Anshul Kundaje

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

69.4Author DataRank

Indexed papers

22in 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 22 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.

Integrative analysis of 111 reference human epigenomes

Nature(2015)10.1038/nature14248

Top 1%

10.0DataRank

Top 1%7189 citations

Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen +93 more

Papers

Driven by 137 papers — median percentile 89. Top paper: “Opportunities and obstacles for deep learning in biology and medicine”.

Opportunities and obstacles for deep learning in biology and medicine

bioRxiv (Cold Spring Harbor Laboratory)(2017)10.1101/142760

N/A

11.2DataRank · unranked

310 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

Integrative analysis of 111 reference human epigenomes

Nature(2015)10.1038/nature14248

Top 1%

10.0DataRank

Top 1%7189 citations

Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen +93 more

Integrative annotation of chromatin elements from ENCODE data

Nucleic Acids Research(2012)10.1093/nar/gks1284

Top 2%

7.9DataRank

Top 2%628 citations

Jason Ernst, Steven P. Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht +10 more

A comparative encyclopedia of DNA elements in the mouse genome

Nature(2014)10.1038/nature13992

Top 2%

7.9DataRank

Top 2%1946 citations

Yong Cheng, Alessandra Breschi, Jost Vielmetter, Weisheng Wu, Tyrone Ryba +150 more

Genome-wide enhancer maps link risk variants to disease genes

Nature(2021)10.1038/s41586-021-03446-x

N/A

7.7DataRank · unranked

764 citations

Drew T. Bergman, Charles P. Fulco, Philine Guckelberger, Benjamin R. Doughty, Tejal A. Patwardhan +27 more

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Nature Genetics(2022)10.1038/s41588-022-01088-x

N/A

7.5DataRank · unranked

331 citations

Stephanie Nevins, Derek C. Chen, Roxanne Chiu, Aaron M. Horning, Tuhin K. Guha +13 more

Modeling gene expression using chromatin features in various cellular contexts

Genome Biology(2012)10.1186/gb-2012-13-9-r53

Top 3%

6.9DataRank

Top 3%299 citations

Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng +6 more

Defining functional DNA elements in the human genome

Proceedings of the National Academy of Sciences(2014)10.1073/pnas.1318948111

Top 3%

6.9DataRank

Top 3%755 citations

Valentina Snetkova, Louis Philip Benoit Bouvrette, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward +29 more

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Nature(2020)10.1038/s41586-020-2493-4

Top 3%

6.4DataRank

Top 3%2615 citations

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal +501 more

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Genome Biology(2012)10.1186/gb-2012-13-9-r48

Top 3%

6.2DataRank

Top 3%269 citations

Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje +7 more

GENCODE: reference annotation for the human and mouse genomes in 2023

Nucleic Acids Research(2022)10.1093/nar/gkac1071

Top 4%

5.1DataRank

Top 4%663 citations

Sílvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E Loveland, Jonathan M. Mudge +57 more

GENCODE 2025: reference gene annotation for human and mouse

Nucleic Acids Research(2024)10.1093/nar/gkae1078

Top 8%

2.7DataRank

Top 8%348 citations

Sílvia Carbonell Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt, Irwin Jungreis +51 more

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

Nature Genetics(2022)10.1038/s41588-022-01069-0

N/A

2.5DataRank · unranked

159 citations

Shengen Shawn Hu, José Verdezoto Mosquera, Wei Feng, Chani J. Hodonsky, Doris Wong +19 more

The ENCODE Uniform Analysis Pipelines

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.04.535623

Top 11%

2.0DataRank

Top 11%102 citations

Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud +55 more

An encyclopedia of enhancer-gene regulatory interactions in the human genome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.09.563812

Top 11%

1.9DataRank

Top 11%120 citations

Kristy S. Mualim, Alireza Karbalayghareh, Maya U. Sheth, Kushal K. Dey, Evelyn Jagoda +41 more

Predicting gene expression in massively parallel reporter assays: A comparative study

Human Mutation(2017)10.1002/humu.23197

N/A

1.7DataRank · unranked

52 citations

Haoyang Zeng, Matthew D. Edwards, Gamze Gürsoy, Kevin Tian, R. Alan Harris +20 more

Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum

Nature Genetics(2021)10.1038/s41588-021-00848-5

N/A

1.7DataRank · unranked

68 citations

Alexandro E. Trevino, T. Xiang, Anshul Kundaje, Arthur Grossman, William J. Greenleaf +1 more

Latent human herpesvirus 6 is reactivated in CAR T cells

Nature(2023)10.1038/s41586-023-06704-2

N/A

1.6DataRank · unranked

53 citations

Yajie Yin, Katie Maurer, Katalin Sandor, Bence Dániel, Garima Yagnik +35 more

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

Genome Research(2014)10.1101/gr.168807.113

N/A

1.6DataRank · unranked

34 citations

Christopher A. Bristow, Robert K. Arthur, Yanxiao Zhang, Anshul Kundaje, Nicolas Nègre +18 more

Single-cell multi-cohort dissection of the schizophrenia transcriptome

Science(2024)10.1126/science.adg5136

N/A

1.3DataRank · unranked

125 citations

Shahin Mohammadi, José Dávila-Velderrain, Sivan Subburaju, Daniel Reed Tso, Makayla Hourihan +196 more

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

Nature Genetics(2023)10.1038/s41588-023-01433-8

N/A

1.3DataRank · unranked

53 citations

Sonia M. Dubois, Frank A. Buquicchio, Yu-Hsin Hsieh, Kopal Garg, Pauline Kautz +25 more

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Genome Research(2012)10.1101/gr.136184.111

N/A

1.2DataRank · unranked

2212 citations

Georgi K. Marinov, Anshul Kundaje, Yanxiao Zhang, Florencia Pauli, Serafim Batzoglou +46 more

Opportunities and obstacles for deep learning in biology and medicine

Journal of The Royal Society Interface(2018)10.1098/rsif.2017.0387

N/A

1.2DataRank · unranked

2203 citations

Daniel S. Himmelstein, Brett K. Beaulieu‐Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way +31 more

Massively parallel characterization of regulatory elements in the developing human cortex

Science(2024)10.1126/science.adh0559

N/A

1.2DataRank · unranked

61 citations

Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki, Fumitaka Inoue +197 more

Deciphering the impact of genomic variation on function

Nature(2024)10.1038/s41586-024-07510-0

N/A

1.1DataRank · unranked

89 citations

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon +95 more

Architecture of the human regulatory network derived from ENCODE data

Nature(2012)10.1038/nature11245

N/A

1.1DataRank · unranked

1548 citations

Anshul Kundaje, Manoj Hariharan, Stephen G. Landt, Koon-Kiu Yan, Chao Cheng +58 more

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.09.483684

Top 19%

1.1DataRank

Top 19%27 citations

Surag Nair, Rui Li, Katerina Kraft, Anusri Pampari, Aman Patel +5 more

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1

Blood(2022)10.1182/blood.2021013753

N/A

1.1DataRank · unranked

30 citations

Caleb A. Lareau, Erik L. Bao, Nan Liu, Taiju Utsugisawa, Alex M. Tseng +27 more

Multicenter integrated analysis of noncoding CRISPRi screens

Nature Methods(2024)10.1038/s41592-024-02216-7

Top 20%

1.0DataRank

Top 20%54 citations

Josh Tycko, Jin Woo Oh, Lexi R. Bounds, Sager J. Gosai, Lazaros Lataniotis +29 more

Linking disease associations with regulatory information in the human genome

Genome Research(2012)10.1101/gr.136127.111

N/A

0.996DataRank · unranked

765 citations

Beatrice Borsari, Anshul Kundaje, Serafim Batzoglou, Valentina Snetkova, Marc A. Schaub

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

Nature(2015)10.1038/nature14252

N/A

0.968DataRank · unranked

634 citations

Andreas R. Pfenning, Hansruedi Mathys, Richard Sandstrom, Anshul Kundaje, Li-Huei Tsai +3 more

Transparency and reproducibility in artificial intelligence

Nature(2020)10.1038/s41586-020-2766-y

N/A

0.929DataRank · unranked

487 citations

George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Massive Analysis Quality Control (MAQC) Society Board of Directors, Matthias Fischer +26 more

Comparative analysis of metazoan chromatin organization

Nature(2014)10.1038/nature13415

N/A

0.910DataRank · unranked

429 citations

Youngsook L. Jung, Tao Liu, Burak H. Alver, Soohyun Lee, Kohta Ikegami +83 more

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Nature Genetics(2020)10.1038/s41588-020-00721-x

N/A

0.895DataRank · unranked

388 citations

Anna Shcherbina, Soumya Kundu, Michael J. Gloudemans, Laure Frésard, Jeffrey M. Granja +13 more

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

Genome Research(2019)10.1101/gr.240093.118

N/A

0.891DataRank · unranked

379 citations

Elizabeth A. Pollina, Param Priya Singh, Salah Mahmoudi, Itamar Harel, Kerriann M. Casey +4 more

Extensive Variation in Chromatin States Across Humans

Science(2013)10.1126/science.1242510

N/A

0.891DataRank · unranked

378 citations

Sofia Kyriazopoulou-Panagiotopoulou, Mark T. Groudine, Judith B. Zaugg, Anshul Kundaje, Yuling Liu +14 more

Comparative analysis of regulatory information and circuits across distant species

Nature(2014)10.1038/nature13668

N/A

0.818DataRank · unranked

232 citations

Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng +40 more

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Genome Research(2012)10.1101/gr.136366.111

N/A

0.796DataRank · unranked

201 citations

Sofia Kyriazopoulou-Panagiotopoulou, Max Libbrecht, Cheryl L. Smith, Debasish Raha, Elliott E. Winters +6 more

Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders

Science Translational Medicine(2024)10.1126/scitranslmed.adh9974

Top 27%

0.733DataRank

Top 27%22 citations

Cuihua Xia, Yi Jiang, Yu Chen, Jiaqi Zhou, Rujia Dai +95 more

Identification of constrained sequence elements across 239 primate genomes

Nature(2023)10.1038/s41586-023-06798-8

N/A

0.713DataRank · unranked

115 citations

Jacob C. Ulirsch, Sabrina Mohd Rashid, Mohamed Ameen, Laksshman Sundaram, Hickey, Glenn +87 more

JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models

Nucleic Acids Research(2025)10.1093/nar/gkaf1209

Top 29%

0.692DataRank

Top 29%56 citations

Ieva Rauluševičiūtė, Dina Ruud Aronsen, Romain Blanc‐Mathieu, Ine Bonthuis, Herman De Beukelaer +29 more

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

Genome Biology(2023)10.1186/s13059-023-02915-y

N/A

0.692DataRank · unranked

17 citations

Carles B. Adsera, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang +46 more

Genome-Wide Gene–Environment Interaction Analyses to Understand the Relationship between Red Meat and Processed Meat Intake and Colorectal Cancer Risk

Cancer Epidemiology Biomarkers & Prevention(2023)10.1158/1055-9965.epi-23-0717

Top 31%

0.635DataRank

Top 31%17 citations

Joel Sanchez Mendez, Andre E. Kim, Mireia Obón‐Santacana, Ferrán Moratalla-Navarro, Vicente Martín +67 more

Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci

Cellular and Molecular Gastroenterology and Hepatology(2021)10.1016/j.jcmgh.2021.02.003

N/A

0.564DataRank · unranked

42 citations

Christopher H. Dampier, Ferran Moratalla-Navarro, Matthew Devall, Sarah J. Plummer, Anna Díez-Villanueva +11 more

Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.04.560808

N/A

0.564DataRank · unranked

42 citations

Mohamed Ameen, Laksshman Sundaram, Anusri Pampari, Jacob Matthew Schreiber, Akshay Balsubramani +7 more

The ENCODE Uniform Analysis Pipelines

Research Square(2023)10.21203/rs.3.rs-3111932/v1

N/A

0.553DataRank · unranked

39 citations

Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud +57 more

Dissecting the cis-regulatory syntax of transcription initiation with deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.28.596138

N/A

0.505DataRank · unranked

28 citations

Melody Yin, Anika Mantripragada, Jacob Matthew Schreiber, Georgi K. Marinov, Sagar Shah +4 more

Transcriptomics and chromatin accessibility in multiple African population samples

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.04.564839

Top 38%

0.505DataRank

Top 38%13 citations

Pagé C. Goddard, Emre Karakoç, Soumya Kundu, Stephanie M. Yan, Daniel Nachun +27 more

Multiomic profiling reveals that prostaglandin E2 reverses aged muscle stem cell dysfunction, leading to increased regeneration and strength

Cell stem cell(2025)10.1016/j.stem.2025.05.012

N/A

0.499DataRank · unranked

26 citations

Adelaida R. Palla, Andrew Tri Van Ho, Daniel C.L. Robinson, Meenakshi Ravichandran, Glenn J. Markov +14 more

An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity

Developmental Cell(2024)10.1016/j.devcel.2024.10.003

N/A

0.490DataRank · unranked

11 citations

Koushambi Mitra, Kaitlyn Spees, AkshatKumar Nigam, Katherine Liu, Camille Januel +8 more

CXCL12 drives natural variation in coronary artery anatomy across diverse populations

Cell(2025)10.1016/j.cell.2025.02.005

N/A

0.487DataRank · unranked

13 citations

Jiayan Zhou, Xiaochen Fan, Daniela Zanetti, Jeffrey A. Naftaly, Pratima Prabala +25 more

Global loss of promoter–enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis

Nature Cancer(2024)10.1038/s43018-024-00823-z

N/A

0.457DataRank · unranked

20 citations

Hayan Lee, Shannon White, Annika K. Weimer, Emma Monte, Aaron M. Horning +21 more

Beyond GWAS of Colorectal Cancer: Evidence of Interaction with Alcohol Consumption and Putative Causal Variant for the 10q24.2 Region

Cancer Epidemiology Biomarkers & Prevention(2022)10.1158/1055-9965.epi-21-1003

N/A

0.442DataRank · unranked

18 citations

Anna Shcherbina, Andre E. Kim, Yu‐Ru Su, Yi Lin, Jun Wang +89 more

A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk

Cancer Research(2023)10.1158/0008-5472.can-22-3713

N/A

0.434DataRank · unranked

17 citations

Andre E. Kim, Yi Lin, Conghui Qu, Marina Evangelou, Ren Yu +95 more

Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

British Journal of Cancer(2023)10.1038/s41416-023-02312-z

N/A

0.416DataRank · unranked

15 citations

Andre E. Kim, Orlagh Flanagan, Neil Murphy, Virginia Díez‐Obrero, Anna Shcherbina +83 more

Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis

Nature Cancer(2024)10.1038/s43018-024-00831-z

N/A

0.416DataRank · unranked

15 citations

Casey Hanson, Si Wu, Aaron M. Horning, Nasim Barapour, Stephanie Nevins +30 more

Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.09.531820

N/A

0.416DataRank · unranked

15 citations

X. Rosa, Vivian Yeong, Garrett M. Ginell, Jian-Hua Chen, Jacob A. Blum +18 more

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.26.629296

Top 45%

0.416DataRank

Top 45%12 citations

Henry Pratt, Kaili Fan, Nishigandha Phalke, Jonathan Fisher, Shaimae I. Elhajjajy +37 more

Single-cell epigenomic identification of inherited risk loci in Alzheimer’s and Parkinson’s disease

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.06.896159

N/A

0.406DataRank · unranked

14 citations

Anna Shcherbina, Soumya Kundu, Michael J. Gloudemans, Laure Frésard, Jeffrey M. Granja +12 more

Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.28.272690

N/A

0.405DataRank · unranked

8 citations

Devon Chandler‐Brown, Jacob Kim, Maurice Langhinrichs, Georgi K. Marinov, William J. Greenleaf +4 more

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders

Cell(2024)10.1016/j.cell.2024.09.014

N/A

0.399DataRank · unranked

8 citations

Joseph G. Arthur, Hanmin Guo, Taeyoung Kim, Yi‐Ling Huang, Reenal Pattni +32 more

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

Cell Genomics(2025)10.1016/j.xgen.2025.100780

N/A

0.385DataRank · unranked

12 citations

Seungsoo Kim, Saman Tabatabaee, Anusri Pampari, Anshul Kundaje, Jonathan K. Pritchard +2 more

SLC12A9 is a lysosome-detoxifying ammonium – chloride co-transporter

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.22.541801

N/A

0.360DataRank · unranked

10 citations

Koushambi Mitra, AkshatKumar Nigam, Kaitlyn Spees, Pravin Hivare, Katherine Liu +4 more

The chromatin landscape of the euryarchaeon Haloferax volcanii

Genome biology(2023)10.1186/s13059-023-03095-5

N/A

0.360DataRank · unranked

10 citations

S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje, William J. Greenleaf +1 more

A cell and transcriptome atlas of human arterial vasculature

Cell Genomics(2025)10.1016/j.xgen.2025.101034

N/A

0.350DataRank · unranked

8 citations

Albert J Pedroza, Disha Sharma, Wenduo Gu, Alex R. Dalal, Chad S. Weldy +20 more

Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes

Digital Discovery(2024)10.1039/d4dd00006d

N/A

0.345DataRank · unranked

9 citations

Matthew F. D. Hurley, Fengling Li, Eva Konkoľová, Martin Klíma, Jana Trylčová +21 more

Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response

Cancer Epidemiology Biomarkers & Prevention(2022)10.1158/1055-9965.epi-22-0763

N/A

0.330DataRank · unranked

8 citations

Andre E. Kim, Yi Lin, Virginia Díez‐Obrero, Stephanie A. Bien, Conghui Qu +84 more

The dynseq browser track shows context-specific features at nucleotide resolution

Nature Genetics(2022)10.1038/s41588-022-01194-w

N/A

0.312DataRank · unranked

7 citations

Arjun Barrett, Daofeng Li, Brian J. Raney, Brian T. Lee, Peter Kerpedjiev +7 more

Characterization of Additive Gene–environment Interactions For Colorectal Cancer Risk

Epidemiology(2024)10.1097/ede.0000000000001795

Top 54%

0.306DataRank

Top 54%4 citations

Yi Lin, Michelle Kim, Eric S. Kawaguchi, Conghui Qu, Caroline Y. Um +74 more

The chromatin landscape of the histone-possessingBacteriovoraxbacteria

Genome Research(2024)10.1101/gr.279418.124

N/A

0.245DataRank · unranked

4 citations

Benjamin R. Doughty, Anshul Kundaje, William J. Greenleaf, Georgi K. Marinov

Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.07.447388

N/A

0.241DataRank · unranked

4 citations

Shengen Shawn Hu, José Verdezoto Mosquera, Wei Feng, Chani J. Hodonsky, Doris Wong +18 more

Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.23.537997

N/A

0.241DataRank · unranked

4 citations

Yajie Yin, Jacob C. Gutierrez, Ryan S. Dhindsa, Anne-Sophie Gribling-Burrer, Yu-Hsin Hsieh +25 more

Cell type–specific purifying selection of synonymous mitochondrial DNA variation

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2505704122

N/A

0.241DataRank · unranked

4 citations

Patrick Maschmeyer, Yajie Yin, Jacob C. Gutierrez, Ryan S. Dhindsa, Anne-Sophie Gribling-Burrer +25 more

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

Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.16.440202

N/A

0.208DataRank · unranked

3 citations

Samuel H. Kim, S. Tansu Bagdatli, Alexandro E. Trevino, Josh Tycko, Tong Wu +6 more

The chromatin landscape of the euryarchaeon Haloferax volcanii

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.22.501187

N/A

0.208DataRank · unranked

3 citations

S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje, William J. Greenleaf +1 more

The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.30.502157

N/A

0.190DataRank · unranked

2 citations

Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang +40 more

CXCL12 drives natural variation in coronary artery anatomy across diverse populations

medRxiv(2023)10.1101/2023.10.27.23297507

N/A

0.174DataRank · unranked

2 citations

Daniela Zanetti, Jiayan Zhou, Jeffrey A. Naftaly, Pratima Prabala, Azalia M. Martínez Jaimes +25 more

Multi-omic Analysis of Familial Adenomatous Polyposis Reveals Molecular Pathways and Polyclonal Spreading Associated with Early Tumorigenesis

Research Square(2021)10.21203/rs.3.rs-515393/v1

N/A

0.165DataRank · unranked

2 citations

Aaron M. Horning, Edward D. Esplin, Si Wu, Casey Hanson, Nasim Bararpour +27 more

Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.03.560722

N/A

0.165DataRank · unranked

2 citations

Matthew F. D. Hurley, Fengling Li, Eva Konkoľová, Martin Klíma, Jana Trylčová +21 more

Decoding Chromatin Dynamics in Cardiac Organoids Reveals Genetic Drivers of Human Heart Development and Disease

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.15.680997

N/A

0.104DataRank · unranked

1 citations

Ryan Zhao, Salil Deshpande, Jackson Powell, Megha Agarwal, Yuan Liu +13 more

Transcription-dependent domain-scale 3D genome organization in dinoflagellates

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.01.181685

N/A

0DataRank · unranked

5 citations

Alexandro E. Trevino, T. Xiang, Anshul Kundaje, Arthur Grossman, William J. Greenleaf +1 more

Deciphering the Impact of Genetic Variation on Human Polyadenylation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.09.491198

N/A

0DataRank · unranked

1 citations

Anshul Kundaje, Georg Seelig, Johannes Linder

Rewriting regulatory DNA to dissect and reprogram gene expression

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.20.572268

N/A

0DataRank · unranked

19 citations

Michael T. Montgomery, H. Spencer Jones, Katherine Guo, Benjamin R. Doughty, Johannes Linder +11 more

The epigenomic landscape of single vascular cells reflects developmental origin and identifies disease risk loci

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.18.492517

N/A

0DataRank · unranked

3 citations

Soumya Kundu, João P. Monteiro, Wenduo Gu, Albert J Pedroza, Alex R. Dalal +13 more

Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.20.520743

N/A

0DataRank · unranked

8 citations

Melanie Weilert, Sabrina Krueger, Anusri Pampari, Hsiao‐Yun Liu, Ally Yang +5 more

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.11.540401

N/A

0DataRank · unranked

9 citations

Connor A. Horton, Avanti Shrikumar, Nilay Shah, Eileen Li, Melanie Weilert +5 more

CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.09.527751

N/A

0DataRank · unranked

8 citations

Hans‐Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao +5 more

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.30.564843

N/A

0DataRank · unranked

1 citations

Benjamin R. Doughty, Anshul Kundaje, William J. Greenleaf, Georgi K. Marinov

Data from A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk

(2023)10.1158/0008-5472.c.6769316

N/A

0DataRank · unranked

0 citations

Andre E. Kim, Yi Lin, Conghui Qu, Marina Evangelou, Ren Yu +95 more

Data from A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk

(2023)10.1158/0008-5472.c.6769316.v1

N/A

0DataRank · unranked

0 citations

Andre E. Kim, Yi Lin, Conghui Qu, Marina Evangelou, Ren Yu +95 more

Disease diagnostics using machine learning of immune receptors

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.26.489314

N/A

0DataRank · unranked

19 citations

Erin Craig, Jackson Michuda, Nidhi Sehgal, Nikhil Ram-Mohan, Ji-Yeun Lee +31 more

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.24.493321

N/A

0DataRank · unranked

20 citations

Amr M. Alexandari, Michael G.B. Hayes, Emil Marklund, Julia M. Schaepe, Arjun K. Aditham +9 more

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.16.342857

N/A

0DataRank · unranked

17 citations

Viviana I. Risca, David L. Reynolds, James Chappell, Adam J. Rubin, Namyoung Jung +11 more

Multiplexed single-cell characterization of alternative polyadenylation regulators

Cell(2024)10.1016/j.cell.2024.06.005

N/A

0DataRank · unranked

48 citations

Hans‐Hermann Wessels, Johannes Linder, Carol Dalgarno, Isabella Mascio, Saket Choudhary +5 more

High-throughput discovery and characterization of human transcriptional effectors

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.09.288324

N/A

0DataRank · unranked

19 citations

Nicole DelRosso, Gaelen T. Hess, Aradhana, Abhimanyu Banerjee, Adi Mukund +10 more

A single cell spatial temporal atlas of skeletal muscle reveals cellular neighborhoods that orchestrate regeneration and become disrupted in aging

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.10.494732

N/A

0DataRank · unranked

27 citations

Colin Holbrook, James N. Hamilton, Jasmin Garoussian, Mohsen Afshar, Shiqi Su +7 more

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

Nature Communications(2021)10.1038/s41467-021-22489-2

N/A

0DataRank · unranked

26 citations

Tao Sun, Anna Shcherbina, Qin Li, Inga Jarmoskaite, Kalli Kappel +5 more

Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer

EBioMedicine(2024)10.1016/j.ebiom.2024.105146

N/A

0DataRank · unranked

13 citations

Andre Kim, Eric S. Kawaguchi, John L. Morrison, Virginia Díez‐Obrero, Demetrius Albanes +60 more

Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk

British Journal of Cancer(2024)10.1038/s41416-024-02638-2

N/A

0DataRank · unranked

11 citations

Yi Lin, Conghui Qu, Volker Arndt, James W. Baurley, Sonja I. Berndt +73 more

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Genome Research(2022)10.1101/gr.275394.121

N/A

0DataRank · unranked

45 citations

Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross C. Hardison, Anshul Kundaje +2 more

Genome-Wide Interaction Analysis of Genetic Variants With Menopausal Hormone Therapy for Colorectal Cancer Risk

JNCI Journal of the National Cancer Institute(2022)10.1093/jnci/djac094

N/A

0DataRank · unranked

4 citations

Andre E. Kim, Stephanie A. Bien, Yi Lin, Conghui Qu, Tabitha A. Harrison +72 more

Two genome-wide interaction loci modify the association of nonsteroidal anti-inflammatory drugs with colorectal cancer

Science Advances(2024)10.1126/sciadv.adk3121

N/A

0DataRank · unranked

8 citations

Andre E. Kim, Yi Lin, Conghui Qu, John L. Morrison, Juan Pablo Lewinger +77 more

The chromatin organization of a chlorarachniophyte nucleomorph genome

Genome biology(2022)10.1186/s13059-022-02639-5

N/A

0DataRank · unranked

8 citations

Xinyi Chen, Tong Wu, Chuan He, Arthur Grossman, Anshul Kundaje +2 more

Accelerating in silico saturation mutagenesis using compressed sensing

Bioinformatics(2022)10.1093/bioinformatics/btac385

N/A

0DataRank · unranked

12 citations

Surag Nair, Akshay Balsubramani, Anshul Kundaje, Jacob Matthew Schreiber

Protocol for mapping the three-dimensional organization of dinoflagellate genomes

STAR Protocols(2024)10.1016/j.xpro.2024.102941

N/A

0DataRank · unranked

1 citations

Anshul Kundaje, William J. Greenleaf, Arthur Grossman, Georgi K. Marinov

fastISM: performant in silico saturation mutagenesis for convolutional neural networks

Bioinformatics(2022)10.1093/bioinformatics/btac135

N/A

0DataRank · unranked

26 citations

Avanti Shrikumar, Jacob Matthew Schreiber, Anshul Kundaje, Surag Nair

Deciphering the impact of genetic variation on human polyadenylation using APARENT2

Genome biology(2022)10.1186/s13059-022-02799-4

N/A

0DataRank · unranked

59 citations

Samantha E. Koplik, Anshul Kundaje, Georg Seelig, Johannes Linder

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.28.596078

N/A

0DataRank · unranked

8 citations

Seungsoo Kim, Saman Tabatabaee, Anusri Pampari, Anshul Kundaje, Jonathan K. Pritchard +2 more

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA

arXiv (Cornell University)(2024)10.52202/079017-1981

N/A

0DataRank · unranked

7 citations

Arpita Singhal, Austin Wang, Anusri Pampari, Maya Kasowski, Anshul Kundaje +1 more

Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease

Cell(2022)10.1016/j.cell.2022.11.028

N/A

0DataRank · unranked

107 citations

Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair +15 more

Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.06.611737

N/A

0DataRank · unranked

3 citations

Boyang Zhang, Anusri Pampari, Jennifer A. Akiyama, Ingrid Playzer-Frick, Catherine S. Novak +12 more

Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

UNC Libraries(2024)10.17615/f3mg-7f39

N/A

0DataRank · unranked

0 citations

Jenny Chang‐Claude, Jukka‐Pekka Mecklin, Emily White, Amanda E. Toland, Mireia Obón‐Santacana +95 more

Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk

UNC Libraries(2024)10.17615/qvhd-8x35

N/A

0DataRank · unranked

0 citations

D. Timothy Bishop, Alicja Wolk, Temitope O. Keku, Virginia Díez‐Obrero, Hermann Brenner +73 more

Landscape of cohesin-mediated chromatin loops in the human genome

Nature(2020)10.1038/s41586-020-2151-x

N/A

0DataRank · unranked

238 citations

Rohith Srivas, Damek V. Spacek, Maya Kasowski, Mariana Ruiz-Velasco, Nicholas A. Sinnott-Armstrong +13 more

RNA polymerase II dynamics and mRNA stability feedback scale mRNA in proportion to cell size

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.20.461005

N/A

0DataRank · unranked

20 citations

Georgi K. Marinov, Huan Zheng, Crystal Yee Tsui, Andrew W. Jones, J. Greenwood +5 more

Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.24.436532

N/A

0DataRank · unranked

12 citations

Stephanie Nevins, Derek C. Chen, Roxanne Chiu, Aaron M. Horning, Rozelle Laquindanum +12 more

Domain adaptive neural networks improve cross-species prediction of transcription factor binding

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.13.431115

N/A

0DataRank · unranked

7 citations

Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross C. Hardison, Anshul Kundaje +2 more

Using gene-environment interactions to explore pathways for colorectal cancer risk

EBioMedicine(2025)10.1016/j.ebiom.2025.105964

N/A

0DataRank · unranked

3 citations

Ren Yu, Andre E. Kim, Georgios Markozannes, Neil Murphy, Demetrius Albanes +58 more

Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.18.638922

N/A

0DataRank · unranked

6 citations

Soumya Kundu, Evin M. Padhi, Salil Deshpande, Austin Wang, E. Robb +9 more

Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk

medRxiv(2025)10.1101/2025.08.28.25334684

N/A

0DataRank · unranked

5 citations

Chad S. Weldy, Soumya Kundu, Quanyi Zhao, D. Li, Kayla Brand +19 more

Vascular smooth muscle cell atherosclerosis trajectories characterized at single cell resolution identify causal transcriptomic and epigenomic mechanisms of disease risk

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.04.655863

N/A

0DataRank · unranked

3 citations

Soumya Kundu, Paul Cheng, Wenduo Gu, Will Jackson, Quanyi Zhao +12 more

Genetic risk factors modulate the association between physical activity and colorectal cancer

Research Square(2025)10.21203/rs.3.rs-7350654/v1

N/A

0DataRank · unranked

1 citations

Mireia Obón‐Santacana, Andre E. Kim, Eric S. Kawaguchi, Yubo Fu, Conghui Qu +69 more

TGF-β-pathway-based polygenic risk score modifies the association between red meat intake and colorectal cancer risk: Application of a novel pathway-based PRS method

medRxiv(2025)10.1101/2025.06.13.25329599

N/A

0DataRank · unranked

0 citations

Bryan Queme, Yubo Fu, John P. Morrison, Juan Pablo Lewinger, Eric S. Kawaguchi +52 more

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.25.678665

N/A

0DataRank · unranked

0 citations

Selin Jessa, Georgi K. Marinov, Sandy Klemm, Anshul Kundaje, William J. Greenleaf +1 more

Predicting chromatin conformation contact maps

PLoS ONE(2025)10.1371/journal.pone.0331124

N/A

0DataRank · unranked

0 citations

Jacob Matthew Schreiber, Anshul Kundaje, William Stafford Noble, Alan Min

High-Throughput Discovery and Characterization of Human Transcriptional Effectors

Cell(2020)10.1016/j.cell.2020.11.024

N/A

0DataRank · unranked

181 citations

Nicole DelRosso, Gaelen T. Hess, Aradhana, Abhimanyu Banerjee, Adi Mukund +10 more

Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses

medRxiv(2022)10.1101/2022.10.16.22280490

N/A

0DataRank · unranked

0 citations

Andre E. Kim, Orlagh Flanagan, Neil Murphy, Virginia Díez‐Obrero, Anna Shcherbina +83 more

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Developmental Cell(2023)10.1016/j.devcel.2023.07.007

N/A

0DataRank · unranked

78 citations

Melanie Weilert, Sabrina Krueger, Anusri Pampari, Hsiao‐Yun Liu, Ally Yang +6 more

MTSplice predicts effects of genetic variants on tissue-specific splicing

Genome biology(2021)10.1186/s13059-021-02273-7

N/A

0DataRank · unranked

69 citations

Muhammed Hasan Çelik, Anshul Kundaje, Jun Cheng

Base-resolution models of transcription-factor binding reveal soft motif syntax

Nature Genetics(2021)10.1038/s41588-021-00782-6

N/A

0DataRank · unranked

702 citations

Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr M. Alexandari, Khyati Dalal +6 more

Global loss of fine-scale chromatin architecture and rebalancing of gene expression during early colorectal cancer development

Research Square(2022)10.21203/rs.3.rs-2003187/v1

N/A

0DataRank · unranked

0 citations

Yizhou Zhu, Hayan Lee, Annika K. Weimer, Aaron M. Horning, Stephanie Nevins +17 more

Comparative analysis of metazoan chromatin organization

DSpace@MIT (Massachusetts Institute of Technology)(2020)10.17615/6z12-pm44

N/A

0DataRank · unranked

0 citations

Dalal Asker, Artyom A. Alekseyenko, Eric M. Bishop, Ron A.-J. Chen, Anshul Kundaje +27 more

The dynseq genome browser track enables visualization of context-specific, dynamic DNA sequence features at single nucleotide resolution

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.26.493621

N/A

0DataRank · unranked

0 citations

Arjun Barrett, Daofeng Li, Brian J. Raney, Brian T. Lee, Peter Kerpedjiev +7 more

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping

Genome biology(2023)10.1186/s13059-023-02930-z

N/A

0DataRank · unranked

13 citations

Samuel H. Kim, S. Tansu Bagdatli, Soon Il Higashino, Alexandro E. Trevino, Josh Tycko +7 more

Elucidating the Risk of Colorectal Cancer for Variants in Hereditary Colorectal Cancer Genes

(2023)10.1053/j.gastro.2023.06.032

N/A

0DataRank · unranked

7 citations

Minta Thomas, Conghui Qu, Xiaoliang Wang, Jeroen R. Huyghe, Jihoon E. Joo +77 more

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.26.505505

N/A

0DataRank · unranked

1 citations

Hayan Lee, Shannon White, Annika K. Weimer, Emma Monte, Aaron Horning +21 more

Anshul Kundaje

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