Alan P. Boyle, Ph.D.

Current lab member

Alan P. Boyle, Ph.D.

Professor, Computational Biology & Bioinformatics and Human Genetics

Principal Investigator

Boyle Lab history

  • Principal Investigator since September 2014
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Research

Research areas

  • Non-coding variation
  • Gene Regulation
  • High-throughput genomics
  • Nanopore sequencing

Training

Education

  • B.S.Biochemistry, Mississippi State University (2005)
  • B.S.Computer Science, Mississippi State University (2005)
  • Ph.D.Computational Biology and Bioinformatics, Duke University (2009)
  • PostdocStanford University (2014)

Biography

Background

Alan Boyle is Professor of Computational Medicine and Bioinformatics and Professor of Human Genetics at the University of Michigan Medical School. He earned his PhD in Computational Biology and Bioinformatics at Duke University, where he developed experimental and computational methods for mapping open chromatin, including DNase-seq. He completed his postdoctoral training in Genetics at Stanford University, where he developed methods for interpreting non-coding genetic variation and contributed to the ENCODE and modENCODE projects. His laboratory combines computational genomics, high-throughput functional assays, and long-read sequencing to understand how variation in regulatory and repetitive regions of the genome alters gene regulation and contributes to human disease. Current research includes interpreting regulatory variants through the IGVF Consortium, developing long-read approaches to study somatic mosaicism through the SMaHT Network, and investigating the effects of mobile elements, tandem repeats, and other structural variants on genome function.

Research output

Boyle Lab publications

87 publications

The IGVF catalog—from genetic variation to function

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 JM , Love MI , Engreitz JM , Hitz BC , Wang T
Nucleic Acids Research 2026 54(D1):D1437--D1445
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Multi-platform framework for mapping somatic retrotransposition in human tissues

Preprint
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 HJE , Park PJ , SMaHT MEI Working Group , Boyle AP †, Mills RE †, Zhou W †, Lee EA †
bioRxiv 2025
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The Somatic Mosaicism across Human Tissues Network

Coorens THH , Oh JW , Choi YA , Lim NS , Zhao B , Voshall A , Abyzov A , Antonacci-Fulton L , Aparicio S , Ardlie KG , Bell TJ , Bennett JT , Bernstein BE , Blanchard TG , Boyle AP , Buenrostro JD , Burns KH , Chen F , Chen R , Choudhury S , Doddapaneni HV , Eichler EE , Evrony GD , Faith MA , Fazzio TG , Fulton RS , Garber M , Gehlenborg N , Germer S , Getz G , Gibbs RA , Hernandez RG , Jin F , Korbel JO , Landau DA , Lawson HA , Lennon NJ , Li H , Li Y , Loh PR , Marth G , McConnell MJ , Mills RE , Montgomery SB , Natarajan P , Park PJ , Satija R , Sedlazeck FJ , Shao DD , Shen H , Stergachis AB , Underhill HR , Urban AE , VonDran MW , Walsh CA , Wang T , Wu TP , Zong C , Lee EA , Vaccarino FM , Somatic Mosaicism across Human Tissues Network
Nature 2025 643(8070):47--59
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Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Nielsen JB , Fritsche LG , Zhou W , Teslovich TM , Holmen OL , Gustafsson S , Gabrielsen ME , Schmidt EM , Beaumont R , Wolford BN , Lin M , Brummett CM , Preuss MH , Refsgaard L , Bottinger EP , Graham SE , Surakka I , Chu Y , Skogholt AH , Dalen H , Boyle AP , Oral H , Herron TJ , Kitzman J , Jalife J , Svendsen JH , Olesen MS , Njølstad I , Løchen ML , Baras A , Gottesman O , Marcketta A , O'Dushlaine C , Ritchie MD , Wilsgaard T , Loos RJF , Frayling TM , Boehnke M , Ingelsson E , Carey DJ , Dewey FE , Kang HM , Abecasis GR , Hveem K , Willer CJ
American Journal of Human Genetics 2018 102(1):103--115
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Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve.

Yang B *, Zhou W *, Jiao J *, Nielsen JB , Mathis MR , Heydarpour M , Lettre G , Folkersen L , Prakash S , Schurmann C , Fritsche L , Farnum GA , Lin M , Othman M , Hornsby W , Driscoll A , Levasseur A , Thomas M , Farhat L , Dubé MP , Isselbacher EM , Franco-Cereceda A , Guo DC , Bottinger EP , Deeb GM , Booher A , Kheterpal S , Chen YE , Kang HM , Kitzman J , Cordell HJ , Keavney BD , Goodship JA , Ganesh SK , Abecasis G , Eagle KA , Boyle AP , Loos RJF , Eriksson P †, Tardif JC †, Brummett CM †, Milewicz DM †, Body SC †, Willer CJ †
Nature Communications 2017 8(1):15481
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A comparative encyclopedia of DNA elements in the mouse genome.

Yue F *, Cheng Y *, Breschi A *, Vierstra J *, Wu W *, Ryba T *, Sandstrom R *, Ma Z *, Davis C *, Pope BD *, Shen Y *, Pervouchine DD , Djebali S , Thurman RE , Kaul R , Rynes E , Kirilusha A , Marinov GK , Williams BA , Trout D , Amrhein H , Fisher-Aylor K , Antoshechkin I , DeSalvo G , See LH , Fastuca M , Drenkow J , Zaleski C , Dobin A , Prieto P , Lagarde J , Bussotti G , Tanzer A , Denas O , Li K , Bender MA , Zhang M , Byron R , Groudine MT , McCleary D , Pham L , Ye Z , Kuan S , Edsall L , Wu YC , Rasmussen MD , Bansal MS , Kellis M , Keller CA , Morrissey CS , Mishra T , Jain D , Dogan N , Harris RS , Cayting P , Kawli T , Boyle AP , Euskirchen G , Kundaje A , Lin S , Lin Y , Jansen C , Malladi VS , Cline MS , Erickson DT , Kirkup VM , Learned K , Sloan CA , Rosenbloom KR , Lacerda de Sousa B , Beal K , Pignatelli M , Flicek P , Lian J , Kahveci T , Lee D , Kent WJ , Ramalho Santos M , Herrero J , Notredame C , Johnson A , Vong S , Lee K , Bates D , Neri F , Diegel M , Canfield T , Sabo PJ , Wilken MS , Reh TA , Giste E , Shafer A , Kutyavin T , Haugen E , Dunn D , Reynolds AP , Neph S , Humbert R , Hansen RS , De Bruijn M , Selleri L , Rudensky A , Josefowicz S , Samstein R , Eichler EE , Orkin SH , Levasseur D , Papayannopoulou T , Chang KH , Skoultchi A , Gosh S , Disteche C , Treuting P , Wang Y , Weiss MJ , Blobel GA , Cao X , Zhong S , Wang T , Good PJ , Lowdon RF , Adams LB , Zhou XQ , Pazin MJ , Feingold EA , Wold B , Taylor J , Mortazavi A , Weissman SM , Stamatoyannopoulos JA , Snyder MP , Guigo R , Gingeras TR , Gilbert DM , Hardison RC , Beer MA , Ren B , Mouse ENCODE Consortium
Nature 2014 515(7527):355--364
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Comparative analysis of regulatory information and circuits across distant species.

Boyle AP *, Araya CL *, Brdlik C , Cayting P , Cheng C , Cheng Y , Gardner K , Hillier LW , Janette J , Jiang L , Kasper D , Kawli T , Kheradpour P , Kundaje A , Li JJ , Ma L , Niu W , Rehm EJ , Rozowsky J , Slattery M , Spokony R , Terrell R , Vafeados D , Wang D , Weisdepp P , Wu YC , Xie D , Yan KK , Feingold EA , Good PJ , Pazin MJ , Huang H , Bickel PJ , Brenner SE , Reinke V , Waterston RH , Gerstein M , White KP †, Kellis M †, Snyder M †
Nature 2014 512(7515):453--456
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Architecture of the human regulatory network derived from ENCODE data

Gerstein MB *, Kundaje A *, Hariharan M *, Landt SG *, Yan KK *, Cheng C *, Mu XJ *, Khurana E *, Rozowsky J *, Alexander R *, Min R *, Alves P *, Abyzov A , Addleman N , Bhardwaj N , Boyle AP , Cayting P , Charos A , Chen DZ , Cheng Y , Clarke D , Eastman C , Euskirchen G , Frietze S , Fu Y , Gertz J , Grubert F , Harmanci A , Jain P , Kasowski M , Lacroute P , Leng J , Lian J , Monahan H , O'Geen H , Ouyang Z , Partridge EC , Patacsil D , Pauli F , Raha D , Ramirez L , Reddy TE , Reed B , Shi M , Slifer T , Wang J , Wu L , Yang X , Yip KY , Zilberman-Schapira G , Batzoglou S , Sidow A , Farnham PJ , Myers RM , Weissman SM , Snyder M
Nature 2012 489(7414):91--100
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Personal omics profiling reveals dynamic molecular and medical phenotypes

Chen R *, Mias GI *, Li-Pook-Than J *, Jiang L *, Lam HYK , Chen R , Miriami E , Karczewski KJ , Hariharan M , Dewey FE , Cheng Y , Clark MJ , Im H , Habegger L , Balasubramanian S , O'Huallachain M , Dudley JT , Hillenmeyer S , Haraksingh R , Sharon D , Euskirchen G , Lacroute P , Bettinger K , Boyle AP , Kasowski M , Grubert F , Seki S , Garcia M , Whirl-Carrillo M , Gallardo M , Blasco MA , Greenberg PL , Snyder P , Klein TE , Altman RB , Butte AJ , Ashley EA , Gerstein M , Nadeau KC , Tang H , Snyder M
Cell 2012 148(6):1293--1307
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Clustering of archael gene regulatory regions

Conference
Boyle AP , Bridges S
FASEB Journal 2003 17(5):A985
BibTeX