Alan P Boyle, PhD
Associate Professor of Computational Medicine and Bioinformatics
Associate Professor of Human Genetics
Computational Medicine and Bioinformatics
100 Washtenaw Ave
Ann Arbor, MI 48109
[email protected]

Available to mentor

Alan P Boyle, PhD
Associate Professor
  • Qualifications
  • Center Memberships
  • Research Overview
  • Links
  • Recent Publications
  • Qualifications
    • Postdoctoral Scholar
      Stanford University, Genetics, 2014
    • Postdoctoral Associate
      Duke University, Computational Biology, 2010
    • PhD
      Duke University, Durham, 2009
    Center Memberships
    • Center Member
      Rogel Cancer Center
    • Center Member
      Precision Health Initiative
    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.

    • Boyle Lab
    Recent Publications See All Publications
    • Journal Article
      CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
      Critical Assessment of Genome Interpretation Consortium . Genome Biol, 2024 Feb 22; 25 (1): 53 DOI:10.1186/s13059-023-03113-6
      PMID: 38389099
    • Journal Article
      HaplotagLR: An efficient and configurable utility for haplotagging long reads.
      Holmes MJ, Mahjour B, Castro CP, Farnum GA, Diehl AG, Boyle AP. PLoS One, 2024 19 (3): e0298688 DOI:10.1371/journal.pone.0298688
      PMID: 38478504
    • Journal Article
      Enhancing Portability of Trans-Ancestral Polygenic Risk Scores through Tissue-Specific Functional Genomic Data Integration
      Crone B, Boyle AP. 2024.02.07.579365 DOI:10.1101/2024.02.07.579365
    • Journal Article
      Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants.
      McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H. Cell Genom, 2023 Oct 11; 3 (10): 100404 DOI:10.1016/j.xgen.2023.100404
      PMID: 37868037
    • Proceeding / Abstract / Poster
      Mechanisms of Intrinsic Radioresistance in Breast Cancer Identify Potential Therapeutic Vulnerabilities
      McBean B, Michmerhuizen AR, Wilder-Romans K, Chandler B, Lerner L, Ward C, Liu M, Boyle AP, Speers C. International Journal of Radiation Oncology • Biology • Physics, 2023 Oct; 117 (2): e250 DOI:10.1016/j.ijrobp.2023.06.1191
    • Journal Article
      Organ-specific prioritization and annotation of non-coding regulatory variants in the human genome
      Zhao N, Dong S, Boyle AP. 2023.09.07.556700 DOI:10.1101/2023.09.07.556700
    • Presentation
      Deciphering Human Regulatory Variation
      Boyle AP. 2023 Sep;
    • Journal Article
      Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1.
      Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu Y-C, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS. Nat Struct Mol Biol, 2023 Aug; 30 (8): 1077 - 1091. DOI:10.1038/s41594-023-01033-4
      PMID: 37460896