Shaun Mahony

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 30 papers. Top paper: “The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes”.

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes

Cell Reports(2022)10.1016/j.celrep.2022.110524

N/A

0.840DataRank · unranked

22 citations

Congyi Lu, Alexis Morrissey, Lorena S. Lopez-Zepeda, Yingzhen Pei, Simon E. Vidal +8 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

DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Nucleic Acids Research(2024)10.1093/nar/gkae585

N/A

0.467DataRank · unranked

16 citations

Yuning Zhang, Alan S. Brown, J.R. Horton, Gabrielle A. Josling, Tsu-Pei Chiu +5 more

Accurate allocation of multimapped reads enables regulatory element analysis at repeats

Genome Research(2024)10.1101/gr.278638.123

N/A

0.428DataRank · unranked

11 citations

Jeffrey Shi, D. James, Shaun Mahony, Alexis Morrissey

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Genome Research(2024)10.1101/gr.277950.123

N/A

0.404DataRank · unranked

9 citations

Xi He, Belinda Giardine, Kathryn J. Isaac, Dylan J. Taylor, Rajiv C. McCoy +29 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

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

G3 Genes Genomes Genetics(2025)10.1093/g3journal/jkaf270

N/A

0.104DataRank · unranked

1 citations

Sohini Mukherjee, C. G. Cannon, Shaun Mahony, D. James

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types

Bioinformatics(2021)10.1093/bioinformatics/btab148

N/A

0DataRank · unranked

14 citations

Belinda Giardine, Shaun Mahony, Yu Zhang, Ross C. Hardison, Guanjue Xiang

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

PEGR: a flexible management platform for reproducible epigenomic and genomic research

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.26.453821

N/A

0DataRank · unranked

0 citations

Gretta D. Kellogg, Ali Nematbakhsh, Prashant Kumar Kuntala, Shaun Mahony, B. Franklin Pugh +2 more

PEGR: a flexible management platform for reproducible epigenomic and genomic research

Genome biology(2022)10.1186/s13059-022-02671-5

N/A

0DataRank · unranked

8 citations

Gretta D. Kellogg, Ali Nematbakhsh, Prashant Kumar Kuntala, Shaun Mahony, B. Franklin Pugh +2 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

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.06.561228

N/A

0DataRank · unranked

8 citations

Jianyu Yang, Tomohiko Akiyama, D. James, Alexis Morrissey, Thomas R. Blanda +6 more

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.02.535219

N/A

0DataRank · unranked

4 citations

Xi He, Belinda Giardine, Kathryn J. Isaac, Dylan J. Taylor, Rajiv C. McCoy +29 more

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.08.566246

N/A

0DataRank · unranked

4 citations

Holly Kleinschmidt, Jianyu Yang, Erik M. Leith, Jenna K. Johnson, Song Tan +3 more

Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.12.556916

N/A

0DataRank · unranked

2 citations

Jeffrey Shi, D. James, Shaun Mahony, Alexis Morrissey

SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.17.562727

N/A

0DataRank · unranked

0 citations

Kuangyu Yen, Shaun Mahony, Jianyu Yang

Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1

Molecular Cell(2024)10.1016/j.molcel.2024.06.022

N/A

0DataRank · unranked

18 citations

Holly Kleinschmidt, Jianyu Yang, Erik M. Leith, Jenna K. Johnson, Song Tan +3 more

Perspective on recent developments and challenges in regulatory and systems genomics

Bioinformatics Advances(2024)10.1093/bioadv/vbaf106

N/A

0DataRank · unranked

11 citations

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

Size-based expectation maximization for characterizing nucleosome positions and subtypes

Genome Research(2024)10.1101/gr.279138.124

N/A

0DataRank · unranked

3 citations

Kuangyu Yen, Shaun Mahony, Jianyu Yang

Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.10.612038

N/A

0DataRank · unranked

2 citations

Alexis Morrissey, Aswathy Sebastian, Belinda Giardine, Courtney Smith, Oluwasegun T. Akinniyi +6 more

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

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.14.670389

N/A

0DataRank · unranked

1 citations

Sohini Mukherjee, C. G. Cannon, Shaun Mahony, D. James

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells v1

(2025)10.17504/protocols.io.3byl46jjjgo5/v1

N/A

0DataRank · unranked

0 citations

Sohini Mukherjee, C. G. Cannon, Shaun Mahony, D. James

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

Genome Biology(2025)10.1186/s13059-025-03494-w

N/A

0DataRank · unranked

0 citations

Carles B. Adsera, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang +45 more

TPCAV: Interpreting deep learning genomics models via concept attribution

bioRxiv (Cold Spring Harbor Laboratory)(2026)10.64898/2026.01.20.700723

N/A

0DataRank · unranked

0 citations

Shaun Mahony, Jianyu Yang

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein–DNA complexes

Nucleic Acids Research(2020)10.1093/nar/gkaa618

N/A

0DataRank · unranked

7 citations

Matthew J. Rossi, Nina Farrell, B. Franklin Pugh, Shaun Mahony, Naomi Yamada

The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.27.355685

N/A

0DataRank · unranked

7 citations

Joana Santos, Lindsey Orchard, Naomi Yamada, Riëtte van Biljon, Heather J. Painter +3 more

PEGR: a management platform for ChIP-based next generation sequencing pipelines

Practice and Experience in Advanced Research Computing(2020)10.1145/3311790.3396621

N/A

0DataRank · unranked

3 citations

Gretta D. Kellogg, Shaun Mahony, William Lai, B. Franklin Pugh, Danying Shao

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.23.391771

N/A

0DataRank · unranked

3 citations

Congyi Lu, Alexis Morrissey, Lorena S. Lopez-Zepeda, Simon E. Vidal, Begüm Aydın +6 more