100 Washtenaw Ave
Ann Arbor, MI 48109
Available to mentor
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Postdoctoral ScholarStanford University, Genetics, 2014
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Postdoctoral AssociateDuke University, Computational Biology, 2010
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PhDDuke University, 2009
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Center MemberRogel Cancer Center
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Center MemberPrecision Health Initiative
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
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McBean B, Abou Zeidane R, Lichtman-Mikol S, Hauk B, Speers J, Tidmore S, Flores CL, Rana PS, Pisano C, Liu M, Santola A, Montero A, Boyle AP, Speers CW. International Journal of Molecular Sciences, 2025 Mar 1; 26 (5):Journal ArticleMELK as a Mediator of Stemness and Metastasis in Aggressive Subtypes of Breast Cancer
DOI:10.3390/ijms26052245 PMID: 40076867 -
Van Deynze K, Mumm C, Maltby CJ, Switzenberg JA, Todd PK, Boyle AP. Nucleic Acids Research, 2025 Jan 27; 53 (2):Journal ArticleEnhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing
DOI:10.1093/nar/gkae1202 PMID: 39676678 -
Yee C, Xiao Y, Chen H, Reddy AR, Xu B, Medwig-Kinney TN, Zhang W, Boyle AP, Herbst WA, Xiang YK, Matus DQ, Shen K. Nature Neuroscience, 2025 Jan 1;Journal ArticleCorrection to: An activity-regulated transcriptional program directly drives synaptogenesis (Nature Neuroscience, (2024), 27, 9, (1695-1707), 10.1038/s41593-024-01728-x)
DOI:10.1038/s41593-025-01950-1 -
Zhou W, Mumm C, Gan Y, Switzenberg JA, Wang J, De Oliveira P, Kathuria K, Losh SJ, McDonald TL, Bessell B, Van Deynze K, McConnell MJ, Boyle AP, Mills RE. 2024 Dec 23; bioRxiv,PreprintA personalized multi-platform assessment of somatic mosaicism in the human frontal cortex
DOI:10.1101/2024.12.18.629274 -
Jain S, Bakolitsa C, Brenner SE, Radivojac P, Moult J, Repo S, Hoskins RA, Andreoletti G, Barsky D, Chellapan A, Chu H, Dabbiru N, Kollipara NK, Ly M, Neumann AJ, Pal LR, Odell E, Pandey G, Peters-Petrulewicz RC, Srinivasan R, Yee SF, Yeleswarapu SJ, Zuhl M, Adebali O, Patra A, Beer MA, Hosur R, Peng J, Bernard BM, Berry M, Dong S, Boyle AP, Adhikari A, Chen J, Hu Z, Wang R, Wang Y, Miller M, Wang Y, Bromberg Y, Turina P, Capriotti E, Han JJ, Ozturk K, Carter H, Babbi G, Bovo S, Di Lena P, Martelli PL, Savojardo C, Casadio R, Cline MS, De Baets G, Bonache S, Díez O, Gutiérrez-Enríquez S, Fernández A, Montalban G, Ootes L, Özkan S, Padilla N, Riera C, De la Cruz X, Diekhans M, Huwe PJ, Wei Q, Xu Q, Dunbrack RL, Gotea V, Elnitski L, Margolin G, Fariselli P, Kulakovskiy IV, Makeev VJ, Penzar DD, Vorontsov IE, Favorov AV, Forman JR, Hasenahuer M, Fornasari MS, Parisi G, Avsec Z, Çelik MH, Nguyen TYD, Gagneur J, Shi FY, Edwards MD, Guo Y, Tian K, Zeng H, Gifford DK, Göke J, Zaucha J, Gough J, Ritchie GRS, Frankish A, Mudge JM, Harrow J, Young EL, Yu Y. Genome Biology, 2024 Dec 1; 25 (1):Journal ArticleCAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
DOI:10.1186/s13059-023-03113-6 PMID: 38389099 -
McDonald T, Mumm C, Switzenberg J, Boyle A. 2024 Nov 26; ZappyLab, Inc.,PreprintTEnCATS - Transposable Element nanopore Cas9-Targeted Sequencing v1
DOI:10.17504/protocols.io.kqdg3q66ev25/v1 -
Zhou W. 2024 Aug 21;PresentationA personalized multi-platform assessment of somatic mosaicism in the human frontal cortex
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Maltby CJ, Krans A, Grudzien SJ, Palacios Y, Muiños J, Suárez A, Asher M, Willey S, Van Deynze K, Mumm C, Boyle AP, Cortese A, Ndayisaba A, Khurana V, Barmada SJ, Dijkstra AA, Todd PK. Science Advances, 2024 Sep 6; 10 (36):Journal ArticleAAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS neurons
DOI:10.1126/sciadv.adn2321 PMID: 39231235
