Harvard Catalyst Profiles

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Martin Joseph Ankrah Aryee, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Ligorio M, Sil S, Malagon-Lopez J, Nieman LT, Misale S, Di Pilato M, Ebright RY, Karabacak MN, Kulkarni AS, Liu A, Vincent Jordan N, Franses JW, Philipp J, Kreuzer J, Desai N, Arora KS, Rajurkar M, Horwitz E, Neyaz A, Tai E, Magnus NKC, Vo KD, Yashaswini CN, Marangoni F, Boukhali M, Fatherree JP, Damon LJ, Xega K, Desai R, Choz M, Bersani F, Langenbucher A, Thapar V, Morris R, Wellner UF, Schilling O, Lawrence MS, Liss AS, Rivera MN, Deshpande V, Benes CH, Maheswaran S, Haber DA, Fernandez-Del-Castillo C, Ferrone CR, Haas W, Aryee MJ, Ting DT. Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer. Cell. 2019 May 23. PMID: 31155233.
    Citations:    
  2. Gaiti F, Chaligne R, Gu H, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. Nature. 2019 May; 569(7757):576-580. PMID: 31092926.
    Citations:    
  3. Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun. 2019 04 23; 10(1):1903. PMID: 31015418.
    Citations:    
  4. Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature. 2019 May; 569(7756):433-437. PMID: 30995674.
    Citations:    
  5. Kangeyan D, Dunford A, Iyer S, Stewart C, Hanna M, Getz G, Aryee MJ. A (fire)cloud-based DNA methylation data preprocessing and quality control platform. BMC Bioinformatics. 2019 Mar 29; 20(1):160. PMID: 30922215.
    Citations:    
  6. Bhan I, Aryee M, Ting DT. Reply. Gastroenterology. 2019 05; 156(6):1933-1934. PMID: 30928436.
    Citations:    
  7. Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet. 2019 04; 51(4):683-693. PMID: 30858613.
    Citations:    
  8. Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 Mar 07; 176(6):1325-1339.e22. PMID: 30827679.
    Citations:    
  9. Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 03; 37(3):276-282. PMID: 30742127.
    Citations:    
  10. Lareau C, Kangeyan D, Aryee MJ. Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets. Methods Mol Biol. 2019; 1935:187-202. PMID: 30758828.
    Citations:    
  11. Lazzarotto CR, Nguyen NT, Tang X, Malagon-Lopez J, Guo JA, Aryee MJ, Joung JK, Tsai SQ. Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq. Nat Protoc. 2018 11; 13(11):2615-2642. PMID: 30341435.
    Citations:    Fields:    
  12. Bhan I, Mosesso K, Goyal L, Philipp J, Kalinich M, Franses JW, Choz M, Oklu R, Toner M, Maheswaran S, Haber DA, Zhu AX, Chung RT, Aryee M, Ting DT. Detection and Analysis of Circulating Epithelial Cells in Liquid Biopsies From Patients With Liver Disease. Gastroenterology. 2018 12; 155(6):2016-2018.e11. PMID: 30218669.
    Citations:    Fields:    Translation:HumansCells
  13. Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature. 2018 09; 561(7723):416-419. PMID: 30209390.
    Citations:    Fields:    
  14. Pelikan RC, Kelly JA, Fu Y, Lareau CA, Tessneer KL, Wiley GB, Wiley MM, Glenn SB, Harley JB, Guthridge JM, James JA, Aryee MJ, Montgomery C, Gaffney PM. Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. Nat Commun. 2018 07 25; 9(1):2905. PMID: 30046115.
    Citations:    Fields:    Translation:HumansCells
  15. Lee K, Zhang Y, Kleinstiver BP, Guo JA, Aryee MJ, Miller J, Malzahn A, Zarecor S, Lawrence-Dill CJ, Joung JK, Qi Y, Wang K. Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize. Plant Biotechnol J. 2019 02; 17(2):362-372. PMID: 29972722.
    Citations:    Fields:    
  16. Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ. Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell. 2018 05 31; 173(6):1535-1548.e16. PMID: 29706549.
    Citations: 5     Fields:    
  17. Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L. Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods. 2018 04; 15(4):238-239. PMID: 29600992.
    Citations: 1     Fields:    
  18. Lareau CA, Aryee MJ. hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data. Nat Methods. 2018 02 28; 15(3):155-156. PMID: 29489746.
    Citations: 1     Fields:    
  19. Lareau CA, Aryee MJ. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. Bioinformatics. 2018 02 15; 34(4):672-674. PMID: 29028898.
    Citations: 1     Fields:    Translation:HumansCells
  20. 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 09; 12(9):793-803. PMID: 28678605.
    Citations: 2     Fields:    Translation:HumansCells
  21. 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 Oct 02; 214(10):2875-2887. PMID: 28878000.
    Citations: 5     Fields:    Translation:AnimalsCells
  22. 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 Jun; 14(6):607-614. PMID: 28459458.
    Citations: 23     Fields:    Translation:Cells
  23. 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. Cancer Discov. 2017 03; 7(3):288-301. PMID: 28213356.
    Citations: 4     Fields:    Translation:HumansCells
  24. 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 02 09; 2(3):e91078. PMID: 28194445.
    Citations: 1     Fields:    
  25. 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 12 15; 64(6):1088-1101. PMID: 27984744.
    Citations: 6     Fields:    Translation:AnimalsCells
  26. Gomez-Cabrero D, Almgren M, Sjöholm LK, Hensvold AH, Ringh MV, Tryggvadottir R, Kere J, Scheynius A, Acevedo N, Reinius L, Taub MA, Montano C, Aryee MJ, Feinberg JI, Feinberg AP, Tegnér J, Klareskog L, Catrina AI, Ekström TJ. High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis. Genome Med. 2016 11 22; 8(1):124. PMID: 27876072.
    Citations: 2     Fields:    Translation:HumansCells
  27. 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 08; 34(8):869-74. PMID: 27347757.
    Citations: 73     Fields:    Translation:HumansCells
  28. Tsai SQ, Topkar VV, Joung JK, Aryee MJ. Open-source guideseq software for analysis of GUIDE-seq data. Nat Biotechnol. 2016 05 06; 34(5):483. PMID: 27153277.
    Citations: 7     Fields:    Translation:Cells
  29. 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 Apr; 21(4):481-6. PMID: 27022036.
    Citations: 8     Fields:    Translation:Humans
  30. 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 Mar 01; 183(5):507-14. PMID: 26867775.
    Citations:    Fields:    Translation:Humans
  31. 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 Jul 23; 523(7561):481-5. PMID: 26098369.
    Citations: 256     Fields:    Translation:HumansAnimalsCells
  32. 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 Jul 15; 83:118-27. PMID: 25913717.
    Citations: 4     Fields:    Translation:HumansCells
  33. Van Rechem C, Black JC, Boukhali M, Aryee MJ, Gräslund S, Haas W, Benes CH, Whetstine JR. Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Cancer Discov. 2015 Mar; 5(3):255-63. PMID: 25564516.
    Citations: 15     Fields:    Translation:HumansCells
  34. 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 Feb; 33(2):187-197. PMID: 25513782.
    Citations: 310     Fields:    Translation:HumansCells
  35. Ziller MJ, Hansen KD, Meissner A, Aryee MJ. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods. 2015 Mar; 12(3):230-2, 1 p following 232. PMID: 25362363.
    Citations: 42     Fields:    Translation:HumansCells
  36. 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 Nov 10; 26(5):668-681. PMID: 25453903.
    Citations: 52     Fields:    Translation:HumansAnimalsCells
  37. Yip WK, Fier H, DeMeo DL, Aryee M, Laird N, Lange C. A novel method for detecting association between DNA methylation and diseases using spatial information. Genet Epidemiol. 2014 Dec; 38(8):714-21. PMID: 25250875.
    Citations: 2     Fields:    Translation:HumansCells
  38. 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 Jun; 32(6):569-76. PMID: 24770325.
    Citations: 245     Fields:    Translation:HumansCells
  39. 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 Apr 03; 94(4):485-95. PMID: 24656863.
    Citations: 30     Fields:    Translation:HumansCells
  40. 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 May 15; 30(10):1363-9. PMID: 24478339.
    Citations: 420     Fields:    Translation:HumansCells
  41. Zou J, Lippert C, Heckerman D, Aryee M, Listgarten J. Epigenome-wide association studies without the need for cell-type composition. Nat Methods. 2014 Mar; 11(3):309-11. PMID: 24464286.
    Citations: 58     Fields:    Translation:HumansCells
  42. Simcha DM, Younes L, Aryee MJ, Geman D. Identification of direction in gene networks from expression and methylation. BMC Syst Biol. 2013 Nov 01; 7:118. PMID: 24182195.
    Citations: 3     Fields:    Translation:Cells
  43. Lanata CF, Fischer-Walker CL, Olascoaga AC, Torres CX, Aryee MJ, Black RE. Global causes of diarrheal disease mortality in children <5 years of age: a systematic review. PLoS One. 2013; 8(9):e72788. PMID: 24023773.
    Citations: 109     Fields:    Translation:Humans
  44. Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics. 2013 Mar; 8(3):290-302. PMID: 23426267.
    Citations: 83     Fields:    Translation:HumansCells
  45. 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 Jan 23; 5(169):169ra10. PMID: 23345608.
    Citations: 74     Fields:    Translation:HumansCells
  46. 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 Feb; 31(2):142-7. PMID: 23334450.
    Citations: 272     Fields:    Translation:HumansCells
  47. Lim SS, Vos T, Flaxman AD, Danaei G, Shibuya K, Adair-Rohani H, Amann M, Anderson HR, Andrews KG, Aryee M, Atkinson C, Bacchus LJ, Bahalim AN, Balakrishnan K, Balmes J, Barker-Collo S, Baxter A, Bell ML, Blore JD, Blyth F, Bonner C, Borges G, Bourne R, Boussinesq M, Brauer M, Brooks P, Bruce NG, Brunekreef B, Bryan-Hancock C, Bucello C, Buchbinder R, Bull F, Burnett RT, Byers TE, Calabria B, Carapetis J, Carnahan E, Chafe Z, Charlson F, Chen H, Chen JS, Cheng AT, Child JC, Cohen A, Colson KE, Cowie BC, Darby S, Darling S, Davis A, Degenhardt L, Dentener F, Des Jarlais DC, Devries K, Dherani M, Ding EL, Dorsey ER, Driscoll T, Edmond K, Ali SE, Engell RE, Erwin PJ, Fahimi S, Falder G, Farzadfar F, Ferrari A, Finucane MM, Flaxman S, Fowkes FG, Freedman G, Freeman MK, Gakidou E, Ghosh S, Giovannucci E, Gmel G, Graham K, Grainger R, Grant B, Gunnell D, Gutierrez HR, Hall W, Hoek HW, Hogan A, Hosgood HD, Hoy D, Hu H, Hubbell BJ, Hutchings SJ, Ibeanusi SE, Jacklyn GL, Jasrasaria R, Jonas JB, Kan H, Kanis JA, Kassebaum N, Kawakami N, Khang YH, Khatibzadeh S, Khoo JP, Kok C, Laden F, Lalloo R, Lan Q, Lathlean T, Leasher JL, Leigh J, Li Y, Lin JK, Lipshultz SE, London S, Lozano R, Lu Y, Mak J, Malekzadeh R, Mallinger L, Marcenes W, March L, Marks R, Martin R, McGale P, McGrath J, Mehta S, Mensah GA, Merriman TR, Micha R, Michaud C, Mishra V, Mohd Hanafiah K, Mokdad AA, Morawska L, Mozaffarian D, Murphy T, Naghavi M, Neal B, Nelson PK, Nolla JM, Norman R, Olives C, Omer SB, Orchard J, Osborne R, Ostro B, Page A, Pandey KD, Parry CD, Passmore E, Patra J, Pearce N, Pelizzari PM, Petzold M, Phillips MR, Pope D, Pope CA, Powles J, Rao M, Razavi H, Rehfuess EA, Rehm JT, Ritz B, Rivara FP, Roberts T, Robinson C, Rodriguez-Portales JA, Romieu I, Room R, Rosenfeld LC, Roy A, Rushton L, Salomon JA, Sampson U, Sanchez-Riera L, Sanman E, Sapkota A, Seedat S, Shi P, Shield K, Shivakoti R, Singh GM, Sleet DA, Smith E, Smith KR, Stapelberg NJ, Steenland K, Stöckl H, Stovner LJ, Straif K, Straney L, Thurston GD, Tran JH, Van Dingenen R, van Donkelaar A, Veerman JL, Vijayakumar L, Weintraub R, Weissman MM, White RA, Whiteford H, Wiersma ST, Wilkinson JD, Williams HC, Williams W, Wilson N, Woolf AD, Yip P, Zielinski JM, Lopez AD, Murray CJ, Ezzati M, AlMazroa MA, Memish ZA. A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012 Dec 15; 380(9859):2224-60. PMID: 23245609.
    Citations: 1933     Fields:    Translation:Humans
  48. Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci. 2012 Oct; 15(10):1371-3. PMID: 22983211.
    Citations: 67     Fields:    Translation:AnimalsCells
  49. Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, Murakami P, Lessard A, Yolken RH, Feinberg AP, Potash JB. Genome-wide DNA methylation scan in major depressive disorder. PLoS One. 2012; 7(4):e34451. PMID: 22511943.
    Citations: 40     Fields:    Translation:HumansCells
  50. Fischer Walker CL, Perin J, Aryee MJ, Boschi-Pinto C, Black RE. Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review. BMC Public Health. 2012 Mar 21; 12:220. PMID: 22436130.
    Citations: 115     Fields:    Translation:Humans
  51. Easwaran H, Johnstone SE, Van Neste L, Ohm J, Mosbruger T, Wang Q, Aryee MJ, Joyce P, Ahuja N, Weisenberger D, Collisson E, Zhu J, Yegnasubramanian S, Matsui W, Baylin SB. A DNA hypermethylation module for the stem/progenitor cell signature of cancer. Genome Res. 2012 May; 22(5):837-49. PMID: 22391556.
    Citations: 92     Fields:    Translation:HumansCells
  52. Mathias DK, Plieskatt JL, Armistead JS, Bethony JM, Abdul-Majid KB, McMillan A, Angov E, Aryee MJ, Zhan B, Gillespie P, Keegan B, Jariwala AR, Rezende W, Bottazzi ME, Scorpio DG, Hotez PJ, Dinglasan RR. Expression, immunogenicity, histopathology, and potency of a mosquito-based malaria transmission-blocking recombinant vaccine. Infect Immun. 2012 Apr; 80(4):1606-14. PMID: 22311924.
    Citations: 14     Fields:    Translation:HumansAnimals
  53. Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD. DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. Int J Epidemiol. 2012 Feb; 41(1):188-99. PMID: 22422452.
    Citations: 25     Fields:    Translation:HumansCells
  54. Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C. nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinformatics. 2012 Mar 01; 28(5):726-8. PMID: 22247278.
    Citations: 4     Fields:    Translation:Humans
  55. Walker CL, Aryee MJ, Boschi-Pinto C, Black RE. Estimating diarrhea mortality among young children in low and middle income countries. PLoS One. 2012; 7(1):e29151. PMID: 22235266.
    Citations: 33     Fields:    Translation:Humans
  56. 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 Nov 27; 29(12):1117-9. PMID: 22119740.
    Citations: 198     Fields:    Translation:HumansCells
  57. Lee RS, Tamashiro KL, Aryee MJ, Murakami P, Seifuddin F, Herb B, Huo Y, Rongione M, Feinberg AP, Moran TH, Potash JB. Adaptation of the CHARM DNA methylation platform for the rat genome reveals novel brain region-specific differences. Epigenetics. 2011 Nov; 6(11):1378-90. PMID: 22048247.
    Citations: 11     Fields:    Translation:AnimalsCells
  58. Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, Nelson WG. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. BMC Genomics. 2011 Jun 13; 12:313. PMID: 21669002.
    Citations: 22     Fields:    Translation:HumansCells
  59. Koh CM, Gurel B, Sutcliffe S, Aryee MJ, Schultz D, Iwata T, Uemura M, Zeller KI, Anele U, Zheng Q, Hicks JL, Nelson WG, Dang CV, Yegnasubramanian S, De Marzo AM. Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene. Am J Pathol. 2011 Apr; 178(4):1824-34. PMID: 21435462.
    Citations: 32     Fields:    Translation:HumansAnimalsCells
  60. Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, Lanahan AA, Taylor JM, Holmes C, Hahn WC, Zhao JJ, Iglehart JD, Quackenbush J. Therapeutic implications of GIPC1 silencing in cancer. PLoS One. 2010 Dec 30; 5(12):e15581. PMID: 21209904.
    Citations: 12     Fields:    Translation:HumansCells
  61. Wu Z, Aryee MJ. Subset quantile normalization using negative control features. J Comput Biol. 2010 Oct; 17(10):1385-95. PMID: 20976876.
    Citations: 19     Fields:    Translation:Humans
  62. 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 Apr; 12(2):197-210. PMID: 20858772.
    Citations: 41     Fields:    Translation:HumansCells
  63. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic memory in induced pluripotent stem cells. Nature. 2010 Sep 16; 467(7313):285-90. PMID: 20644535.
    Citations: 760     Fields:    Translation:AnimalsCells
  64. Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, Eiriksdottir G, Harris TB, Launer L, Gudnason V, Fallin MD. Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med. 2010 Sep 15; 2(49):49ra67. PMID: 20844285.
    Citations: 123     Fields:    Translation:HumansCells
  65. 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 Sep 16; 467(7313):338-42. PMID: 20720541.
    Citations: 246     Fields:    Translation:AnimalsCells
  66. 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 Aug; 42(8):668-75. PMID: 20601956.
    Citations: 171     Fields:    Translation:HumansCells
  67. Ladd-Acosta C, Aryee MJ, Ordway JM, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Curr Protoc Hum Genet. 2010 Apr; Chapter 20:Unit 20.1.1-19. PMID: 20373514.
    Citations: 17     Fields:    Translation:Cells
  68. Aryee MJ, Gutiérrez-Pabello JA, Kramnik I, Maiti T, Quackenbush J. An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinformatics. 2009 Dec 10; 10:409. PMID: 20003283.
    Citations: 42     Fields:    
  69. 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 Dec; 41(12):1350-3. PMID: 19881528.
    Citations: 456     Fields:    Translation:HumansCells
  70. Aryee MJ, Quackenbush J. An optimized predictive strategy for interactome mapping. J Proteome Res. 2008 Sep; 7(9):4089-94. PMID: 18642945.
    Citations: 1     Fields:    Translation:Cells
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.