Alan P Boyle, PhD
Computational Medicine and Bioinformatics
100 Washtenaw Ave
Ann Arbor, MI 48109
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Qualifications
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Postdoctoral ScholarStanford University, Genetics, United States
2010 - 2014
Postdoctoral Fellowship
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Postdoctoral AssociateDuke University, Computational Biology, MI, United States
2010 - 2010
Postdoctoral Fellowship
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PhD, Computational Biology and BioinformaticsDuke University, Durham, NC; Advisor: Dr. Terrence S. Furey and Dr. Gregory E. Crawford, United States
2005 - 2009
Center Memberships
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Center MemberAI and Digital Health Innovation
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Center MemberRogel Cancer Center
Research Overview
My research group aims to combine both computational and wet lab strategies to answer questions related to the transcriptional regulatory control of human genes. We believe that a complex regulatory control determines the fates of individual non-coding regulatory elements and that the integration of diverse genetic, epigenetic, and disease data is the best way to explore this control. As such, it is important to map and understand how sequence variations in individuals are responsible for mediating differences in gene expression and their phenotypic consequences. The goal of my research is to understand the biological mechanisms underlying transcriptional regulation and how human variation at regulatory regions affects this process.
I was involved in developing the first genome-wide map of open chromatin regions using DNase-seq as a member of the ENCODE project. This was some of the first work done using the now ubiquitous high- throughput sequencing data. I was further involved in demonstrating that heritable genomic variation can result in changes in open chromatin states. I now continue this work in annotation of regulatory regions through a mix of machine learning and wet lab approaches through the web resource RegulomeDB and through membership in the IGVF and SMaHT consortia. My recent work has also focused on using long-read sequencing technology to directly measure the effect of conformational changes in the human genome that can be driven through the movement of transposable elements. This work has also expanded to study short tandem repeat expansions in the human genome with a focus on identification of new disease-associated repeats.
Links
Boyle Lab
Recent Publications
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McBean BN, Rana PS, Zeidane RA, Davis A, Mercer V, Hauk B, Michmerhuizen A, Lichtman-Mikol S, Diedrich C, Wilder-Romans K, Tao M, Boyle AP, Speers C. Cancer Research, 2026 Apr 5; 86 (7_Supplement): 4645 - 4645.Journal ArticleAbstract 4645: Integrative transcriptomic and CRISPRi screening identifies determinants of intrinsic radiosensitivity in breast cancer
DOI:10.1158/1538-7445.am2026-4645 -
Rabbani M, Apell Z, Parnell TJ, Moritz L, Kim S, Srinivasan S, Agrawal R, Vargo A, Orchard P, Xie W, Freddolino L, Boyle AP, Li JZ, Lesch BJ, Cairns B, Kim M, Wilson TE, Hammoud SS. 2026 Mar 14; bioRxiv,Preprint3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis
DOI:10.64898/2026.03.10.710708 -
Li S, Chou E, Wang K, Boyle AP, Sartor MA. 2026 Mar 8; bioRxiv,PreprintTFBSpedia: a comprehensive human and mouse transcription factor binding sites database
DOI:10.64898/2026.03.04.709638 -
McBean B, Hauk B, Michmerhuizen AR, Chandler BC, Pesch AM, Lerner LM, Gurdak D, Ward C, Rana P, Zeidane RA, Mercer V, Tao M, Hochmuth E, Jungles KM, The S, Liu M, Spratt DE, Boyle AP, Pierce LJ, Speers CW. NPJ Breast Cancer, 2026 Feb 24;Journal ArticleTranscriptomic analysis to uncover the mechanism of radiosensitization of AR-positive triple-negative breast cancers with AR inhibition.
DOI:10.1038/s41523-026-00916-1 PMID: 41735341 -
Li D, Liu S, Assis PR, Li M, Dong S, Whaling I, Jolanki O, Kagda M, Zhang W, Macias-Velasco JF, Liu T, Cody S, Antonacci-Fulton L, Huang Y, Liu J, Montgomery MT, Zeiberg D, Jain S, Pejaver V, Bergquist T, Chen Y, Radivojac P, Gersbach CA, Sherpa RN, Castro CP, Boyle AP, Starita LM, Fowler DM, Ahituv N, Dey KK, Majoros WH, Reddy TE, Craven M, Sinha R, Sverchkov Y, Cai X, Nzima MZ, Calderwood MA, Rozowsky J, Gerstein M, Ma J, Yue F, Cherry MM, Love MI, Engreitz JM, Hitz BC, Wang T. Nucleic Acids Research, 2026 Jan 6; 54 (1): D1437 - D1445.Journal ArticleThe IGVF catalog—from genetic variation to function
DOI:10.1093/nar/gkaf1341 PMID: 41359121 -
Zhou W, Mumm C, Gan Y, Switzenberg JA, Wang J, Oliveira PD, Kathuria K, Losh SJ, McDonald TL, Bessell B, Deynze KV, McConnell MJ, Boyle AP, Mills RE. Alzheimer S Dementia the Journal of the Alzheimer S Association, 2025 Dec 1; 21: e103962Proceeding / Abstract / PosterBasic Science and Pathogenesis
DOI:10.1002/alz70855_103962 PMID: 41437633 -
Wang S, Bae M, Wang J, Zhao B, Nguyen K, Mallett S, Switzenberg JA, Losh SJ, Sexton CE, Miao B, Dong S, Zeng X, Wang Z, McDonald TL, Mumm C, Gadde RK, Tariq AM, Chen Z, Feng WC, Burn A, Park J, Chu C, Shen H, Wang T, Urban AE, Zhu X, Li H, Burns KH, Chun H-JE, Park PJ, SMaHT MEI Working Group , Boyle AP, Mills RE, Zhou W, Lee EA. 2025 Oct 7;PreprintMulti-platform framework for mapping somatic retrotransposition in human tissues.
DOI:10.1101/2025.10.07.680917 PMID: 41278868 -
Parana P, Mumm C, McConnell MJ, Boyle AP. Microbiology Resource Announcements, 2025 May 13;Journal ArticleDraft De-Novo Genome Construction of Scytonema sp. PRP1: Identified from Single-Cell Sequencing Library Preparation
Featured News & Stories
Highlighted Publications: August - December 2025
Congratulations on Department of Human Genetics Faculty Promotions
Highlighted Publications - July 2025
