Sushmita Roy

Also affiliated with Wisconsin Institutes for Discovery

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 2%percentile

3.1Author 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 →

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Science(2010)10.1126/science.1198374

Top 9%

2.4DataRank

Top 9%1089 citations

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Yanxiao Zhang, Richard S. Sandstrom +172 more

Papers

Driven by 45 papers — median percentile 50. Top paper: “Reliable prediction of regulator targets using 12 Drosophila genomes”.

Reliable prediction of regulator targets using 12 Drosophila genomes

Genome Research(2007)10.1101/gr.7090407

N/A

6.4DataRank · unranked

162 citations

Alexander Stark, Sushmita Roy, Sharon L. R. Kardia, Yanxiao Zhang

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Genome Research(2012)10.1101/gr.127191.111

N/A

4.3DataRank · unranked

126 citations

Sushmita Roy, Ferhat Ay, Patrick E. Meyer, Rogerio Candeias, Christopher A. Bristow +2 more

Evolutionary principles of modular gene regulation in yeasts

eLife(2013)10.7554/elife.00603

N/A

3.2DataRank · unranked

90 citations

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Science(2010)10.1126/science.1198374

Top 9%

2.4DataRank

Top 9%1089 citations

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Yanxiao Zhang, Richard S. Sandstrom +172 more

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

PLoS Computational Biology(2013)10.1371/journal.pcbi.1003252

N/A

2.3DataRank · unranked

101 citations

Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron Stewart, Audrey P. Gasch +1 more

Current and future directions in network biology

Bioinformatics Advances(2024)10.1093/bioadv/vbae099

N/A

1.6DataRank · unranked

100 citations

Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Krishnan, Arjun +32 more

Comparative Functional Genomics of the Fission Yeasts

Science(2011)10.1126/science.1203357

N/A

0.940DataRank · unranked

524 citations

Zehua Chen, Moran Yassour, Brian J. Haas, Naomi Habib, Ilan Wapinski +64 more

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

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

N/A

0.788DataRank · unranked

190 citations

Prisca Liberali, Sushmita Roy, Dawn Thompson

Correction: Evolutionary principles of modular gene regulation in yeasts

eLife(2013)10.7554/elife.01114

N/A

0.734DataRank · unranked

13 citations

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

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

Genome biology(2021)10.1186/s13059-021-02378-z

N/A

0.529DataRank · unranked

33 citations

Sushmita Roy, Da-Inn Lee

Data integration for inferring context-specific gene regulatory networks

Current Opinion in Systems Biology(2020)10.1016/j.coisb.2020.09.005

N/A

0.449DataRank · unranked

19 citations

Junha Shin, Shilu Zhang, Sushmita Roy, Brittany Baur

Perspective on recent developments and challenges in regulatory and systems genomics

Bioinformatics Advances(2024)10.1093/bioadv/vbaf106

N/A

0.373DataRank · unranked

11 citations

Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony +3 more

Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft

Scientific Reports(2023)10.1038/s41598-023-32568-7

N/A

0.360DataRank · unranked

10 citations

Maggie A. Marshall, Narmeen S Rashid, Jacqueline M. Grible, Aaron D. Valentine, Amy L. Olex +11 more

ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants

Frontiers in Genetics(2020)10.3389/fgene.2020.00730

Top 50%

0.356DataRank

Top 50%6 citations

Yi Zhang, Shilu Zhang, Sushmita Roy, Pablo Pérez‐Piñera, Jun S. Song +1 more

Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE

Methods in molecular biology(2022)10.1007/978-1-0716-2257-5_24

Top 56%

0.292DataRank

Top 56%3 citations

Sara Knaack, Sushmita Roy, Shilu Zhang

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation

PLoS Computational Biology(2023)10.1371/journal.pcbi.1011286

N/A

0.253DataRank · unranked

4 citations

Junha Shin, Jacob Matthew Schreiber, Shilu Zhang, Yi Zhang, Mohith Manjunath +4 more

Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.29.458098

N/A

0.234DataRank · unranked

3 citations

Jacob Matthew Schreiber, Junha Shin, Shilu Zhang, Yi Zhang, Mohith Manjunath +4 more

Current and future directions in network biology

arXiv (Cornell University)(2023)10.48550/arxiv.2309.08478

N/A

0.208DataRank · unranked

3 citations

Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Krishnan, Arjun +32 more

A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.11.538573

N/A

0.208DataRank · unranked

3 citations

Saptarshi Pyne, Spencer Halberg, Sung Chul Park, Hyewon Seo, Aidan Schmidt +5 more

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

10.21203/rs.3.rs-1892655/v1

N/A

0.104DataRank · unranked

1 citations

Saptarshi Pyne, Stefan Pietrzak, Alireza Siahpirani, Rupa Sridha, Sushmita Roy +1 more

Author response: Evolutionary principles of modular gene regulation in yeasts

(2013)10.7554/elife.00603.031

N/A

0DataRank · unranked

0 citations

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

Defining the role of β-cell IRE1α/XBP1 pathway and its gene regulatory network components in non-obese diabetic mice

Nature Communications(2025)10.1038/s41467-025-65635-w

N/A

0DataRank · unranked

3 citations

Khagani Eynullazada, Qianqian Ou, Junha Shin, Sushmita Roy, Feyza Engin +1 more

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Genome Research(2025)10.1101/gr.280357.124

N/A

0DataRank · unranked

4 citations

Tiegh Taylor, Kumaragurubaran Rathnakumar, Nadiya Khyzha, Minggao Liang, Azad Alizada +12 more

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Genome Research(2025)10.1101/gr.279930.124

N/A

0DataRank · unranked

1 citations

Sushmita Roy, Da-Inn Lee

Thioredoxin interacting protein (TXNIP), a redox regulator, mediates the EPAC-RAP1 signaling dependency of primary melanoma

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.29.696903

N/A

0DataRank · unranked

0 citations

Mithalesh Kumar Singh, Sarah Altameemi, Sonia Gude, Sushmita Roy, Ryan Rossman +6 more

Author Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft

Scientific Reports(2024)10.1038/s41598-024-82374-y

N/A

0DataRank · unranked

0 citations

Maggie A. Marshall, Narmeen S Rashid, Jacqueline M. Grible, Aaron D. Valentine, Amy L. Olex +11 more

Combinatorics of Cis‐Regulatory Element Evolution in Stress Response Modules of Ascomycete Yeasts

The FASEB Journal(2012)10.1096/fasebj.26.1_supplement.731.11

N/A

0DataRank · unranked

0 citations

Sushmita Roy, Dawn Thompson, Prisca Liberali, Aurian P. García-González, Jay H. Konieczka +1 more

Human iPSC Modeling Reveals Mutation-Specific Responses to Gene Therapy in a Genotypically Diverse Dominant Maculopathy

The American Journal of Human Genetics(2020)10.1016/j.ajhg.2020.06.011

N/A

0DataRank · unranked

58 citations

Benjamin Steyer, Pawan K. Shahi, Katherine P. Mueller, Rasa Valiauga, Kimberly L. Edwards +14 more

Identification of FMR1-regulated molecular networks in human neurodevelopment

Genome Research(2020)10.1101/gr.251405.119

N/A

0DataRank · unranked

68 citations

Junha Shin, Ryan D. Risgaard, Molly Parries, Jianyi Wang, Deborah Chasman +5 more

Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.17.254615

N/A

0DataRank · unranked

6 citations

Sushmita Roy, Da-Inn Lee

Dynamic regulatory module networks for inference of cell type-specific transcriptional networks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.18.210328

N/A

0DataRank · unranked

1 citations

Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart +3 more

The NIH Somatic Cell Genome Editing program

Nature(2021)10.1038/s41586-021-03191-1

N/A

0DataRank · unranked

132 citations

Erik J. Sontheimer, Philip J. Brooks, Melinda R. Dwinell, Charles A. Gersbach, David R. Liu +70 more

Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder

PLoS Genetics(2021)10.1371/journal.pgen.1009309

N/A

0DataRank · unranked

23 citations

Yuchang Wu, Junha Shin, Ye Zheng, Alireza Fotuhi Siahpirani, Yupei Lin +8 more

Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.01.446671

N/A

0DataRank · unranked

11 citations

Alireza Fotuhi Siahpirani, Jiaxin Li, Saptarshi Pyne, Matthew R. Stone, Viswesh Periyasamy +3 more

Faculty Opinions recommendation of Quantifying the effect of experimental perturbations at single-cell resolution.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature(2021)10.3410/f.739508592.793584255

N/A

0DataRank · unranked

0 citations

Sushmita Roy

Dynamic regulatory module networks for inference of cell type–specific transcriptional networks

Genome Research(2022)10.1101/gr.276542.121

N/A

0DataRank · unranked

6 citations

Sara Knaack, Deborah Chasman, Morten Seirup, Rupa Sridharan, Ron Stewart +3 more

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.25.513724

N/A

0DataRank · unranked

1 citations

Tiegh Taylor, Kumaragurubaran Rathnakumar, Nadiya Khyzha, Minggao Liang, Azad Alizada +11 more

Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

Nature Communications(2023)10.1038/s41467-023-38637-9

N/A

0DataRank · unranked

115 citations

Saptarshi Pyne, Stefan Pietrzak, Spencer Halberg, Sunnie Grace McCalla, Alireza Fotuhi Siahpirani +3 more

Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data

G3 Genes Genomes Genetics(2023)10.1093/g3journal/jkad004

N/A

0DataRank · unranked

53 citations

Alireza Fotuhi Siahpirani, Jiaxin Li, Saptarshi Pyne, Matthew R. Stone, Viswesh Periyasamy +3 more

Protective effects of dietary grape against atopic dermatitis-like skin lesions in NC/NgaTndCrlj mice

Frontiers in Immunology(2023)10.3389/fimmu.2022.1051472

N/A

0DataRank · unranked

10 citations

Charlotte A. Mintie, Mary A. Ndiaye, Gagan Chhabra, Sushmita Roy, Ruth Sullivan +4 more

Identifying molecular and functional similarities and differences between human primary cardiac valve interstitial cells and ventricular fibroblasts

Frontiers in Bioengineering and Biotechnology(2023)10.3389/fbioe.2023.1102487

N/A

0DataRank · unranked

5 citations

Fathima Shabnam, Sophie Givens, Vaidehi A. Patil, Yunfeng Ding, Grace Li +7 more

Human left ventricular cardiac fibroblasts undergo a dynamic shift in secretome and gene expression toward a cardiac myofibroblast phenotype during early passage in typical culture expansion conditions

Cytotherapy(2023)10.1016/j.jcyt.2023.10.001

N/A

0DataRank · unranked

1 citations

Sushmita Roy, Tianhua Zhou, Delani Wille, Sophie Mixon Reeves, James J. Conklin +2 more

Examining dynamics of three-dimensional genome organization with multi-task matrix factorization

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.25.554883

N/A

0DataRank · unranked

1 citations

Sushmita Roy, Da-Inn Lee

Predicting patient-specific enhancer-promoter interactions

Cell Reports Methods(2023)10.1016/j.crmeth.2023.100594

N/A

0DataRank · unranked

0 citations

Sushmita Roy, Brittany Baur

Perspective on recent developments and challenges in regulatory and systems genomics

arXiv (Cornell University)(2024)10.48550/arxiv.2411.04363

N/A

0DataRank · unranked

0 citations

Sushmita Roy, Ferhat Ay, Anthony Mathelier, Alejandra Medina-Rivera, Shaun Mahony +3 more

Sushmita Roy

Indexed papers

Top data-sharing exemplar

Papers