Alan P. Boyle

ORCID: 0000-0002-2081-1105

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 6%percentile

0.219Author DataRank

Indexed papers

1in 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 1 indexed paper 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.

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

Papers

Driven by 39 papers — median percentile 37. Top paper: “Perspectives on ENCODE”.

Perspectives on ENCODE

Nature(2020)10.1038/s41586-020-2449-8

N/A

4.7DataRank · unranked

227 citations

Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken +95 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

Annotating and prioritizing human non-coding variants with RegulomeDB v.2

Nature Genetics(2023)10.1038/s41588-023-01365-3

N/A

0.776DataRank · unranked

176 citations

Nanxiang Zhao, Emma Spragins, Meenakshi S. Kagda, Mingjie Li, Pedro Assis +6 more

An activity-regulated transcriptional program directly drives synaptogenesis

Nature Neuroscience(2024)10.1038/s41593-024-01728-x

N/A

0.406DataRank · unranked

14 citations

Yutong Xiao, Hongwen Chen, Anay R. Reddy, Bing Xu, Taylor N. Medwig-Kinney +7 more

Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing

Nucleic Acids Research(2024)10.1093/nar/gkae1202

N/A

0.269DataRank · unranked

5 citations

Camille Mumm, Connor J. Maltby, Jessica A. Switzenberg, Peter K. Todd, Alan P. Boyle +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

Multi-platform framework for mapping somatic retrotransposition in human tissues

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.07.680917

N/A

0.104DataRank · unranked

1 citations

Mingyun Bae, Jinhao Wang, Boxun Zhao, Khue Nguyen, Shayna Mallett +30 more

Cas9 targeted enrichment of mobile elements using nanopore sequencing

Nature Communications(2021)10.1038/s41467-021-23918-y

N/A

0DataRank · unranked

68 citations

Weichen Zhou, Christopher P. Castro, Camille Mumm, Jessica A. Switzenberg, Ryan E. Mills +2 more

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome

Nucleic Acids Research(2021)10.1093/nar/gkab924

N/A

0DataRank · unranked

23 citations

Alan P. Boyle, Shengcheng Dong

F-Seq2: improving the feature density based peak caller with dynamic statistics

NAR Genomics and Bioinformatics(2021)10.1093/nargab/lqab012

N/A

0DataRank · unranked

11 citations

Alan P. Boyle, Nanxiang Zhao

Single residue substitution in protamine 1 disrupts sperm genome packaging and embryonic development in mice

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.16.460631

N/A

0DataRank · unranked

14 citations

Samantha B. Schon, Mashiat Rabbani, Sheng Yi, Devon F. Pendlebury, Ritvija Agrawal +13 more

Real-Time, Direct Classification of Nanopore Signals with SquiggleNet

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.15.426907

N/A

0DataRank · unranked

6 citations

Jack Wadden, John R. Erb‐Downward, Piyush Ranjan, Weichen Zhou, T. L. McDonald +6 more

Cas9 targeted enrichment of mobile elements using nanopore sequencing

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.10.430605

N/A

0DataRank · unranked

4 citations

Weichen Zhou, Christopher P. Castro, Camille Mumm, Jessica A. Switzenberg, Ryan E. Mills +2 more

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.09.434619

N/A

0DataRank · unranked

1 citations

Alan P. Boyle, Shengcheng Dong

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions

BMC Bioinformatics(2022)10.1186/s12859-022-04865-x

N/A

0DataRank · unranked

8 citations

Alan P. Boyle, Sierra S. Nishizaki

OnRamp: rapid nanopore plasmid validation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.15.484480

N/A

0DataRank · unranked

7 citations

Melissa L. Drexel, T. L. McDonald, Adam Diehl, Jessica A. Switzenberg, Alan P. Boyle +1 more

Quantitative assessment of association between noncoding variants and transcription factor binding

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.22.517559

N/A

0DataRank · unranked

5 citations

Alan P. Boyle, Ningxin Ouyang

Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.05.515231

N/A

0DataRank · unranked

0 citations

Adam Diehl, Alan P. Boyle, Christopher P. Castro

Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants

Cell Genomics(2023)10.1016/j.xgen.2023.100404

N/A

0DataRank · unranked

47 citations

Sool Lee, Jiseok Lee, Jessica Bell, Oleh Krupa, Jessica E. Davis +12 more

Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1

Nature Structural & Molecular Biology(2023)10.1038/s41594-023-01033-4

N/A

0DataRank · unranked

28 citations

Samantha B. Schon, Mashiat Rabbani, Yi Sheng, Ritvija Agrawal, Juniper Glass-Klaiber +16 more

Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes

Human Genetics and Genomics Advances(2023)10.1016/j.xhgg.2023.100210

N/A

0DataRank · unranked

3 citations

Adam Diehl, Alan P. Boyle, Christopher P. Castro

Multiplexed long-read plasmid validation and analysis using OnRamp

Genome Research(2023)10.1101/gr.277369.122

N/A

0DataRank · unranked

18 citations

Melissa L. Drexel, T. L. McDonald, Adam Diehl, Jessica A. Switzenberg, Alan P. Boyle +1 more

LRphase: an efficient method for assigning haplotype identity to long reads

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.18.524565

N/A

0DataRank · unranked

1 citations

Babak Mahjour, Christopher P. Castro, G.A. Farnum, Adam Diehl, Alan P. Boyle +1 more

Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration

PLoS Genetics(2024)10.1371/journal.pgen.1011356

N/A

0DataRank · unranked

4 citations

Alan P. Boyle, Bradley Crone

HaplotagLR: An efficient and configurable utility for haplotagging long reads

PLoS ONE(2024)10.1371/journal.pone.0298688

N/A

0DataRank · unranked

1 citations

Babak Mahjour, Christopher P. Castro, G.A. Farnum, Adam Diehl, Alan P. Boyle +1 more

A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.18.629274

N/A

0DataRank · unranked

5 citations

Camille Mumm, Yanming Gan, Jessica A. Switzenberg, Jinhao Wang, Paulo De Oliveira +8 more

Enhanced Detection and Genotyping of Disease-Associated Tandem Repeats Using HMMSTR and Targeted Long-Read Sequencing

medRxiv(2024)10.1101/2024.05.01.24306681

N/A

0DataRank · unranked

3 citations

Camille Mumm, Connor J. Maltby, Jessica A. Switzenberg, Peter K. Todd, Alan P. Boyle +1 more

Enhancing Portability of Trans-Ancestral Polygenic Risk Scores through Tissue-Specific Functional Genomic Data Integration

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.07.579365

N/A

0DataRank · unranked

1 citations

Alan P. Boyle, Bradley Crone

An activity-regulated transcriptional program directly drives synaptogenesis

UNC Libraries(2024)10.17615/73xp-4k72

N/A

0DataRank · unranked

0 citations

Wendy A. Herbst, Hongwen Chen, Yang K. Xiang, David Q. Matus, Kang Shen +7 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

Long-term immune reprogramming of classical monocytes with altered ontogeny mediates enhanced lung injury in sepsis survivors

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.16.654442

N/A

0DataRank · unranked

1 citations

Breanna McBean, Alan P. Boyle, Brett C. Arenberg, Matthias Mack, Bethany B. Moore +9 more

Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.27.650888

N/A

0DataRank · unranked

0 citations

Katelyn M. Green, Bradley Crone, Jessica A. Switzenberg, Elizabeth M.H. Tank, Amy Krans +8 more

GPatch enables chromosome-scale, gap-free pseudoassemblies from fragmented draft genomes

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.22.655567

N/A

0DataRank · unranked

0 citations

Alan P. Boyle, Adam Diehl

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions

NAR Genomics and Bioinformatics(2020)10.1093/nargab/lqaa006

N/A

0DataRank · unranked

27 citations

Raymond G. Cavalcante, Chee Khoon Lee, Tingting Qin, Snehal Patil, Shuze Wang +4 more

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

BMC Bioinformatics(2020)10.1186/s12859-020-03742-9

N/A

0DataRank · unranked

3 citations

Alan P. Boyle, Adam Diehl

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

Genome Research(2020)10.1101/gr.258228.119

N/A

0DataRank · unranked

26 citations

Alan P. Boyle, Ningxin Ouyang

SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.13.250118

N/A

0DataRank · unranked

1 citations

Alan P. Boyle, Sierra S. Nishizaki

DNA methylation directs nucleosome positioning in RNA-mediated transcriptional silencing

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.29.359794

N/A

0DataRank · unranked

1 citations

Shriya Sethuraman, Jakub Dolata, Alan P. Boyle, Andrzej Wierzbicki, M. Hafiz Rothi

SquiggleNet: real-time, direct classification of nanopore signals

Genome biology(2021)10.1186/s13059-021-02511-y

N/A

0DataRank · unranked

88 citations

Jack Wadden, John R. Erb‐Downward, Piyush Ranjan, Weichen Zhou, T. L. McDonald +6 more

Alan P. Boyle

Indexed papers

Top data-sharing exemplar

Papers