🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Lukas M. Simon

Baylor College of Medicine

ORCID: 0000-0001-6148-8861
Biochemistry, Genetics and Molecular BiologyMedicine

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 2%percentile
3.5Author DataRank

Indexed papers

4in 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 4 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 →

Top data-sharing exemplar

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

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

Papers

Driven by 50 papers — median percentile 38. Top paper: “GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency”.

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

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

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

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

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

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
N/A
1.1DataRank · unranked
1780 citations

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

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

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

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

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

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

Spliceosome-targeted therapies trigger an antiviral immune response in triple-negative breast cancer

Cell(2021)10.1016/j.cell.2020.12.031
N/A
0.814DataRank · unranked
227 citations

Jarey H. Wang, Fade Gong, William Wu, Nicholas J. Neill, Ik Sun Kim +32 more

Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization

Cell Reports(2022)10.1016/j.celrep.2022.111576
N/A
0.784DataRank · unranked
28 citations

Chuangye Qi, Ruoyu Wang, Joo‐Hyung Lee, Jiaofang Shao, Lanxin Bei +10 more

Single-cell multiomics decodes regulatory programs for mouse secondary palate development

Nature Communications(2024)10.1038/s41467-024-45199-x
N/A
0.643DataRank · unranked
23 citations

Akiko Suzuki, Chihiro Iwaya, Guangsheng Pei, Xian Chen, Hiroki Yoshioka +5 more

Single-Cell RNA Sequencing Uncovers Paracrine Functions of the Epicardial-Derived Cells in Arrhythmogenic Cardiomyopathy

Circulation(2021)10.1161/circulationaha.120.052928
N/A
0.593DataRank · unranked
51 citations

Sirisha Cheedipudi, Leila Rouhi, Siyang Fan, Lukas M. Simon, Zhongming Zhao +4 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

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

The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma

Experimental Hematology and Oncology(2024)10.1186/s40164-024-00484-9
N/A
0.494DataRank · unranked
26 citations

Changying Jiang, Alexa A Jordan, Yuxuan Che, Yang Liu, Qingsong Cai +18 more

deCS : A Tool for Systematic Cell Type Annotations of Single-Cell RNA Sequencing Data Among Human Tissues

Genomics Proteomics & Bioinformatics(2022)10.1016/j.gpb.2022.04.001
N/A
0.483DataRank · unranked
24 citations

Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao +1 more

Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders

Genome Research(2020)10.1101/gr.265769.120
N/A
0.470DataRank · unranked
22 citations

Yin‐Ying Wang, Lukas M. Simon, Yulin Dai, Zhongming Zhao, Peilin Jia +1 more

EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data

Patterns(2021)10.1016/j.patter.2021.100311
N/A
0.425DataRank · unranked
16 citations

Zhongming Zhao, Lukas M. Simon, Fangfang Yan

Let-7 restrains an epigenetic circuit in AT2 cells to prevent fibrogenic intermediates in pulmonary fibrosis

Nature Communications(2025)10.1038/s41467-025-59641-1
N/A
0.406DataRank · unranked
14 citations

Md Shafiquzzaman, Maria E. Ruiz-Echartea, Rupa S. Kanchi, Brandon T. Tran, Lukas M. Simon +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

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

DeepFace: Deep-learning-based framework to contextualize orofacial-cleft-related variants during human embryonic craniofacial development

Human Genetics and Genomics Advances(2024)10.1016/j.xhgg.2024.100312
N/A
0.360DataRank · unranked
10 citations

Toshiyuki Itai, Guangsheng Pei, Fangfang Yan, Yan Chu, Xiaoqian Jiang +7 more

TCA cycle mode switch determines the fate of pirtobrutinib-tolerant persister cells in mantle cell lymphoma

Blood(2025)10.1182/blood.2024026919
N/A
0.330DataRank · unranked
7 citations

Qingsong Cai, Yang Liu, Lei Nie, Heng‐Huan Lee, Fangfang Yan +24 more

deCS : A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.19.460993
N/A
0.292DataRank · unranked
6 citations

Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao +1 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

Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease

Science Advances(2025)10.1126/sciadv.adw4917
Top 58%
0.272DataRank
Top 58%5 citations

Citu Citu, Nitesh Enduru, Xian Chen, Chia-Hao Tung, Tirthankar Sinha +10 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

SMARCA4 regulates spatially restricted metabolic plasticity in 3D multicellular tissue

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.21.436346
N/A
0.241DataRank · unranked
4 citations

Eric A. Smith, Yuen San Chan, Mario Loeza Cabrera, Courtney Chambers, Maria Jarvis +9 more

Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin’s Protective Mechanisms in Experimental Bronchopulmonary Dysplasia

Genes(2024)10.3390/genes15060806
N/A
0.230DataRank · unranked
3 citations

Amrit Kumar Shrestha, Shyam Thapa, Sandra L. Grimm, Cristian Coarfa, Fabian Theis +3 more

Investigating gene functions and single-cell expression profiles of de novo variants in orofacial clefts

Human Genetics and Genomics Advances(2024)10.1016/j.xhgg.2024.100313
N/A
0.208DataRank · unranked
3 citations

Fangfang Yan, Andi Liu, Yulin Dai, Chihiro Iwaya, Sarah W. Curtis +7 more

Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer's disease

Research Square(2024)10.21203/rs.3.rs-4622123/v1
N/A
0.208DataRank · unranked
3 citations

Andi Liu, Citu Citu, Nitesh Enduru, Xian Chen, Astrid M. Manuel +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

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

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

EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.15.426387
N/A
0.104DataRank · unranked
1 citations

Zhongming Zhao, Lukas M. Simon, Fangfang Yan

Single-nucleus multiomics reveals the disrupted regulatory programs in three brain regions of sporadic early-onset Alzheimer’s disease

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.25.600720
Top 78%
0.104DataRank
Top 78%1 citations

Citu Citu, Nitesh Enduru, Xian Chen, Astrid M. Manuel, Tirthankar Sinha +8 more

MitoTrace: A Computational Framework for Analyzing Mitochondrial Variation in Single-Cell RNA Sequencing Data

Genes(2023)10.3390/genes14061222
N/A
0DataRank · unranked
67 citations

Wankun Deng, David C. Samuels, Zhongming Zhao, Lukas M. Simon, Mingqiang Wang

Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.02.514609
N/A
0DataRank · unranked
1 citations

Akiko Suzuki, Chihiro Iwaya, Guangsheng Pei, Xian Chen, Hiroki Yoshioka +5 more

Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches

Genes(2021)10.3390/genes12050635
N/A
0DataRank · unranked
20 citations

Johnathan Jia, Yulin Dai, Lukas M. Simon, Zhongming Zhao, Hyun-Hwan Jeong

Let-7 restrains an oncogenic circuit in AT2 cells to prevent fibrogenic cell intermediates in pulmonary fibrosis

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.22.595205
N/A
0DataRank · unranked
1 citations

Md Shafiquzzaman, Maria E. Ruiz-Echartea, Rupa S. Kanchi, Brandon T. Tran, Lukas M. Simon +14 more

Single-cell multiome characterizing intercellular communication and intracellular regulation of epithelium and mesenchymal during secondary palate development in mice

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.09.031
N/A
0DataRank · unranked
0 citations

Yulin Dai, Andi Liu, Toshiyuki Itai, Fangfang Yan, Lukas M. Simon +2 more

Bio-primed machine learning to enhance discovery of relevant biomarkers

npj Precision Oncology(2025)10.1038/s41698-025-00825-9
N/A
0DataRank · unranked
14 citations

Alexander Renwick, Joseph R. Zoeller, Jitendra K. Meena, Nicholas J. Neill, Elizabeth A. Bowling +4 more

INSCT: Integrating millions of single cells using batch-aware triplet neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.16.100024
N/A
0DataRank · unranked
5 citations

Yin‐Ying Wang, Zhongming Zhao, Lukas M. Simon

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data

GigaScience(2020)10.1093/gigascience/giaa122
N/A
0DataRank · unranked
17 citations

Fangfang Yan, Zhongming Zhao, Lukas M. Simon

Longitudinal single-cell transcriptomics of gamma herpesvirus infection in mouse lungs

03.02 - Airway cell biology and immunopathology(2020)10.1183/23120541.lsc-2020.33
N/A
0DataRank · unranked
0 citations

Ilias Angelidis, Meshal Ansari, Christoph H. Mayr, Maximilian Strunz, Lukas M. Simon +3 more

MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer

Cancer Discovery(2024)10.1158/2159-8290.cd-22-0649
N/A
0DataRank · unranked
17 citations

Jarey H. Wang, Nicholas J. Neill, Dianne T. Keough, Nagireddy Putluri, Panagiotis Katsonis +29 more