Photo of Alan Boyles

Alan Boyle, Ph.D.

Michigan Neuroscience Institute Affiliate
Associate Professor of Computational Medicine and Bioinformatics
Associate Professor of Human Genetics
Palmer Commons
Room 2049A 
Ann Arbor, MI 48109

Areas of Interest

Dr. Boyle's 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. Using innovative computational and wet lab approaches the lab both characterizes the function of these regulatory elements as well as examines the effect of genetic variation in these regions.

Honors & Awards

  • Endowment for the Basic Sciences Teaching Award (2019)
  • First Place in CAGI5 Regulation Saturation Challenge (2018)
  • NSF CAREER Award (2017)
  • Alfred P. Sloan Foundation Fellowship in Computational & Evolutionary Molecular Biology (2015)


  • Ph.D., Computational Biology and Bioinformatics, Duke University, Durham, NC (2009)
  • B.S., Biochemistry and Molecular Biology, Mississippi State University, Starkville, MS (2005)
  • B.S., Computer Science, Mississippi State University, Starkville, MS (2005)

Published Articles or Reviews

  • Dong S, Boyle AP. “Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.” Nucleic Acids Research 2021, 50:e6–e6. PMID: 34648033.
  • *McDonald TL, *Zhou W, Castro CP, Mumm C, Switzenberg JA, †Mills RE, †Boyle AP. “Cas9 targeted enrichment of mobile elements using nanopore sequencing.” Nature Communications 2021, 12:3586. PMID: 34117247.
  • Ouyang N, Boyle AP. “TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.” Genome Research 2020, 30:1040–1046. PMID: 32660981.
  • Diehl AG, Ouyang N, Boyle AP. “Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.” Nature Communications 2020, 11:1796. PMID: 32286261.

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