950-0

Top 5%

4.3DataRank

Top 5%574 citations

BRAIN Initiative Cell Census Network (BICCN) Corresponding authors, Edward M. Callaway, Joseph R. Ecker, Z. Josh Huang, Ed S. Lein +252 more

γδ T cells regulate the intestinal response to nutrient sensing

Science(2021)10.1126/science.aba8310

N/A

4.3DataRank · unranked

157 citations

William Khoury-Hanold, Jaechul Lim, Indresh Singh, Moshe Biton, Bernardo S. Reis +14 more

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Nature Methods(2018)10.1038/s41592-018-0014-2

N/A

4.3DataRank · unranked

141 citations

Adam L. Haber, Sean K. Simmons, Pradeep Natarajan, Zhe Ji, Michele A. Busby +8 more

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Nature(2021)10.1038/s41586-021-03500-8

Top 5%

4.2DataRank

Top 5%389 citations

Julie A. Harris, Fangming Xie, Stephan Fischer, Ricky S. Adkins, Andrew I. Aldridge +81 more

Cell Atlas of The Human Fovea and Peripheral Retina

Scientific Reports(2020)10.1038/s41598-020-66092-9

Top 5%

4.2DataRank

Top 5%298 citations

Yi-Rong Peng, Tavé van Zyl, Prisca Liberali, Karthik Shekhar, Dejan Juric +3 more

Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

Clinical Cancer Research(2020)10.1158/1078-0432.ccr-19-3958

N/A

4.2DataRank · unranked

185 citations

Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +15 more

Joint single-cell measurements of nuclear proteins and RNA in vivo

Nature Methods(2021)10.1038/s41592-021-01278-1

N/A

4.1DataRank · unranked

137 citations

Christopher N. Parkhurst, Emma M. Magee, Devan R. Phillips, Ehsan Habibi, Fei Chen +5 more

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

Cell Reports(2019)10.1016/j.celrep.2019.05.046

N/A

4.1DataRank · unranked

178 citations

Caleb A. Lareau, Erik L. Bao, Satish K. Nandakumar, Christoph Muus, Jacob C. Ulirsch +8 more

QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis

Science(2021)10.1126/science.abb6896

N/A

4.1DataRank · unranked

149 citations

Lingfei Wang, Chih-Hung Chou, Kai Liu, Toru Nakata, Alok Jaiswal +9 more

B-cell-specific checkpoint molecules that regulate anti-tumour immunity

Nature(2023)10.1038/s41586-023-06231-0

N/A

4.1DataRank · unranked

171 citations

Yoon-Chul Kye, Jingwen Shi, Elena Torlai Triglia, Alexandra Schnell, Johannes Fessler +22 more

Genome-wide identification and characterization of replication origins by deep sequencing

Genome Biology(2012)10.1186/gb-2012-13-4-r27

N/A

3.9DataRank · unranked

100 citations

Yoshimi Yanagisawa, Alexander M. Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula +13 more

A roadmap for the Human Developmental Cell Atlas

Nature(2021)10.1038/s41586-021-03620-1

Top 6%

3.9DataRank

Top 6%194 citations

Deanne Taylor, Sten Linnarsson, Bruce J. Aronow, Samirkumar B. Amin, Roger A. Barker +53 more

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate

Molecular Cell(2019)10.1016/j.molcel.2018.10.032

N/A

3.9DataRank · unranked

150 citations

Christopher Frederick Mugler, Abdurrahman Keskin, Stefanie Hodapp, Leon Yen-Lee Chan, Karsten Weis +7 more

The Organoid Cell Atlas

Nature Biotechnology(2020)10.1038/s41587-020-00762-x

Top 6%

3.8DataRank

Top 6%172 citations

Michael Boutros, J. Gray Camp, Hans Clevers, Juergen A. Knoblich, Prisca Liberali +7 more

Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma

Cancer Cell(2020)10.1016/j.ccell.2020.06.004

N/A

3.8DataRank · unranked

165 citations

Bernhard Englinger, Li Jiang, Jens M Hübner, Olivia A. Hack, Sibylle Madlener +38 more

The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression

Immunity(2015)10.1016/j.immuni.2015.05.017

N/A

3.7DataRank · unranked

98 citations

Jimmy L. Zhao, Nikita Sinha, Georgi K. Marinov, Mati Mann, Monika S. Kowalczyk +8 more

A transcription factor atlas of directed differentiation

Cell(2023)10.1016/j.cell.2022.11.026

Top 6%

3.6DataRank

Top 6%232 citations

Sai Ma, Tristan Tay, Paul C. Kirchgatterer, Vanessa K. Verdine, Baolin Guo +14 more

RBPJ Controls Development of Pathogenic Th17 Cells by Regulating IL-23 Receptor Expression

Cell Reports(2016)10.1016/j.celrep.2016.05.088

N/A

3.6DataRank · unranked

112 citations

Chuan Wu, Chao Wang, Le Cong, Mathias Pawlak, Youjin Lee +5 more

Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma

Nature Medicine(2021)10.1038/s41591-020-01212-6

N/A

3.5DataRank · unranked

127 citations

Cyril Neftel, Marni E. Shore, Hannah R. Weisman, Nathan D. Mathewson, Matthew J. McBride +50 more

A quantitative framework for characterizing the evolutionary history of mammalian gene expression

Genome Research(2018)10.1101/gr.237636.118

N/A

3.5DataRank · unranked

149 citations

Ross Swofford, Jeremy Johnson, Beryl B. Cummings, Noga Rogel, Broad Institute Sequencing Platform and Whole Genome Assembly Team +5 more

Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

Cell(2022)10.1016/j.cell.2022.09.010

Top 6%

3.5DataRank

Top 6%238 citations

Amanda J. Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim +14 more

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

medRxiv(2020)10.1101/2020.09.08.20190561

N/A

3.4DataRank · unranked

132 citations

Jacob C. Ulirsch, Nathan Y. Cheng, Brian L. Trippe, Rebecca S. Fine, Jenkai Miao +24 more

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

Genome Research(2011)10.1101/gr.122267.111

N/A

3.3DataRank · unranked

86 citations

Yoshimi Yanagisawa, Nicholas Rhind, Prisca Liberali, Oliver J. Rando, Nick Rhind +1 more

A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq

Molecular Therapy(2020)10.1016/j.ymthe.2020.07.023

N/A

3.3DataRank · unranked

111 citations

Rebecca C. Larson, Nemanja Despot Marjanovic, Kirk Gosik, Ana P. Castano, Selena J. Lorrey +17 more

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data

Nature Biotechnology(2022)10.1038/s41587-022-01288-0

N/A

3.3DataRank · unranked

128 citations

Prisca Liberali, Livnat Jerby‐Arnon, Livnat Jerby-Arnon

Blood and immune development in human fetal bone marrow and Down syndrome

Nature(2021)10.1038/s41586-021-03929-x

N/A

3.2DataRank · unranked

160 citations

Simone Webb, Issac Goh, Mariana Quiroga Londoño, Gary Reynolds, Michael Mather +60 more

A human breast atlas integrating single-cell proteomics and transcriptomics

Developmental Cell(2022)10.1016/j.devcel.2022.05.003

Top 7%

3.2DataRank

Top 7%163 citations

Carman Man-Chung Li, Jennifer M. Rosenbluth, Laura M. Selfors, Nomeda Girnius, Ron C.J. Schackmann +15 more

Evolutionary principles of modular gene regulation in yeasts

eLife(2013)10.7554/elife.00603

N/A

3.2DataRank · unranked

90 citations

Sushmita Roy, Mark P Styczynsky, Jenna Pfiffner, Courtney French, Amanda Socha +11 more

Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells*

Molecular & Cellular Proteomics(2019)10.1074/mcp.ra118.001259

N/A

3.2DataRank · unranked

120 citations

Andrew Rhoads, Alexandra R. Cocco, Ryan Peckner, Adam L. Haber, Lawrence D. Schweitzer +8 more

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

Nature Communications(2021)10.1038/s41467-021-22851-4

N/A

3.0DataRank · unranked

107 citations

Prisca Liberali, Jiarui Ding

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

Cell(2021)10.1016/j.cell.2021.04.032

N/A

2.9DataRank · unranked

100 citations

Christopher O. Barnes, Basak Eraslan, Andrew Hudak, Jennifer R. Keeffe, Lisa A. Cosimi +34 more

Towards a Human Cell Atlas: Taking Notes from the Past

Trends in Genetics(2021)10.1016/j.tig.2021.03.007

Top 8%

2.9DataRank

Top 8%97 citations

Prisca Liberali, Sarah A. Teichmann, Rik G.H. Lindeboom

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

Compressed sensing for highly efficient imaging transcriptomics

Nature Biotechnology(2021)10.1038/s41587-021-00883-x

N/A

2.8DataRank · unranked

49 citations

Brooke Simonton, Jon Bezney, Evan Murray, Shahul Alam, Anubhav Sinha +6 more

Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing

PLOS Biology(2022)10.1371/journal.pbio.3001532

N/A

2.7DataRank · unranked

107 citations

Alok Jaiswal, Mukund Varma, Tyler Laszewski, Angelo Grauel, Abdifatah S. Omar +11 more

Spatial host–microbiome sequencing reveals niches in the mouse gut

Nature Biotechnology(2023)10.1038/s41587-023-01988-1

N/A

2.7DataRank · unranked

121 citations

Martin Stražar, James G. Wilson, Prisca Liberali, Sanja Vicković, Preben Bo Mortensen +1 more

Using viral load and epidemic dynamics to optimize pooled testing in resource-constrained settings

Science Translational Medicine(2021)10.1126/scitranslmed.abf1568

N/A

2.7DataRank · unranked

59 citations

James A. Hay, Brendan Blumenstiel, Maegan Harden, Michelle Cipicchio, Jon Bezney +8 more

Gene duplication and the evolution of ribosomal protein gene regulation in yeast

Proceedings of the National Academy of Sciences(2010)10.1073/pnas.0911905107

N/A

2.6DataRank · unranked

74 citations

Jenna Pfiffner, Courtney French, Amanda Socha, Prisca Liberali, Courtney E. French +2 more

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization

BMC Bioinformatics(2018)10.1186/s12859-018-2255-6

N/A

2.6DataRank · unranked

59 citations

Prisca Liberali, Carl G. de Boer

Building a high-quality Human Cell Atlas

Nature Biotechnology(2021)10.1038/s41587-020-00812-4

N/A

2.6DataRank · unranked

80 citations

Jay W. Shin, Anna Hupalowska, Prisca Liberali, Holger Heyn, Orit Rozenblatt–Rosen +1 more

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Molecular Systems Biology(2012)10.1038/msb.2012.50

N/A

2.6DataRank · unranked

51 citations

Ilan Wapinski, Hanah Margalit, Prisca Liberali, Nir Friedman, Naomi Habib

ImmVar project: Insights and design considerations for future studies of “healthy” immune variation

Seminars in Immunology(2015)10.1016/j.smim.2015.03.003

Top 9%

2.5DataRank

Top 9%67 citations

Nir Hacohen, Diane Mathis, Prisca Liberali, Barbara E. Stranger, Christophe Benoıst +1 more

A single-cell and single-nucleus RNA-seq toolbox for fresh and frozen human tumors

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/761429

N/A

2.5DataRank · unranked

68 citations

Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Indresh Singh +44 more

Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

Cell(2024)10.1016/j.cell.2024.07.035

N/A

2.5DataRank · unranked

109 citations

Anna Hupalowska, Prisca Liberali, Jennifer E. Rood

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity

Journal of Experimental Medicine(2016)10.1084/jem.20151118

N/A

2.5DataRank · unranked

62 citations

Takaaki Kondo, Sheng Xiao, Nir Yosef, Jellert T. Gaublomme, Chuan Wu +6 more

Brain Chimeroids reveal individual susceptibility to neurotoxic triggers

Nature(2024)10.1038/s41586-024-07578-8

N/A

2.5DataRank · unranked

90 citations

Irene Faravelli, Tyler Faits, Sophia Andreadis, Sebastiano Trattaro, Xian Adiconis +10 more

An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

Cell Reports(2020)10.1016/j.celrep.2020.108433

N/A

2.5DataRank · unranked

90 citations

Asaf Madi, Nir Yosef, Norio Chihara, Amit Awasthi, Caroline Pot +20 more

GeNets: a unified web platform for network-based genomic analyses

Nature Methods(2018)10.1038/s41592-018-0039-6

N/A

2.4DataRank · unranked

63 citations

April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld, David An +21 more

EZH2 promotes a bi-lineage identity in basal-like breast cancer cells

Oncogene(2012)10.1038/onc.2012.390

N/A

2.4DataRank · unranked

37 citations

T Hadar, Y. Karamansha, L Liberman, I Waldhorn, Irit Gat-Viks +14 more

The Human Cell Atlas from a cell census to a unified foundation model

Nature(2024)10.1038/s41586-024-08338-4

Top 9%

2.4DataRank

Top 9%134 citations

Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah A. Teichmann +4 more

Transcriptome-scale RNase-footprinting of RNA-protein complexes

Nature Biotechnology(2016)10.1038/nbt.3441

N/A

2.4DataRank · unranked

75 citations

Ruisheng Song, Hailiang Huang, Prisca Liberali, Kevin Struhl, Zhe Ji

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.31.016972

N/A

2.4DataRank · unranked

90 citations

Nikolas L. Jorstad, Qiwen Hu, Blue B. Lake, Wei Tian, Brian E. Kalmbach +99 more

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

Genome Research(2018)10.1101/gr.240390.118

N/A

2.3DataRank · unranked

78 citations

Jenny Chen, Rachel E. Gate, Meena Subramaniam, Tushar Bhangale, Mark N. Lee +18 more

Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain

Nature Genetics(2024)10.1038/s41588-024-01685-y

Top 9%

2.3DataRank

Top 9%179 citations

Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C. White, Bernard Ng +22 more

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium

Communications Biology(2022)10.1038/s42003-022-03050-3

N/A

2.2DataRank · unranked

83 citations

Denis Schapiro, Konstantin Carlberg, Britta Lötstedt, Ludvig Larsson, Franziska Hildebrandt +9 more

Scalable genetic screening for regulatory circuits using compressed Perturb-seq

Nature Biotechnology(2023)10.1038/s41587-023-01964-9

N/A

2.2DataRank · unranked

96 citations

Loic Binan, Jon Bezney, Brooke Simonton, Jahanara Freedman, Chris J. Frangieh +8 more

The Human Cell Atlas White Paper

arXiv (Cornell University)(2018)10.17863/cam.40032

Top 10%

2.2DataRank

Top 10%41 citations

Sarah A. Teichmann, Orit Rozenblatt‐Rosen, Michael J. T. Stubbington, Kristin G. Ardlie, Ido Amit +76 more

The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis

ImmunoHorizons(2020)10.4049/immunohorizons.1900099

N/A

2.2DataRank · unranked

81 citations

Y Grace Cao, Matthew B. Gologorsky, Jessica A. Li, Adam L. Haber, Moshe Biton +5 more

A cell atlas foundation model for scalable search of similar human cells

Nature(2024)10.1038/s41586-024-08411-y

N/A

2.1DataRank · unranked

114 citations

Tony Kuo, Daryle J. DePianto, Omar Salem, Tobias Heigl, Nathaniel Diamant +9 more

Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion

Molecular and Cellular Biology(2015)10.1128/mcb.01105-14

N/A

2.1DataRank · unranked

55 citations

Catherine Callister, Alon Goren, Nir Yosef, Neha Garg, Vahid Khoddami +4 more

A single cell atlas of human and mouse white adipose tissue

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.09.466968

N/A

2.0DataRank · unranked

57 citations

Christopher Jacobs, Adam L. Essene, Deepti Pant, Danielle Tenen, Georgia Colleluori +38 more

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

Nature Communications(2020)10.1038/s41467-020-15022-4

N/A

2.0DataRank · unranked

81 citations

Carl G. de Boer, Charles P. Fulco, Caleb A. Lareau, Masahiro Kanai, Jacob C. Ulirsch +12 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

N/A

2.0DataRank · unranked

43 citations

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

An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease

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0.852DataRank · unranked

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0.851DataRank · unranked

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Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2001250117

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.10.376509

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Science(2014)10.1126/science.1254665

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0.820DataRank · unranked

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0.819DataRank · unranked

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Proceedings of the National Academy of Sciences(2019)10.1073/pnas.1821068116

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0.815DataRank · unranked

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0.813DataRank · unranked

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Nature Neuroscience(2017)10.1038/nn.4537

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0.808DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.07.515446

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0.808DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/461228

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0.803DataRank · unranked

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Nature Immunology(2013)10.1038/ni.2587

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0.796DataRank · unranked

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Nature(2017)10.1038/nature24480

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0.792DataRank · unranked

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Cell Reports(2018)10.1016/j.celrep.2018.11.056

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0.791DataRank · unranked

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Nature Cell Biology(2017)10.1038/ncb3563

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0.790DataRank · unranked

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Annual Review of Cell and Developmental Biology(2015)10.1146/annurev-cellbio-100913-012908

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0.788DataRank · unranked

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Cell(2011)10.1016/j.cell.2011.10.022

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0.781DataRank · unranked

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Nano Letters(2012)10.1021/nl3042917

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0.776DataRank · unranked

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0.768DataRank · unranked

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Cell(2021)10.1016/j.cell.2021.08.020

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0.766DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.14.338418

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0.760DataRank · unranked

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Molecular Biology and Evolution(1998)10.1093/oxfordjournals.molbev.a025992

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0.747DataRank · unranked

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0.746DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.912717

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0.737DataRank · unranked

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eLife(2013)10.7554/elife.01114

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0.734DataRank · unranked

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Nature Immunology(2017)10.1038/ni.3683

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0.729DataRank · unranked

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Nature Methods(2009)10.1038/nmeth.1404

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0.716DataRank · unranked

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0.709DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.20.890327

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0.702DataRank · unranked

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0.701DataRank · unranked

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(2017)10.7554/elife.27041.011

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0.700DataRank

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Stem Cell Reports(2013)10.1016/j.stemcr.2013.07.004

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0.700DataRank · unranked

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0.697DataRank · unranked

103 citations

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arXiv (Cornell University)(2022)10.48550/arxiv.2211.03553

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0.684DataRank · unranked

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0.680DataRank · unranked

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0.677DataRank · unranked

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0.676DataRank

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.16.383307

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0.673DataRank · unranked

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0.673DataRank · unranked

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0.661DataRank · unranked

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0.653DataRank · unranked

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0.649DataRank

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0.644DataRank · unranked

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Current Biology(2010)10.1016/j.cub.2010.06.022

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0.644DataRank · unranked

72 citations

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0.641DataRank · unranked

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Developmental Cell(2012)10.1016/j.devcel.2012.08.009

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0.628DataRank · unranked

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Leukemia(2012)10.1038/leu.2012.33

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0.627DataRank · unranked

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Nature Immunology(2023)10.1038/s41590-023-01437-w

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0.626DataRank · unranked

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0.617DataRank · unranked

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Cancer Cell(2022)10.1016/j.ccell.2022.04.005

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0.617DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.18.500470

N/A

0.614DataRank · unranked

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Nature Methods(2023)10.1038/s41592-023-01766-6

N/A

0.612DataRank · unranked

58 citations

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Cold Spring Harbor Perspectives in Biology(2020)10.1101/cshperspect.a035733

N/A

0.605DataRank · unranked

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Nature Reviews Immunology(2011)10.1038/nri3109

N/A

0.598DataRank · unranked

53 citations

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Oncogene(1998)10.1038/sj.onc.1202250

N/A

0.596DataRank · unranked

52 citations

Sarit Cohen, Esther Cohen, Irit Bar-Am, Sara Lavi, Esther Ganelin Cohen +2 more

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Science(2016)10.1126/science.aaf5453

N/A

0.590DataRank · unranked

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Bioinformatics(2002)10.1093/bioinformatics/18.suppl_1.s258

N/A

0.581DataRank · unranked

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Nature(2023)10.1038/s41586-023-06445-2

Top 34%

0.569DataRank

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Cell(2024)10.1016/j.cell.2024.04.038

N/A

0.567DataRank · unranked

14 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/773408

N/A

0.565DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.01.322420

N/A

0.564DataRank · unranked

11 citations

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Nature Medicine(2020)10.1038/s41591-020-0975-4

N/A

0.564DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.29.563503

N/A

0.564DataRank · unranked

11 citations

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MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis

Genome Biology(2012)10.1186/gb-2012-13-1-r6

N/A

0.561DataRank · unranked

41 citations

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Nature Methods(2024)10.1038/s41592-024-02495-0

N/A

0.557DataRank · unranked

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Nature Biotechnology(2013)10.1038/nbt.2519

N/A

0.554DataRank · unranked

37 citations

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An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

Nature Communications(2014)10.1038/ncomms5893

N/A

0.546DataRank · unranked

37 citations

Jason Trigg, Prisca Liberali, Bonnie Berger, Leonid Chindelevitch

Physical Module Networks: an integrative approach for reconstructing transcription regulation

Bioinformatics(2011)10.1093/bioinformatics/btr222

N/A

0.546DataRank · unranked

37 citations

Prisca Liberali, Nir Friedman, Noa Novershtern

Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq

Nature Communications(2024)10.1038/s41467-024-47290-9

N/A

0.542DataRank · unranked

36 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/743039

N/A

0.535DataRank · unranked

8 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/191056

N/A

0.533DataRank · unranked

34 citations

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Science Advances(2021)10.1126/sciadv.abd2710

N/A

0.524DataRank · unranked

32 citations

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The π-calculus as an Abstraction for Biomolecular Systems

Natural Computing Series(2004)10.1007/978-3-642-18734-6_11

N/A

0.524DataRank · unranked

32 citations

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Alzheimer's & Dementia(2020)10.1002/alz.038589

N/A

0.505DataRank · unranked

28 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.23.525200

N/A

0.505DataRank · unranked

9 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.03.587267

N/A

0.495DataRank · unranked

14 citations

Sara Whiteman, Tal Gilboa, Wendy Trieu, Siddharth Iyer, Bogdan Budnik +11 more

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Nature Communications(2023)10.1038/s41467-023-43790-2

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0.494DataRank · unranked

26 citations

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Journal of Experimental Medicine(2018)10.1084/jem.20180300

N/A

0.489DataRank · unranked

25 citations

Orr Ashenberg, Jason Pyrdol, Adrienne M. Luoma, Matan Hofree, Elena Christian +10 more

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.26.482041

N/A

0.489DataRank · unranked

12 citations

Alexandra Schnell, Maryann Zhao, Linglin Huang, Yu Hou, Elena Christian +13 more

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Nature Biotechnology(2020)10.1038/s41587-020-0665-2

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0.485DataRank · unranked

7 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.19.639050

N/A

0.483DataRank · unranked

24 citations

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Nature Immunology(2021)10.1038/s41590-021-00895-4

N/A

0.470DataRank · unranked

22 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.11.245472

N/A

0.469DataRank · unranked

8 citations

Prisca Liberali, Livnat Jerby‐Arnon, Livnat Jerby-Arnon

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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

Author Correction: A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

Nature(2022)10.1038/s41586-021-04373-7

N/A

0.460DataRank · unranked

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eLife(2017)10.7554/elife.20937

N/A

0.442DataRank · unranked

18 citations

Jinsuk Kang, Arvind Shakya, Marcin Tabaka, Elke A. Jarboe, Prisca Liberali +2 more

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arXiv (Cornell University)(2020)10.48550/arxiv.2012.12961

N/A

0.438DataRank · unranked

10 citations

Prisca Liberali, Brian Cleary

scSVA: an interactive tool for big data visualization and exploration in single-cell omics

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/512582

N/A

0.434DataRank · unranked

17 citations

Joshua Gould, Prisca Liberali, Marcin Tabaka

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.27.449937

N/A

0.434DataRank · unranked

17 citations

Bo Yuan, Jessica X. Hjaltelin, Chunlei Zheng, Chen Yuan, Jihye Kim +22 more

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bioRxiv (Cold Spring Harbor Laboratory)(2015)10.1101/031385

N/A

0.425DataRank · unranked

9 citations

Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Jacob H. Hanna +4 more

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bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/605436

N/A

0.425DataRank · unranked

16 citations

Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +15 more

Pan-cancer single cell RNA-seq uncovers recurring programs of cellular heterogeneity

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/807552

N/A

0.425DataRank · unranked

16 citations

Rotem Tal, Zhanna Orlova, Michael S. Cuoco, James M. McFarland, Allison C. Warren +21 more

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Nature Genetics(2024)10.1038/s41588-024-01958-6

N/A

0.416DataRank · unranked

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Lecture Notes in Computer Science(2024)10.1007/978-1-0716-3989-4_2

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0.416DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.03.657653

N/A

0.405DataRank · unranked

6 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.29.493705

N/A

0.399DataRank · unranked

1 citations

Gila Lithwick-Yanai, Xian Adiconis, Florian Oberstrass, Nika Iremadze, Kathryn Geiger-Schuller +11 more

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.20.567825

N/A

0.390DataRank · unranked

9 citations

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Nature Biotechnology(2025)10.1038/s41587-025-02702-z

N/A

0.385DataRank · unranked

12 citations

Jure Leskovec, Prisca Liberali, Hanchen Wang

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/853457

N/A

0.385DataRank · unranked

12 citations

Prisca Liberali, Jiarui Ding

MAUDE: Inferring expression changes in sorting-based CRISPR screens

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/819649

N/A

0.382DataRank · unranked

3 citations

John P. Ray, Nir Hacohen, Prisca Liberali, John Ray, Carl G. de Boer

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.27.477911

N/A

0.381DataRank · unranked

6 citations

Kristina M. Holton, Richard M. Giadone, Ceren Ozek, Monika Saxena, Samara Santiago +14 more

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/217133

N/A

0.368DataRank · unranked

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Genome Biology(2025)10.1186/s13059-025-03499-5

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0.363DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.911966

N/A

0.361DataRank · unranked

7 citations

Allon Wagner, Johannes Fessler, Julian Avila-Pacheco, Jim Karminski, Sarah Zaghouani +22 more

TACCO: Unified annotation transfer and decomposition of cell identities for single-cell and spatial omics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.02.508471

Top 49%

0.360DataRank

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Noa Moriel, Evan Murray, Fei Chen, Johanna Klughammer, Prisca Liberali +4 more

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British Journal of Cancer(1995)10.1038/bjc.1995.10

N/A

0.360DataRank · unranked

10 citations

M Lahav, P Raanani, R. Singer, M Sagiv, S Giler +6 more

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.09.471942

N/A

0.357DataRank · unranked

6 citations

Liming Tao, Fulong Yu, Liam D. Cato, Blake Cohen, Xiaotian Liao +7 more

Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/868752

N/A

0.353DataRank · unranked

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Brenton R. Paolella, Allison C. Warren, Kathryn Geiger-Schuller, Tsukasa Shibue, Michael Rothberg +18 more

Author Correction: Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Nature Methods(2018)10.1038/s41592-018-0237-2

N/A

0.352DataRank · unranked

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Nature Cancer(2025)10.1038/s43018-025-01053-7

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0.351DataRank · unranked

9 citations

Thinh T. Nguyen, Atharva Bhagwat, Akhil Kumar, Bruno Giotti, Benjamin Kepecs +29 more

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.28.546977

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0.349DataRank

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Trends in Genetics(1995)10.1016/s0168-9525(00)89117-9

N/A

0.345DataRank · unranked

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Prisca Liberali, Eva Jablonka

A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest

Cell Reports(2020)10.1016/j.celrep.2020.108392

N/A

0.345DataRank · unranked

9 citations

Caroline S. Mock, Veena Venkatachalam, Jose Reyes, Kyle W. Karhohs, Trudy G. Oliver +5 more

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.31.466532

N/A

0.345DataRank · unranked

9 citations

Katherine Tooley, Giulia Escobar, Gitanjali Dandekar, Asaf Madi, Ella Goldschmidt +6 more

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Zenodo (CERN European Organization for Nuclear Research)(2020)10.5281/zenodo.4001718

Top 52%

0.331DataRank

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Neurosurgery(2016)10.1227/01.neu.0000489712.44702.0d

N/A

0.330DataRank · unranked

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Cancer Cell(2025)10.1016/j.ccell.2025.05.009

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0.330DataRank · unranked

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Meng Xiao He, Ziad Bakouny, Abhay Kanodia, Sara Napolitano, Jingyi Wu +25 more

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.11.612340

N/A

0.324DataRank · unranked

5 citations

Steven T. Rutherford, Ziqing Lu, Kerry R. Buchholz, Nicholas J. Skelton, Kangway V. Chuang +16 more

Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse

Nature(2022)10.1038/s41586-022-04562-y

N/A

0.317DataRank · unranked

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.10.627865

N/A

0.312DataRank · unranked

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Xinhao Liu, Minsheng Hao, Tianyu Liu, Prisca Liberali, Yong‐Ju Lee

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Molecular Systems Biology(2015)10.15252/msb.20156548

N/A

0.312DataRank · unranked

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Jason Trigg, Prisca Liberali, Bonnie Berger, Leonid Chindelevitch

The G1/S transition in mammalian stem cells in vivo is autonomously regulated by cell size

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.09.588781

N/A

0.312DataRank · unranked

7 citations

Shuyuan Zhang, Gustavo de Medeiros, Prisca Liberali, Jan M. Skotheim, Shicong Xie

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.23.167098

N/A

0.312DataRank · unranked

7 citations

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Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.05.136358

N/A

0.312DataRank · unranked

7 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.26.477748

N/A

0.312DataRank · unranked

7 citations

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.17.430503

N/A

0.307DataRank · unranked

4 citations

Carl G. de Boer, Moran Yassour, Jennifer Molinet, Lin Fan, Xian Adiconis +6 more

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bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.10.499469

Top 54%

0.307DataRank

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/188961

N/A

0.305DataRank · unranked

3 citations

Jenny Chen, Rachel E. Gate, Meena Subramaniam, Tushar Bhangale, Mark N. Lee +18 more

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bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.05.558331

N/A

0.302DataRank · unranked

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Nature Biotechnology(2025)10.1038/s41587-025-02814-6

N/A

0.300DataRank · unranked

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Steven T. Rutherford, Ziqing Lu, Kerry R. Buchholz, Nathaniel Diamant, Jan-Christian Hütter +16 more

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.30.426796

N/A

0.297DataRank · unranked

4 citations

Matan Hofree, Jonathan Chen, Siranush Sarkizova, Joshua D. Pirl, Vjola Jorgji +71 more

Decoding the development of the blood and immune systems during human fetal liver haematopoiesis

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/654210

N/A

0.296DataRank · unranked

5 citations

Rachel A. Botting, Emily Stephenson, Kile Green, Laura Jardine, Emily F. Calderbank +54 more

A single-cell atlas of human and mouse white adipose tissue

Yearbook of Paediatric Endocrinology(2023)10.1530/ey.20.9.2

Top 56%

0.293DataRank

Top 56%4 citations

Essene AL, Pant D, Forrest Y. Tanaka, Di Vincenzo A, Jorgensen AM +46 more

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Proceedings of the National Academy of Sciences(2009)10.1073/pnas.0904478106

N/A

0.292DataRank · unranked

6 citations

Elizabeth Winzeler, Jill P. Mesirov, Prisca Liberali, Dyann F. Wirth, Johanna P. Daily +2 more

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome

medRxiv(2020)10.1101/2020.06.17.20132555

N/A

0.269DataRank · unranked

3 citations

Xingrong Liu, Indresh Singh, Anita Pandit, Alexander Kurilshikov, Rodrigo Bacigalupe +27 more

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bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.10.420463

N/A

0.269DataRank · unranked

5 citations

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The Journal of Immunology(2021)10.4049/jimmunol.206.supp.68.13

N/A

0.262DataRank · unranked

3 citations

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RPS15 and TP53 Co-Mutation Drives B Cell Malignancy through Altered Translation and MYC Activation in a Murine Model

Blood(2020)10.1182/blood-2020-138900

N/A

0.241DataRank · unranked

4 citations

Tamara Ouspenskaia, Doris Fu, Peyton Waddicor, Anat Biran, Aviv Liani +29 more

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bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.25.457678

N/A

0.241DataRank · unranked

4 citations

Jideofor Ezike, Anton Afanassiev, Laura Greenstreet, Stephen Zhang, Jennifer Whangbo +14 more

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Nature Biotechnology(2025)10.1038/s41587-025-02830-6

Top 61%

0.241DataRank

Top 61%4 citations

Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernández‐García +11 more

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

Cell(2015)10.1016/j.cell.2015.09.044

N/A

0.241DataRank · unranked

4 citations

Nathan Haseley, Douglas Brown, Cristina Penaranda, John J. Trombetta, Rahul Satija +8 more

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bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/091926

N/A

0.241DataRank · unranked

4 citations

Le Cong, Matthew E. Hurles, Prisca Liberali, Brian Cleary

Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.20.517242

N/A

0.233DataRank · unranked

3 citations

Sonia M. Dubois, Frank A. Buquicchio, Yu-Hsin Hsieh, Kopal Garg, Pauline Kautz +24 more

Joint Embedding vs Reconstruction: Provable Benefits of Latent Space Prediction for Self Supervised Learning

arXiv (Cornell University)(2025)10.48550/arxiv.2505.12477

N/A

0.226DataRank · unranked

3 citations

Mark Ibrahim, Tommaso Biancalani, Prisca Liberali, Randall Balestriero, Hugues Van Assel

HTAPP_TST- Nuclei isolation from frozen tissue v2

(2020)10.17504/protocols.io.bhbcj2iw

N/A

0.219DataRank · unranked

1 citations

Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Prisca Liberali, Åsa Segerstolpe +2 more

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bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.22.590125

Top 63%

0.218DataRank

Top 63%3 citations

Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Olena Kuksenko +11 more

Erratum: Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples

Nature Methods(2014)10.1038/nmeth0214-210e

N/A

0.212DataRank · unranked

2 citations

Diego Borges-Rivera, Rahul Satija, David S. DeLuca, Michele A. Busby, Aaron M. Berlin +11 more

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arXiv (Cornell University)(2018)10.48550/arxiv.1811.11790

N/A

0.208DataRank · unranked

3 citations

William Stephenson, Geoffrey Schiebinger, Jonathan H. Huggins, Trevor Campbell, Prisca Liberali +2 more

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bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/655753

N/A

0.208DataRank · unranked

3 citations

Alexandra Schnell, Louis V. Cammarata, Aaron Yao‐Smith, Prisca Liberali, Vijay K. Kuchroo +3 more

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Nature Reviews Genetics(2022)10.1038/s41576-022-00486-5

N/A

0.208DataRank · unranked

3 citations

Prisca Liberali, Eric E. Schadt, Joyce Y. Tung, D. Gary Gilliland

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bioRxiv (Cold Spring Harbor Laboratory)(2018)10.1101/476036

N/A

0.208DataRank · unranked

3 citations

Bo Li, Cristin McCabe, Abigail Knecht, Eugene Drokhlyansky, Nicholas Van Wittenberghe +10 more

Gene context drift identifies drug targets to mitigate cancer treatment resistance

Cancer Cell(2025)10.1016/j.ccell.2025.06.005

N/A

0.208DataRank · unranked

3 citations

Sabrina Terranova, Erica Nathan, Linda P. Hu, Jessica T. Taylor, Katherine E. Masih +29 more

Reconstructing Gene Histories in Ascomycota Fungi

Methods in Enzymology(2010)10.1016/s0076-6879(10)70018-5

N/A

0.208DataRank · unranked

3 citations

Prisca Liberali, Ilan Wapinski

Shuffle-Seq: En masse combinatorial encoding for n -way genetic interaction screens

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/861443

N/A

0.208DataRank · unranked

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Avinash Waghray, Julia Waldman, Isaac Wakiro, Mei-Ju Su, Sébastien Vigneau +6 more

HTAPP_Dissociation of human metastatic breast cancer core needle biopsy to a single-cell suspension for single-cell RNA-seq v1

(2019)10.17504/protocols.io.4j7gurn

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Julia Waldman, Jingyi Wu, Abhay Kanodia, Sébastien Vigneau, Asaf Rotem +5 more

Supplemental Table 4 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

(2023)10.1158/1078-0432.22476824

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Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +16 more

Supplemental Table 3 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22476827.v1

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Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +16 more

HTAPP_Processing human ovarian cancer ascites to a single-cell suspension for single-cell RNA-seq v1

(2019)10.17504/protocols.io.4kbgusn

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Parin Shah, Mei-Ju Su, Isaac Wakiro, Sara Napolitano, Jingyi Wu +7 more

Author response: Enforcement of developmental lineage specificity by transcription factor Oct1

(2017)10.7554/elife.20937.039

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0DataRank · unranked

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Jinsuk Kang, Arvind Shakya, Marcin Tabaka, Elke A. Jarboe, Prisca Liberali +2 more

Supplemental Table 6 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

(2023)10.1158/1078-0432.22476818

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Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +16 more

DroNc-seq step-by-step v1

(2017)10.17504/protocols.io.md2c28e

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Author Correction: Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

Nature Biotechnology(2025)10.1038/s41587-025-02602-2

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Ana M. Meireles, Reuben Moncada, Yushu Chen, Ping Wu, Joshua Gould +38 more

HTAPP_TST- Nuclei isolation from frozen tissue v1

(2019)10.17504/protocols.io.4pggvjw

N/A

0DataRank · unranked

0 citations

Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Orit Rozenblatt–Rosen, Prisca Liberali +2 more

Remodeling of human colon plasma cell repertoire in ulcerative colitis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.14.480403

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0 citations

Basak Eraslan, Andrew Hudak, Eric M. Brown, Dallis Sergio, Toni Marie Delorey +12 more

Author Correction: B-cell-specific checkpoint molecules that regulate anti-tumour immunity

Nature(2025)10.1038/s41586-025-08858-7

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Supplemental Table 4 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22476824.v1

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0 citations

Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +16 more

HTAPP_Designing gene panels for neuroblastoma targeted spatial transcriptomics assays v1

(2021)10.17504/protocols.io.bw86phze

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0DataRank · unranked

0 citations

Orr Ashenberg, Anand G. Patel, Natalie Collins, Xiaowei Zhuang, Orit Rozenblatt–Rosen +6 more

A multimodal atlas of COVID-19 severity identifies hallmarks of dysregulated immunity

medRxiv(2025)10.1101/2025.09.19.25334095

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0DataRank · unranked

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Pritha Sen, Christopher V. Cosgriff, Jessica Tantivit, Thomas Eisenhaure, Thomas J. LaSalle +61 more

Hematopoietic Stem Cells Respond Heterogeneously to Inflammatory Signals in an Age-Dependent Manner

Blood(2016)10.1182/blood.v128.22.566.566

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0DataRank · unranked

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Mati Mann, Monika Kowalczyk, Carl de Boer, Jun Wang, Prisca Liberali +4 more

Data used in ECLIPSER methods paper and GTEx snRNA-seq cross-tissue reference map analysis

Zenodo (CERN European Organization for Nuclear Research)(2021)10.5281/zenodo.5725802

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Jiali Wang, Gökçen Eraslan, Duyen T. Nguyen, Andrew R. Hamel, Brian Cole +5 more

Supplementary Figures S1-S7 from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

INDIGO (University of Illinois at Chicago)(2023)10.1158/2159-8290.22541081.v1

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Sai Ma, Lindsay M. LaFave, Arjun J. Bhutkar, Manyuan Liu, Lydia P. DeAngelo +18 more

HTAPP_EZ Nuclei Isolation from frozen tissue v1

(2019)10.17504/protocols.io.4j9gur6

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Cristin McCabe, Eugene Drokhlyansky, Orit Rozenblatt–Rosen, Prisca Liberali, Orit Rozenblatt‐Rosen +1 more

Supplemental Table 13 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

(2023)10.1158/1078-0432.22476833

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0DataRank · unranked

0 citations

Ofir Cohen, Kailey J. Kowalski, Justin G. Kusiel, Jorge E. Buendia-Buendia, Michael S. Cuoco +16 more

Supplementary Table S4 from Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer

Figshare(2025)10.1158/2159-8290.28367843

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0 citations

Rony Chanoch-Myers, Rafaela Sartore, Bruna Paulsen, Simon Gritsch, Hannah Weisman +9 more

PDTM-32. RESOLVING MEDULLOBLASTOMA CELLULAR ARCHITECTURE BY SINGLE-CELL GENOMICS

Neuro-Oncology(2019)10.1093/neuonc/noz175.808

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0DataRank · unranked

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Volker Hovestadt, Kyle Smith, McKenzie Shaw, Alicia Baumgartner, John DeWitt +52 more

Supplementary Table 6 from Integrative Genomic Analysis Implicates Gain of PIK3CA at 3q26 and MYC at 8q24 in Chronic Lymphocytic Leukemia

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22444134.v1

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Megan Hanna, Bethany Tesar, Lillian Werner, Nathalie Pochet, John M. Asara +13 more

Supplemental Table 11 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

(2023)10.1158/1078-0432.22476839

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Table S1: Somatic Mutations from Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair–Deficient Colorectal Cancer

Figshare(2023)10.1158/2326-6066.22542492.v1

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Data used in ECLIPSER methods paper and GTEx snRNA-seq cross-tissue reference map analysis

Zenodo (CERN European Organization for Nuclear Research)(2021)10.5281/zenodo.5725801

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Table S1: Somatic Mutations from Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair–Deficient Colorectal Cancer

(2023)10.1158/2326-6066.22542492

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Data from AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer

(2023)10.1158/2159-8290.c.6549711.v1

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Single-cell Profiling of Mouse Trachea After Sulfur Dioxide Injury Reveals Drivers of Airway Barrier Remodeling

American Journal of Respiratory and Critical Care Medicine(2025)10.1164/ajrccm.2025.211.abstracts.a3349

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641 Spatially organized multicellular immune hubs in MMRd and MMRp colorectal cancer

Regular and Young Investigator Award Abstracts(2021)10.1136/jitc-2021-sitc2021.641

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Supplementary Data from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22476806.v1

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Supplementary Figure Legends 1-2 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

(2023)10.1158/0008-5472.22373727

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Exact Identification of Topologically Essential Interactions in the Networks Derived from Perturbation Experiments

Biophysical Journal(2011)10.1016/j.bpj.2010.12.379

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0DataRank · unranked

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Supplementary Table S2 from Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer

Figshare(2025)10.1158/2159-8290.28367849

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Reward-Guided Iterative Refinement in Diffusion Models at Test-Time with Applications to Protein and DNA Design

arXiv (Cornell University)(2025)10.48550/arxiv.2502.14944

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Supplementary Figure 2 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

(2023)10.1158/0008-5472.22373730

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HTAPP_Designing gene panels for metastatic breast cancer targeted spatial transcriptomics assays v1

(2021)10.17504/protocols.io.bw83phyn

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EPEN-21. IMPAIRED NEURONAL-GLIAL FATE SPECIFICATION IN PEDIATRIC EPENDYMOMA REVEALED BY SINGLE-CELL RNA-SEQ

Neuro-Oncology(2020)10.1093/neuonc/noaa222.158

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0 citations

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Supplementary Figure from AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer

Figshare(2023)10.1158/2159-8290.22541643.v1

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0 citations

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Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing v1

(2018)10.17504/protocols.io.pbhdij6

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David Gennert, Diana Lu, Rahul Satija, Alex K. Shalek, Prisca Liberali +2 more

HTAPP_OCT embedding of snap frozen tumor tissue v1

(2019)10.17504/protocols.io.4n2gvge

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LGG-05. SINGLE CELL RNA SEQUENCING REVEALS MITOGENIC AND PROGENITOR GENE PROGRAMS IN BRAF-REARRANGED PILOCYTIC ASTROCYTOMAS

Neuro-Oncology(2019)10.1093/neuonc/noz036.148

N/A

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Guillaume Bergthold, Kristine Pelton, Sarah Becker, Robert Jones, Claire Sinai +31 more

Supplementary Tables 1-4 from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

(2023)10.1158/0008-5472.22373724

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Data from Revealing Targeted Therapy for Human Cancer by Gene Module Maps

(2023)10.1158/0008-5472.c.6497181

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Single cell RNA-Seq of hematopoietic stem cells reveals a cell cycle-dependent interplay between aging and differentiation

Experimental Hematology(2014)10.1016/j.exphem.2014.07.075

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Itay Tirosh, Dirk Heckl, Prisca Liberali, Monika S. Kowalczyk, Benjamin L. Ebert +1 more

Supplemental Table 2 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22476830.v1

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Supplemental Table 8 from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

INDIGO (University of Illinois at Chicago)(2023)10.1158/1078-0432.22476812.v1

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Systematically quantifying morphological features reveals constraints on organoid phenotypes

Cell Systems(2022)10.1016/j.cels.2022.05.008

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25 citations

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Organoids as tools for fundamental discovery and translation—a Keystone Symposia report

Annals of the New York Academy of Sciences(2022)10.1111/nyas.14874

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Growth of the maternal intestine during reproduction

Cell(2025)10.1016/j.cell.2025.02.015

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