Mark Gerstein

Biochemistry, 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

38.7Author DataRank

Indexed papers

24in 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 24 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.

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Cell(2022)10.1016/j.cell.2022.08.004

Top 3%

6.3DataRank

Top 3%1056 citations

Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley Abel, Allison A. Regier +37 more

Papers

Driven by 114 papers — median percentile 76. Top paper: “Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing”.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Nature Genetics(2020)10.1038/s41588-019-0576-7

N/A

8.1DataRank · unranked

783 citations

Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung, Lixing Yang +89 more

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Nature Genetics(2020)10.1038/s41588-019-0562-0

N/A

7.0DataRank · unranked

483 citations

Eva G. Alvarez, Adrian Baez‐Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester +80 more

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Cell(2022)10.1016/j.cell.2022.08.004

Top 3%

6.3DataRank

Top 3%1056 citations

Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley Abel, Allison A. Regier +37 more

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Nature Genetics(2020)10.1038/s41588-019-0564-y

N/A

5.9DataRank · unranked

312 citations

Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G.W. Verhaak, Rameen Beroukhim +91 more

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Science(2021)10.1126/science.abf7117

Top 4%

5.7DataRank

Top 4%812 citations

Peter A. Audano, Qihui Zhu, Bernardo Rodríguez–Martín, David Porubsky, Marc Jan Bonder +60 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

An integrative ENCODE resource for cancer genomics

Nature Communications(2020)10.1038/s41467-020-14743-w

Top 5%

4.1DataRank

Top 5%190 citations

Donghoon Lee, Vineet K. Dhiman, Peng Jiang, Jie Xu, Patrick D. McGillivray +53 more

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome

Nucleic Acids Research(2022)10.1093/nar/gkac966

Top 8%

2.7DataRank

Top 8%143 citations

Theodore Arapoglou, Xihao Li, Zilin Li, Xiuwen Zheng, Jill E. Moore +20 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

DeepVelo : Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations

Science Advances(2022)10.1126/sciadv.abq3745

N/A

2.4DataRank · unranked

88 citations

William C. King, Ahyeon Hwang, Mark Gerstein, Jing Zhang, Zhanlin Chen

Pathway and network analysis of more than 2500 whole cancer genomes

Nature Communications(2020)10.1038/s41467-020-14367-0

Top 9%

2.3DataRank

Top 9%117 citations

David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguél Vázquez, Abdullah Kahraman +95 more

Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer

Cancer(2020)10.1002/cncr.32914

N/A

2.1DataRank · unranked

44 citations

Shantao Li, Harvey A. Risch, Ranjit S. Bindra, Patrick D. McGillivray, Mark Gerstein +1 more

Single-cell genomics and regulatory networks for 388 human brains

Science(2024)10.1126/science.adi5199

Top 12%

1.7DataRank

Top 12%155 citations

Jason Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta +91 more

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex

Science(2024)10.1126/science.adh1938

Top 18%

1.2DataRank

Top 18%69 citations

Abby Spangler, Nicholas J. Eagles, Kelsey D. Montgomery, Sang Ho Kwon, Boyi Guo +90 more

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009303

N/A

1.2DataRank · unranked

23 citations

Daniel Spakowicz, Garrett I. Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang +13 more

Transcriptional activity and strain-specific history of mouse pseudogenes

Nature Communications(2020)10.1038/s41467-020-17157-w

Top 19%

1.1DataRank

Top 19%38 citations

Paul Muir, Adam Frankish, Ian T. Fiddes, Mark Diekhans, David Thybert +7 more

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers

Genome Medicine(2021)10.1186/s13073-021-00879-x

Top 22%

0.914DataRank

Top 22%29 citations

Sushant Kumar, Arif Harmanci, Shantao Li, Robert R. Kitchen, Yan Zhang +11 more

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

Genome Research(2011)10.1101/gr.114587.110

N/A

0.831DataRank · unranked

254 citations

Zhi John Lu, Mei Zhong, Mihail Sarov, John I. Murray, Cathleen M. Brdlik +13 more

Origins and characterization of variants shared between databases of somatic and germline human mutations

BMC Bioinformatics(2020)10.1186/s12859-020-3508-8

Top 26%

0.775DataRank

Top 26%18 citations

John Leisman, Fábio C. P. Navarro, Mark Gerstein, Matthew Meyerson

Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

Science(2024)10.1126/science.adh0829

Top 26%

0.765DataRank

Top 26%50 citations

Michael Margolis, Rujia Dai, Pan Zhang, Pawel F. Przytycki, Daniel Vo +95 more

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.10.447896

N/A

0.759DataRank · unranked

22 citations

Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Jose Manuel Gonzalez, Michele Magrane +23 more

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq

Nucleic Acids Research(2020)10.1093/nar/gkaa1155

N/A

0.748DataRank · unranked

19 citations

Michelle Kudron, Alec Victorsen, Jiahao Gao, Haneen Ammouri, Fábio C. P. Navarro +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

Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors

Science Signaling(2023)10.1126/scisignal.abm5518

N/A

0.691DataRank · unranked

21 citations

Claire Song, Jaylissa Torres Robles, Leonidas Salichos, Hua Jane Lou, TuKiet T. Lam +3 more

Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex

Genome Medicine(2022)10.1186/s13073-022-01133-8

N/A

0.674DataRank · unranked

15 citations

Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu +3 more

exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Cell Genomics(2023)10.1016/j.xgen.2023.100303

Top 30%

0.671DataRank

Top 30%19 citations

Alessandra Stürchler, Robert Fullem, David Chen, Anne C Starner, Emmanuel Esquivel +25 more

Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma

Clinical Cancer Research(2024)10.1158/1078-0432.ccr-23-3932

N/A

0.667DataRank · unranked

17 citations

Jonathan Warrell, Sandra Martínez-Morilla, Niki Gavrielatou, Ioannis Vathiotis, Vesal Yaghoobi +4 more

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins

Genome biology(2020)10.1186/s13059-020-01979-4

N/A

0.648DataRank · unranked

11 citations

Jason Liu, Donghoon Lee, Jo-Jo Feng, Lucas Lochovsky, Shaoke Lou +3 more

Child Development and Structural Variation in the Human Genome

Child Development(2013)10.1111/cdev.12051

N/A

0.524DataRank · unranked

32 citations

Rajini Haraksingh, Fabian Grubert, Alexej Abyzov, Mark Gerstein, Sherman Weissman +2 more

DeepVelo: Single-cell Transcriptomic Deep Velocity Field Learning with Neural Ordinary Differential Equations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.15.480564

N/A

0.502DataRank · unranked

6 citations

William C. King, Ahyeon Hwang, Mark Gerstein, Jing Zhang, Zhanlin Chen

Single-cell genomics and regulatory networks for 388 human brains

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.18.585576

Top 44%

0.419DataRank

Top 44%9 citations

Jason J. Liu, Declan Clarke, Matthew L. Jensen, Jonathan Warrell, Chirag Gupta +75 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

Binding profiles for 961DrosophilaandC. eleganstranscription factors reveal tissue-specific regulatory relationships

Genome Research(2024)10.1101/gr.279037.124

N/A

0.416DataRank · unranked

10 citations

Louis Gevirtzman, Alec Victorsen, Bridget C. Lear, Jiahao Gao, Jinrui Xu +20 more

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

BMC Bioinformatics(2020)10.1186/s12859-020-03785-y

N/A

0.398DataRank · unranked

9 citations

Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Chupp, Mark Gerstein +1 more

FANCY: fast estimation of privacy risk in functional genomics data

Bioinformatics(2020)10.1093/bioinformatics/btaa661

N/A

0.342DataRank · unranked

5 citations

Charlotte M. Brannon, Fábio C. P. Navarro, Mark Gerstein, Gamze Gürsoy

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.16.423102

Top 53%

0.322DataRank

Top 53%5 citations

Peter A. Audano, Qihui Zhu, Bernardo Rodríguez–Martín, David Porubsky, Marc Jan Bonder +58 more

Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.18.576242

Top 54%

0.311DataRank

Top 54%5 citations

Louis Gevirtzman, Alec Victorsen, Bridget C. Lear, Jiahao Gao, Jinrui Xu +20 more

Network-based drug repurposing for psychiatric disorders using single-cell genomics

Cell Genomics(2025)10.1016/j.xgen.2025.101003

N/A

0.288DataRank · unranked

5 citations

Noah Cohen Kalafut, Declan Clarke, Jerome J. Choi, Kalpana Hanthanan Arachchilage, Saniya Khullar +6 more

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis

BMC Bioinformatics(2020)10.1186/s12859-020-03758-1

N/A

0.269DataRank · unranked

5 citations

Jason Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee +2 more

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases

Genome Research(2023)10.1101/gr.278322.123

N/A

0.239DataRank · unranked

3 citations

Maya N. Geradi, Gamze Gürsoy, Monica R. Grasty, Andrew D. Miranker, Mark Gerstein +1 more

The IGVF catalog—from genetic variation to function

Nucleic Acids Research(2025)10.1093/nar/gkaf1341

Top 63%

0.219DataRank

Top 63%3 citations

Shane Liu, Pedro Assis, Mingjie Li, Shengcheng Dong, Ian Whaling +42 more

Recent advances and future prospects for blockchain in biomedicine

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101114

N/A

0.165DataRank · unranked

2 citations

Xiangru Tang, Xiao Zhou, Danielle Lee, Ahmed El‐Hussein, Elizabeth Knight +3 more

Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks

Bioinformatics(2024)10.1093/bioinformatics/btae463

N/A

0.165DataRank · unranked

2 citations

Mark Gerstein, Jiahao Gao

Human Genome Annotation

Lecture Notes in Computer Science(2010)10.1007/978-3-642-13078-6_7

Top 70%

0.149DataRank

Top 70%1 citations

Mark Gerstein

FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation

Nucleic Acids Research(2025)10.1093/nar/gkaf1217

Top 72%

0.115DataRank

Top 72%1 citations

Vineet Verma, Xihao Li, Zilin Li, Nicole Shedd, Thomas Cheng Li +12 more

Machine Learning Models Based on Histological Images from Healthy Donors Identify ImageQTLs and Predict Chronological Age

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.04.674328

N/A

0.104DataRank · unranked

1 citations

William Zhu, Christopher J. F. Cameron, Pengyu Ni, Xiao Zhou, Tselmeg Ulammandakh +2 more

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Cell(2024)10.1016/j.cell.2024.09.001

N/A

0DataRank · unranked

93 citations

Dingyao Zhang, Yan Gao, Bo Tao, Daiwei Zhang, Shuozhen Bao +15 more

Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations

Cell(2024)10.1016/j.cell.2024.11.012

N/A

0DataRank · unranked

37 citations

Beatrice Borsari, Yunyang Li, Susanna Liu, Yuan Gao, Xin Xin +10 more

MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations

Bioinformatics(2024)10.1093/bioinformatics/btae260

N/A

0DataRank · unranked

19 citations

Andrew Tran, Jeffrey Too Chuan Tan, Mark Gerstein, Xiangru Tang

Predicting A/B compartments from histone modifications using deep learning

iScience(2024)10.1016/j.isci.2024.109570

N/A

0DataRank · unranked

12 citations

Nitya Thakkar, Hannah L. Harris, Susanna Liu, Megan Zhang, Mark Gerstein +6 more

FAVOR-GPT: a generative natural language interface to whole genome variant functional annotations

Bioinformatics Advances(2024)10.1093/bioadv/vbae143

N/A

0DataRank · unranked

9 citations

Hufeng Zhou, Vineet Verma, Xiangru Tang, Yanjun Shao, Eric Van Buren +6 more

A variational graph-partitioning approach to modeling protein liquid-liquid phase separation

Cell Reports Physical Science(2024)10.1016/j.xcrp.2024.102292

N/A

0DataRank · unranked

3 citations

Jonathan Warrell, Suchen Zheng, Mark Gerstein, Gaoyuan Wang

REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers

Communications Biology(2024)10.1038/s42003-024-07045-0

N/A

0DataRank · unranked

6 citations

Sebastian JH Seager, Fred J. Sigworth, Hemant D. Tagare, Mark Gerstein, Christopher J. F. Cameron

Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c01116

N/A

0DataRank · unranked

7 citations

Prashant S. Emani, Mark Gerstein, Ho‐Joon Lee

Less-is-more: selecting transcription factor binding regions informative for motif inference

Nucleic Acids Research(2024)10.1093/nar/gkad1240

N/A

0DataRank · unranked

7 citations

Jiahao Gao, Pengyu Ni, Mark Gerstein, Jinrui Xu

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding

Briefings in Bioinformatics(2024)10.1093/bib/bbae096

N/A

0DataRank · unranked

6 citations

Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Che-Yu Lee, Feng Yue +5 more

Risks of AI Scientists: Prioritizing Safeguarding Over Autonomy

arXiv (Cornell University)(2024)10.48550/arxiv.2402.04247

N/A

0DataRank · unranked

13 citations

Qiao Jin, Kunlun Zhu, Tongxin Yuan, Yichi Zhang, Wangchunshu Zhou +8 more

Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.18.585480

N/A

0DataRank · unranked

2 citations

Pengyu Ni, Paola Suárez-Meade, Yu Ma, Emily Forrest, Guilin Wang +5 more

Network-based drug repurposing for psychiatric disorders using single-cell genomics

medRxiv(2024)10.1101/2024.12.01.24318008

N/A

0DataRank · unranked

2 citations

Noah Cohen Kalafut, Declan Clarke, Jerome Choi, Kalpana Hanthanan Arachchilage, Saniya Khullar +5 more

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Genome Research(2024)10.1101/gr.279419.124

N/A

0DataRank · unranked

2 citations

Marc Jan Bonder, Sabriya A. Syed, Matthew Jensen, HGSVC Functional Analysis Working Group, Mark Gerstein +9 more

A Variational Graph Partitioning Approach to Modeling Protein Liquid-liquid Phase Separation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.20.576375

N/A

0DataRank · unranked

1 citations

Jonathan Warrell, Suchen Zheng, Mark Gerstein, Gaoyuan Wang

Quantum variational autoencoder utilizing regularized mixed-state latent representations

Physical review. A/Physical review, A(2025)10.1103/physreva.111.042416

N/A

0DataRank · unranked

9 citations

Jonathan Warrell, Prashant S. Emani, Mark Gerstein, Gaoyuan Wang

Aerosol-based exposure to opportunistic pathogens originating from hospital sink drains

American Journal of Infection Control(2025)10.1016/j.ajic.2025.10.030

N/A

0DataRank · unranked

4 citations

Kathleen R. Bowie, Irvan Luhung, Hannah Greenwald, Scott C. Roberts, Trini Mathew +5 more

Machine-learning models based on histological images from healthy donors identify imageQTLs and predict chronological age

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2423469122

N/A

0DataRank · unranked

1 citations

William Zhu, Christopher J. F. Cameron, Pengyu Ni, Xiao Zhou, Tselmeg Ulammandakh +2 more

A discard-and-restart MD algorithm for the sampling of protein intermediate states

Biophysical Journal(2025)10.1016/j.bpj.2025.03.024

N/A

0DataRank · unranked

1 citations

Jonathon Howard, Mark Gerstein, Alan Ianeselli

Structural and transduction patterns of human-specific polymorphic SVA insertions

Mobile DNA(2025)10.1186/s13100-025-00373-w

N/A

0DataRank · unranked

1 citations

Mark Loftus, Emily C. Golba, Haley Abel, Hufsah Ashraf, Peter A. Audano +64 more

Scalable and efficient on-chain data management in blockchain for large biomedical data

Journal of Biomedical Informatics(2025)10.1016/j.jbi.2025.104818

N/A

0DataRank · unranked

1 citations

Elizabeth Knight, Mark Gerstein, Eric Ni

Spatially decoding genotype-associated epigenetic landscapes in human lymphoma FFPE tissues via epi-Patho-DBiT

Nature Communications(2025)10.1038/s41467-026-71576-9

N/A

0DataRank · unranked

0 citations

Bo Tao, Archibald Enninful, Dingyao Zhang, Negin Farzad, Keyi Li +10 more

Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders

Cell(2025)10.1016/j.cell.2024.12.022

N/A

0DataRank · unranked

39 citations

Jessica C. McAfee, Jiseok Lee, Alejandro Gómez, Austin T Ledford, Declan Clarke +7 more

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences

Cell(2020)10.1016/j.cell.2020.01.032

N/A

0DataRank · unranked

169 citations

Jonathan Warrell, Shantao Li, Patrick D. McGillivray, Matthew Meyerson, Leonidas Salichos +14 more

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Nature Methods(2020)10.1038/s41592-020-0907-8

N/A

0DataRank · unranked

120 citations

Mengting Gu, Emrah Gumusgoz, Landon L. Chan, Koon‐Kiu Yan, Joel Rozowsky +20 more

Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts

BMC Medical Genomics(2020)10.1186/s12920-020-00732-x

N/A

0DataRank · unranked

57 citations

Charlotte M. Brannon, Mark Gerstein, Gamze Gürsoy

DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring

BMC Bioinformatics(2020)10.1186/s12859-020-03605-3

N/A

0DataRank · unranked

8 citations

Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy +2 more

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood

Nature Communications(2020)10.1038/s41467-020-17388-x

N/A

0DataRank · unranked

45 citations

Forrest W. Crawford, Mark Gerstein, Shantao Li

SVFX: a machine learning framework to quantify the pathogenicity of structural variants

Genome biology(2020)10.1186/s13059-020-02178-x

N/A

0DataRank · unranked

41 citations

Arif Harmanci, Jagath Vytheeswaran, Mark Gerstein, Sushant Kumar

Epigenome-based splicing prediction using a recurrent neural network

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008006

N/A

0DataRank · unranked

40 citations

Jing Zhang, Jason Liu, Mark Gerstein, Donghoon Lee

Using blockchain to log genome dataset access: efficient storage and query

BMC Medical Genomics(2020)10.1186/s12920-020-0716-z

N/A

0DataRank · unranked

33 citations

Robert Bjornson, Molly E. Green, Mark Gerstein, Gamze Gürsoy

Estimating growth patterns and driver effects in tumor evolution from individual samples

Nature Communications(2020)10.1038/s41467-020-14407-9

N/A

0DataRank · unranked

32 citations

Matthew Meyerson, Jonathan Warrell, Mark Gerstein, Leonidas Salichos

Broad transcriptomic dysregulation across the cerebral cortex in ASD

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.17.423129

N/A

0DataRank · unranked

20 citations

Brie Wamsley, George Chen, Sepideh Parhami, Prashant S. Emani, Nathan Chang +17 more

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.28.959874

N/A

0DataRank · unranked

17 citations

Yucheng T. Yang, John A. Capra, Mark Gerstein, Bian Li

Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.03.168831

N/A

0DataRank · unranked

6 citations

Ryan L. Collins, Wan-Ping Lee, Alexandra M. Weber, Yukyung Jun, Qihui Zhu +18 more

Bayesian Structural Time Series for Biomedical Sensor Data: A Flexible Modeling Framework for Evaluating Interventions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.02.973677

N/A

0DataRank · unranked

4 citations

Daniel Spakowicz, Garrett I. Ash, Rebecca Hoyd, Andrew Zhang, Shaoke Lou +12 more

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.29.123638

N/A

0DataRank · unranked

2 citations

Jing Zhang, Jason Liu, Zixuan Zhang, Jiangqi Zhu, Donghoon Lee +3 more

NIMBus: a Negative Binomial Regression based Integrative Method for Mutation Burden Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.29.124149

N/A

0DataRank · unranked

0 citations

Jason Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee +2 more

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

The American Journal of Human Genetics(2021)10.1016/j.ajhg.2021.03.014

N/A

0DataRank · unranked

137 citations

Ryan L. Collins, Wan‐Ping Lee, Alexandra M. Weber, Yukyung Jun, Qihui Zhu +18 more

Privacy-preserving genotype imputation with fully homomorphic encryption

Cell Systems(2021)10.1016/j.cels.2021.10.003

N/A

0DataRank · unranked

44 citations

Eduardo Chielle, Charlotte M. Brannon, Michail Maniatakos, Mark Gerstein, Gamze Gürsoy

Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders

Sports Medicine(2021)10.1007/s40279-021-01543-5

N/A

0DataRank · unranked

33 citations

Matthew Stults‐Kolehmainen, Michael A. Busa, Allison E. Gaffey, Konstantinos Angeloudis, Borja Muñiz-Pardos +43 more

Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption

IEEE Access(2021)10.1109/access.2021.3093005

N/A

0DataRank · unranked

46 citations

Eduardo Chielle, Gamze Gürsoy, Oleg Mazonka, Mark Gerstein, Michail Maniatakos +1 more

STK11/LKB1 Loss of Function Is Associated with Global DNA Hypomethylation and S -Adenosyl-Methionine Depletion in Human Lung Adenocarcinoma

Cancer Research(2021)10.1158/0008-5472.can-20-3199

N/A

0DataRank · unranked

17 citations

Bernice A. Agana, Jacob M. Kaufman, Michael F. Sharpnack, Walter Wang, Christoph Weigel +9 more

Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology

Journal of Biological Chemistry(2021)10.1016/j.jbc.2021.100937

N/A

0DataRank · unranked

16 citations

Christopher J. F. Cameron, Swapnil C. Devarkar, Sebastian JH Seager, Mark Gerstein, Yong Xiong +2 more

SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments

Bioinformatics(2021)10.1093/bioinformatics/btaa1039

N/A

0DataRank · unranked

17 citations

Jing Zhang, Jason Liu, Zixuan Zhang, Jiangqi Zhu, Donghoon Lee +3 more

Recovering genotypes and phenotypes using allele-specific genes

Genome biology(2021)10.1186/s13059-021-02477-x

N/A

0DataRank · unranked

14 citations

Nancy Lu, Sarah Wagner, Mark Gerstein, Gamze Gürsoy

DECODE: a De ep-learning framework for Co n de nsing enhancers and refining boundaries with large-scale functional assays

Bioinformatics(2021)10.1093/bioinformatics/btab283

N/A

0DataRank · unranked

12 citations

Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min +3 more

Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization

Bioinformatics(2021)10.1093/bioinformatics/btab107

N/A

0DataRank · unranked

1 citations

Tianxiao Li, Jason Liu, Mark Gerstein, Shaoke Lou

Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.07.459322

N/A

0DataRank · unranked

5 citations

Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu +3 more

Nodal Modulator is required to sustain endoplasmic reticulum morphology

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.28.428001

N/A

0DataRank · unranked

2 citations

Christopher J. F. Cameron, Swapnil C. Devarkar, Mark Gerstein, Yong Xiong, Christian Schlieker +1 more

DECODE: A De ep-learning Framework for Co n de nsing Enhancers and Refining Boundaries with Large-scale Functional Assays

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.27.428477

N/A

0DataRank · unranked

0 citations

Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min +3 more

Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD

Nature(2022)10.1038/s41586-022-05377-7

N/A

0DataRank · unranked

294 citations

Jillian R. Haney, Brie Wamsley, Chloe X. Yap, Sepideh Parhami, Prashant S. Emani +21 more

Recurrent repeat expansions in human cancer genomes

Nature(2022)10.1038/s41586-022-05515-1

N/A

0DataRank · unranked

89 citations

Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu +19 more

Insights from incorporating quantum computing into drug design workflows

Bioinformatics(2022)10.1093/bioinformatics/btac789

N/A

0DataRank · unranked

50 citations

Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul W. Merrill +4 more

Storing and analyzing a genome on a blockchain

Genome biology(2022)10.1186/s13059-022-02699-7

N/A

0DataRank · unranked

39 citations

Charlotte M. Brannon, Eric Ni, Sarah Wagner, Amol Khanna, Mark Gerstein +1 more

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

iScience(2022)10.1016/j.isci.2022.104653

N/A

0DataRank · unranked

31 citations

Jennifer Jones, Roger P. Alexander, Eric Alsop, Ji Yeong An, Mohammad H. Asghari +91 more

Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins

Cell Reports(2022)10.1016/j.celrep.2022.111675

N/A

0DataRank · unranked

23 citations

Christopher J. F. Cameron, Maria Fernanda Forni, Renee R. Wasko, Brigitte S. Naughton, Valerie Horsley +3 more

Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations

Nature Communications(2022)10.1038/s41467-022-31107-8

N/A

0DataRank · unranked

18 citations

Jeremy Goldwasser, Philip Tuckman, Jason Liu, Jing Zhang, Mark Gerstein +1 more

Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade

npj Precision Oncology(2022)10.1038/s41698-022-00330-3

N/A

0DataRank · unranked

8 citations

Leonidas Salichos, Sandra Martínez-Morilla, Niki Gavrielatou, Thazin Nwe Aung, Saba Shafi +8 more

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010636

N/A

0DataRank · unranked

7 citations

Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu +3 more

Building integrative functional maps of gene regulation

Human Molecular Genetics(2022)10.1093/hmg/ddac195

N/A

0DataRank · unranked

6 citations

Henry Pratt, Jill E. Moore, Mark Gerstein, Zhiping Weng, Jinrui Xu

Predicting A/B compartments from histone modifications using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.19.488754

N/A

0DataRank · unranked

12 citations

Nitya Thakkar, Hannah L. Harris, Megan Zhang, Susanna Liu, Mark Gerstein +6 more

A genome-wide atlas of recurrent repeat expansions in human cancer

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.24.505159

N/A

0DataRank · unranked

1 citations

Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu +19 more

Minor intron splicing is critical for survival of lethal prostate cancer

Molecular Cell(2023)10.1016/j.molcel.2023.05.017

N/A

0DataRank · unranked

23 citations

Kyle D. Drake, Luca Roma, Ellen Qian, Se Ri Lee, Declan Clarke +16 more

Unified views on variant impact across many diseases

Trends in Genetics(2023)10.1016/j.tig.2023.02.002

N/A

0DataRank · unranked

6 citations

Mark Gerstein, Sushant Kumar

Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011222

N/A

0DataRank · unranked

1 citations

Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang +2 more

Data from STK11/LKB1 Loss of Function Is Associated with Global DNA Hypomethylation and S-Adenosyl-Methionine Depletion in Human Lung Adenocarcinoma

(2023)10.1158/0008-5472.c.6513136.v1

N/A

0DataRank · unranked

0 citations

Bernice A. Agana, Jacob M. Kaufman, Michael F. Sharpnack, Walter Wang, Christoph Weigel +9 more

REPIC — an ensemble learning methodology for cryo-EM particle picking

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.13.540636

N/A

0DataRank · unranked

0 citations

Sebastian JH Seager, Fred J. Sigworth, Hemant D. Tagare, Mark Gerstein, Christopher J. F. Cameron

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