Photo of Martin Aryee,  PhD

Martin Aryee, PhD

Massachusetts General Hospital

Massachusetts General Hospital
Phone: (617) 575-9715


aryee.martin@mgh.harvard.edu

Martin Aryee, PhD

Massachusetts General Hospital

EDUCATIONAL TITLES

  • Assistant Professor, Pathology, Harvard Medical School
  • Assistant Professor, Biostatistics, Harvard T.H. Chan School Of Public Health
  • Associate Member, Epigenomics Program, Broad Institute of MIT and Harvard
  • Assistant Pathologist, Pathology, Massachusetts General Hospital

DF/HCC PROGRAM AFFILIATION

Publications

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  • Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med 2017; 214:2875-2887. PubMed
  • Nordor AV, Nehar-Belaid D, Richon S, Klatzmann D, Bellet D, Dangles-Marie V, Fournier T, Aryee MJ. The early pregnancy placenta foreshadows dna methylation alterations of solid tumors. Epigenetics 2017. PubMed
  • Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods 2017; 14:607-614. PubMed
  • Boulay G, Awad ME, Riggi N, Archer TC, Iyer S, Boonseng WE, Rossetti NE, Naigles B, Rengarajan S, Volorio A, Kim JC, Mesirov JP, Tamayo P, Pomeroy SL, Aryee MJ, Rivera MN. OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma. 2017; 7:288-301. PubMed
  • Desai N, Sajed D, Arora KS, Solovyov A, Rajurkar M, Bledsoe JR, Sil S, Amri R, Tai E, MacKenzie OC, Mino-Kenudson M, Aryee MJ, Ferrone CR, Berger DL, Rivera MN, Greenbaum BD, Deshpande V, Ting DT. Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer. JCI Insight 2017; 2:e91078. PubMed
  • Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M. Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs. Mol Cell 2016; 64:1088-1101. PubMed
  • Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol 2016. PubMed
  • Tsai SQ, Topkar VV, Joung JK, Aryee MJ. Open-source guideseq software for analysis of GUIDE-seq data. Nat Biotechnol 2016; 34:483. PubMed
  • Heist RS, Shim HS, Gingipally S, Mino-Kenudson M, Le L, Gainor JF, Zheng Z, Aryee M, Xia J, Jia P, Jin H, Zhao Z, Pao W, Engelman JA, Iafrate AJ. MET Exon 14 Skipping in Non-Small Cell Lung Cancer. Oncologist 2016; 21:481-6. PubMed
  • Perin J, Fischer Walker CL, Black RE, Aryee MJ. Meta-Analysis With a Continuous Covariate That Is Differentially Categorized Across Studies. Am J Epidemiol 2016; 183:507-14. PubMed
  • Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 2015. PubMed
  • 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. Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer. Methods 2015. PubMed
  • Ziller MJ, Hansen KD, Meissner A, Aryee MJ. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods 2015; 12:230-2, 1 p following 232. PubMed
  • Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 2015; 33:187-97. PubMed
  • 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. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 2014; 26:668-81. PubMed
  • Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014; 32:569-76. PubMed
  • Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 2014. PubMed
  • Liu Y, Li X, Aryee MJ, Ekström TJ, Padyukov L, Klareskog L, Vandiver A, Moore AZ, Tanaka T, Ferrucci L, Fallin MD, Feinberg AP. GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. Am J Hum Genet 2014; 94:485-95. PubMed
  • Zou J, Lippert C, Heckerman D, Aryee M, Listgarten J. Epigenome-wide association studies without the need for cell-type composition. Nat Methods 2014; 11:309-11. PubMed
  • Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, Reinius L, Acevedo N, Taub M, Ronninger M, Shchetynsky K, Scheynius A, Kere J, Alfredsson L, Klareskog L, Ekström TJ, Feinberg AP. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 2013; 31:142-7. PubMed
  • Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med 2013; 5:169ra10. PubMed
  • Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 2011; 29:1117-9. PubMed
  • Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, Irizarry RA. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics 2011; 12:197-210. PubMed
  • Wu Z, Aryee MJ. Subset quantile normalization using negative control features. J Comput Biol 2010; 17:1385-95. PubMed
  • Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, Daley GQ, Weissman IL, Feinberg AP. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 2010; 467:338-42. PubMed
  • Haffner MC, Aryee MJ, Toubaji A, Esopi DM, Albadine R, Gurel B, Isaacs WB, Bova GS, Liu W, Xu J, Meeker AK, Netto G, De Marzo AM, Nelson WG, Yegnasubramanian S. Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat Genet 2010; 42:668-75. PubMed
  • Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 2009; 41:1350-3. PubMed
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