Aryee Lab

Martin J. Aryee, PhD, is a developer of computational methods for genomics and epigenomics. He is a member of the Molecular Pathology Research Unit of Massachusetts General Hospital.

Martin J. Aryee, PhD

Assistant Pathologist,
Massachusetts General Hospital

Assistant Professor of Pathology,
Harvard Medical School


Martin received his PhD in Biostatistics from the Harvard School of Public Health in 2008, and completed a post-doctoral fellowship at the Johns Hopkins Sidney Kimmel Comprehensive Cancer Center. He joined the Massachusetts General Hospital and Harvard Medical School (HMS) Departments of Pathology in 2012. In 2014 he taught a course titled Fundamental Concepts in Gene Mapping at HMS. 

Dr. Aryee specializes in epigenetic mechanisms involved in chemical and physical changes to the structure of DNA without changes in the underlying sequence. Epigenetics allows for fine-tuned control of gene expression and is the basic mechanism whereby a single human genome can give rise to over 200 different cell types in the adult organism. He is interested in the interplay between genetic and epigenetic factors, and their role in determining cell state and disease etiology.

Research Interests

Dr. Aryee's research involves developing statistical tools for mapping genomic and epigenomic landscapes and using this data to understand causes of human disease. For example, in 2014 Dr. Aryee et al published a paper on "Minfi", an open source software package developed in the Molecular Pathology Research Unit at Mass General Hospital. Using Bioconductor, a team of collaborators developed a flexible and comprehensive package for the analysis of Infinium DNA methylation microarrays. This suite of computational tools incorporate state-of-the-art statistical techniques for the analysis of DNAm data. In the paper, they illustrate how their methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods.  

Martin Aryee, PhD
Principal Investigator, Massachusetts General Hospital
Assistant Professor of Pathology, Harvard Medical School
Associate Member, Broad Institute of MIT & Harvard

Robert Howe
Undergraduate Thesis Student, University of Vermont
Robert is a senior at the University of Vermont pursuing degrees in Biochemistry and Computer Science. He hopes to go to medical school in 2016. 

Akpéli Nordor, PharmD
Visiting Research Scholar, Institut Curie & Université Paris Descartes
Akpéli received his PharmD from Université Paris Descartes in 2013. He is currently completing a PhD at the Institut Curie’s Translational Research Department as part of Frontiers in Life Sciences PhD program of the Center for Research and Interdisciplinarity of Paris.

Vishal Thapar, PhD
Research Scientist, Massachusetts General Hospital
Vishal received his PhD in Computer Science from the University of Connecticut in 2008. He did a post-doc at Cold Spring Harbor and then worked as a bioinformatics research scientist at Memorial Sloan Kettering Cancer Center before joining MGH in 2013. He works jointly with The Aryee and Ting labs.

Open Position: Research scientist, programmer/analyst

Molecular Pathology Unit, Massachusetts General Hospital

Please go to the Aryee Lab for details about the open research scientist position and instructions on how to apply.

Aryee Lab Publications

Visit the Aryee Lab Publications page for more information.


View all publications for Martin Aryee on PubMed

Selected Publications from PubMed

  1. Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer. O'Brien TD, Jia P, Xia J, Saxena U, Jin H, Vuong H, Kim P, Wang Q, Aryee MJ, Mino-Kenudson M, Engelman JA, Le LP, Iafrate AJ, Heist RS, Pao W, Zhao Z. Methods. 2015 Apr 23. pii: S1046-2023(15)00162-0. doi: 10.1016/j.ymeth.2015.04.016. [Epub ahead of print]
  2. Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis.
    Van Rechem C, Black JC, Boukhali M, Aryee MJ, Gräslund S, Haas W, Benes CH, Whetstine JR. Cancer Discov. 2015 Mar;5(3):255-63. doi: 10.1158/2159-8290.CD-14-1326. Epub 2015 Jan 6.
  3. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. Nat Biotechnol. 2015 Feb;33(2):187-97. doi: 10.1038/nbt.3117. Epub 2014 Dec 16.
  4. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN.