Daniel J. B. Clarke

Also affiliated with Icahn School of Medicine at Mount Sinai

Agricultural and Biological SciencesBiochemistry, Genetics and Molecular BiologyEconomics, Econometrics and Finance

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

19.2Author DataRank

Indexed papers

19in 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 19 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.

Gene Set Knowledge Discovery with Enrichr

Current Protocols(2021)10.1002/cpz1.90

Top 3%

6.8DataRank

Top 3%3776 citations

Allison Bailey, Maxim V. Kuleshov, Daniel J. B. Clarke, John Erol Evangelista, Sherry L. Jenkins +7 more

Papers

Driven by 46 papers — median percentile 62. Top paper: “Gene Set Knowledge Discovery with Enrichr”.

Gene Set Knowledge Discovery with Enrichr

Current Protocols(2021)10.1002/cpz1.90

Top 3%

6.8DataRank

Top 3%3776 citations

Allison Bailey, Maxim V. Kuleshov, Daniel J. B. Clarke, John Erol Evangelista, Sherry L. Jenkins +7 more

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

Cell Systems(2019)10.1016/j.cels.2019.09.011

N/A

4.7DataRank · unranked

66 citations

Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik +31 more

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules

BMC Bioinformatics(2022)10.1186/s12859-022-04590-5

Top 10%

2.1DataRank

Top 10%112 citations

Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma’ayan +1 more

SigCom LINCS: data and metadata search engine for a million gene expression signatures

Nucleic Acids Research(2022)10.1093/nar/gkac328

Top 11%

2.0DataRank

Top 11%115 citations

Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen +8 more

The FAIR Cookbook - the essential resource for and by FAIR doers

Scientific Data(2023)10.1038/s41597-023-02166-3

N/A

1.8DataRank · unranked

69 citations

Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, Ishwar Chandramouliswaran +57 more

Pan-cancer proteogenomics characterization of tumor immunity

Cell(2024)10.1016/j.cell.2024.01.027

N/A

1.7DataRank · unranked

91 citations

Weiping Ma, Tomer M. Yaron, Francesca Pia Caruso, Nicole Tignor, Joshua M. Wang +95 more

Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources

Nucleic Acids Research(2024)10.1093/nar/gkae1080

Top 15%

1.4DataRank

Top 15%123 citations

Daniel J. B. Clarke, John Erol Evangelista, Nathania Lingam, Avi Ma’ayan, Ido Diamant

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

bioRxiv (Cold Spring Harbor Laboratory)(2019)10.1101/657676

N/A

1.1DataRank · unranked

9 citations

Lily Wang, Alex Jones, Megan L. Wojciechowicz, Denis Torre, Kathleen M. Jagodnik +30 more

Getting Started with LINCS Datasets and Tools

Current Protocols(2022)10.1002/cpz1.487

Top 23%

0.885DataRank

Top 23%35 citations

Eryk Kropiwnicki, Megan L. Wojciechowicz, Kathleen M. Jagodnik, Ingrid Shu, Allison Bailey +10 more

Transforming L1000 profiles to RNA-seq-like profiles with deep learning

BMC Bioinformatics(2022)10.1186/s12859-022-04895-5

Top 23%

0.861DataRank

Top 23%27 citations

Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma’ayan +1 more

Enrichr-KG: bridging enrichment analysis across multiple libraries

Nucleic Acids Research(2023)10.1093/nar/gkad393

N/A

0.819DataRank · unranked

234 citations

Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma’ayan +1 more

Appyters: Turning Jupyter Notebooks into data-driven web apps

Patterns(2021)10.1016/j.patter.2021.100213

N/A

0.729DataRank · unranked

128 citations

Minji Jeon, Daniel Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles S. Dai +19 more

Connecting omics signatures and revealing biological mechanisms with iLINCS

Nature Communications(2022)10.1038/s41467-022-32205-3

N/A

0.719DataRank · unranked

120 citations

Mehdi Fazel‐Najafabadi, Michal Kouril, Behrouz Shamsaei, Juozas Vasiliauskas, Wen Niu +21 more

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs

Database(2023)10.1093/database/baad009

Top 29%

0.701DataRank

Top 29%19 citations

Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon +3 more

Rummagene: massive mining of gene sets from supporting materials of biomedical research publications

Communications Biology(2024)10.1038/s42003-024-06177-7

Top 29%

0.698DataRank

Top 29%26 citations

Giacomo B. Marino, Eden Z. Deng, Zhuorui Xie, John Erol Evangelista, Avi Ma’ayan +1 more

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning

Database(2021)10.1093/database/baab017

N/A

0.542DataRank · unranked

36 citations

John Erol Evangelista, Daniel Stein, Daniel J. B. Clarke, Alexander Lachmann, Maxim V. Kuleshov +4 more

Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics

Cell Reports Methods(2024)10.1016/j.crmeth.2024.100839

Top 37%

0.531DataRank

Top 37%8 citations

Giacomo B. Marino, Daniel J. B. Clarke, Ido Diamant, Adam C. Resnick, Weiping Ma +3 more

Interoperable RNA-Seq analysis in the cloud

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms(2020)10.1016/j.bbagrm.2020.194521

N/A

0.529DataRank · unranked

33 citations

Daniel J. B. Clarke, Denis Torre, Zhuorui Xie, Avi Ma’ayan, Alexander Lachmann

Getting Started with the IDG KMC Datasets and Tools

Current Protocols(2022)10.1002/cpz1.355

Top 38%

0.511DataRank

Top 38%12 citations

Jessica Binder, Jeremy J. Yang, Jayme Holmes, Alexander Lachmann, Daniel J. B. Clarke +7 more

RummaGEO: Automatic mining of human and mouse gene sets from GEO

Patterns(2024)10.1016/j.patter.2024.101072

Top 39%

0.491DataRank

Top 39%17 citations

Daniel J. B. Clarke, Alexander Lachmann, Eden Z. Deng, Avi Ma’ayan, Giacomo B. Marino

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery

Nucleic Acids Research(2023)10.1093/nar/gkad399

Top 39%

0.486DataRank

Top 39%11 citations

Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie +3 more

Making Common Fund data more findable: catalyzing a data ecosystem

GigaScience(2022)10.1093/gigascience/giac105

N/A

0.483DataRank · unranked

24 citations

Arthur Brady, Karl Czajkowski, Jain Aluvathingal, Saranya Canchi, Leonard Hartmanis +38 more

Toxicology knowledge graph for structural birth defects

Communications Medicine(2023)10.1038/s43856-023-00329-2

N/A

0.470DataRank · unranked

22 citations

Daniel J. B. Clarke, Zhuorui Xie, Giacomo B. Marino, Vivian Utti, Sherry L. Jenkins +13 more

Making Common Fund data more findable: Catalyzing a Data Ecosystem

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.05.467504

N/A

0.434DataRank · unranked

6 citations

Arthur Brady, Karl Czajkowski, Jain Aluvathingal, Saranya Canchi, Leonard Hartmanis +33 more

L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine

Nucleic Acids Research(2025)10.1093/nar/gkaf373

Top 44%

0.420DataRank

Top 44%10 citations

John Erol Evangelista, Daniel J. B. Clarke, Avi Ma’ayan, Giacomo B. Marino

Gene set predictor for post-treatment Lyme disease

Cell Reports Medicine(2022)10.1016/j.xcrm.2022.100816

N/A

0.406DataRank · unranked

14 citations

Alison W. Rebman, Jinshui Fan, Mark J. Soloski, John N. Aucott, Avi Ma’ayan +1 more

Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing

Frontiers in Immunology(2021)10.3389/fimmu.2021.636289

N/A

0.406DataRank · unranked

14 citations

Alison W. Rebman, Allison Bailey, Megan L. Wojciechowicz, Sherry L. Jenkins, John Erol Evangelista +11 more

PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices

PeerJ(2023)10.7717/peerj.14927

N/A

0.385DataRank · unranked

12 citations

Kaeli Rizzo, Alon Bartal, Minji Jeon, Daniel J. B. Clarke, Avi Ma’ayan +1 more

The Translational Data Catalog - discoverable biomedical datasets

Scientific Data(2023)10.1038/s41597-023-02258-0

Top 53%

0.325DataRank

Top 53%6 citations

Rocca-Serra, Philippe, Daniel J. B. Clarke, Nirmeen Sallam, François Ancien, Abetare Shabani +8 more

Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.03.560783

Top 54%

0.308DataRank

Top 54%6 citations

Giacomo B. Marino, Eden Z. Deng, Zhuorui Xie, John Erol Evangelista, Avi Ma’ayan +1 more

Playbook workflow builder: Interactive construction of bioinformatics workflows

PLoS Computational Biology(2025)10.1371/journal.pcbi.1012901

N/A

0.269DataRank · unranked

5 citations

John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano R Maurya +36 more

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets

GigaScience(2025)10.1093/gigascience/giaf025

N/A

0.269DataRank · unranked

5 citations

Stephanie Olaiya, John Erol Evangelista, Daniel J. B. Clarke, Avi Ma’ayan, Giacomo B. Marino

Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases

Current Protocols(2025)10.1002/cpz1.70200

N/A

0.241DataRank · unranked

4 citations

Andrew D. Lutsky, Anna I. Byrd, Daniel J. B. Clarke, Abinanda Prabhakaran, Sherry L. Jenkins +2 more

Gene and drug landing page aggregator

Bioinformatics Advances(2022)10.1093/bioadv/vbac013

Top 65%

0.208DataRank

Top 65%3 citations

Maxim V. Kuleshov, Zhuorui Xie, John Erol Evangelista, Marilyn R Meyers, Eryk Kropiwnicki +3 more

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.11.666099

N/A

0.208DataRank · unranked

3 citations

Benjamin Stear, John K. Simmons, Vincent T. Metzger, Praveen Kumar, John Erol Evangelista +39 more

RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.09.588712

Top 65%

0.208DataRank

Top 65%3 citations

Daniel J. B. Clarke, Eden Z. Deng, Avi Ma’ayan, Giacomo B. Marino

D2H2: diabetes data and hypothesis hub

Bioinformatics Advances(2023)10.1093/bioadv/vbad178

Top 66%

0.190DataRank

Top 66%2 citations

Nasheath Ahmed, Zhuorui Xie, Kathleen M. Jagodnik, Jason Han, Daniel J. B. Clarke +5 more

PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.20.427528

N/A

0.165DataRank · unranked

2 citations

Kaeli Rizzo, Alon Bartal, Minji Jeon, Daniel J. B. Clarke, Avi Ma’ayan +1 more

ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.15.508198

N/A

0.104DataRank · unranked

1 citations

Daniel J. B. Clarke, Zhuorui Xie, Giacomo B. Marino, Vivian Utti, Taha M. Ahooyi +13 more

The Translational Data Catalog - discoverable biomedical datasets

Oxford University Research Archive (ORA) (University of Oxford)(2022)10.5281/zenodo.7157285

Top 78%

0.104DataRank

Top 78%1 citations

Rocca-Serra, Philippe, Daniel J. B. Clarke, Nirmeen Sallam, François Ancien, Abetare Shabani +8 more

A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.30.657124

N/A

0DataRank · unranked

0 citations

Giacomo B. Marino, Avi Ma’ayan, Daniel J. B. Clarke

The COVID-19 Drug and Gene Set Library

Patterns(2020)10.1016/j.patter.2020.100090

N/A

0DataRank · unranked

85 citations

Daniel Stein, Daniel J. B. Clarke, Eryk Kropiwnicki, Kathleen M. Jagodnik, Alon Bartal +9 more

EnrichrBot: Twitter bot tracking tweets about human genes

Bioinformatics(2020)10.1093/bioinformatics/btaa240

N/A

0DataRank · unranked

6 citations

Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma’ayan +1 more

Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays

STAR Protocols(2024)10.1016/j.xpro.2024.103457

N/A

0DataRank · unranked

0 citations

Eden Z. Deng, Daniel J. B. Clarke, Ido Diamant, Adam C. Resnick, Weiping Ma +3 more

sc2DAT: workflow for targeting tumor subpopulations of single cells

Bioinformatics Advances(2024)10.1093/bioadv/vbaf237

N/A

0DataRank · unranked

0 citations

Anna I Byrd, Nasheath Ahmed, Daniel J. B. Clarke, Avi Ma’ayan, Giacomo B. Marino

Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells

Aging Cell(2023)10.1111/acel.13809

N/A

0DataRank · unranked

9 citations

Reid H. Fleishman, Zhuorui Xie, Giacomo B. Marino, Daniel J. B. Clarke, Avi Ma’ayan +1 more

Daniel J. B. Clarke

Indexed papers

Top data-sharing exemplar

Papers