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Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets.

Lareau C, Kangeyan D, Aryee MJ.

Methods Mol Biol. 2019;1935:187-202. doi: 10.1007/978-1-4939-9057-3_13.


Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.

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.

Nat Biotechnol. 2019 Feb 11. doi: 10.1038/s41587-018-0011-0. [Epub ahead of print]


Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq.

Lazzarotto CR, Nguyen NT, Tang X, Malagon-Lopez J, Guo JA, Aryee MJ, Joung JK, Tsai SQ.

Nat Protoc. 2018 Nov;13(11):2615-2642. doi: 10.1038/s41596-018-0055-0.


In vivo CRISPR editing with no detectable genome-wide off-target mutations.

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.

Nature. 2018 Sep;561(7723):416-419. doi: 10.1038/s41586-018-0500-9. Epub 2018 Sep 12.


Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.

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.

Nat Commun. 2018 Jul 25;9(1):2905. doi: 10.1038/s41467-018-05328-9.


Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize.

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.

Plant Biotechnol J. 2019 Feb;17(2):362-372. doi: 10.1111/pbi.12982. Epub 2018 Jul 22.


Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ.

Cell. 2018 May 31;173(6):1535-1548.e16. doi: 10.1016/j.cell.2018.03.074. Epub 2018 Apr 26.


Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo".

Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L.

Nat Methods. 2018 Apr;15(4):238-239. doi: 10.1038/nmeth.4541. Epub 2018 Mar 30. No abstract available.


hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data.

Lareau CA, Aryee MJ.

Nat Methods. 2018 Feb 28;15(3):155-156. doi: 10.1038/nmeth.4583. No abstract available.


diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

Lareau CA, Aryee MJ.

Bioinformatics. 2018 Feb 15;34(4):672-674. doi: 10.1093/bioinformatics/btx623.


The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors.

Nordor AV, Nehar-Belaid D, Richon S, Klatzmann D, Bellet D, Dangles-Marie V, Fournier T, Aryee MJ.

Epigenetics. 2017 Sep;12(9):793-803. doi: 10.1080/15592294.2017.1342912. Epub 2017 Nov 24.


CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.

Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK.

Nat Methods. 2017 Jun;14(6):607-614. doi: 10.1038/nmeth.4278. Epub 2017 May 1.


OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma.

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.

Cancer Discov. 2017 Mar;7(3):288-301. doi: 10.1158/2159-8290.CD-16-0844. Epub 2017 Feb 17.


Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer.

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.

JCI Insight. 2017 Feb 9;2(3):e91078. doi: 10.1172/jci.insight.91078.


Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.

Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M.

Mol Cell. 2016 Dec 15;64(6):1088-1101. doi: 10.1016/j.molcel.2016.11.020.


High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis.

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.

Genome Med. 2016 Nov 22;8(1):124.


Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK.

Nat Biotechnol. 2016 Aug;34(8):869-74. doi: 10.1038/nbt.3620. Epub 2016 Jun 27.


Open-source guideseq software for analysis of GUIDE-seq data.

Tsai SQ, Topkar VV, Joung JK, Aryee MJ.

Nat Biotechnol. 2016 May 6;34(5):483. doi: 10.1038/nbt.3534. No abstract available.


Meta-Analysis With a Continuous Covariate That Is Differentially Categorized Across Studies.

Perin J, Fischer Walker CL, Black RE, Aryee MJ.

Am J Epidemiol. 2016 Mar 1;183(5):507-14. doi: 10.1093/aje/kwv140. Epub 2016 Feb 10.


Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ, Joung JK.

Nature. 2015 Jul 23;523(7561):481-5. doi: 10.1038/nature14592. Epub 2015 Jun 22.


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 Jul 15;83:118-27. doi: 10.1016/j.ymeth.2015.04.016. Epub 2015 Apr 23.


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.


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):187-197. doi: 10.1038/nbt.3117. Epub 2014 Dec 16.


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.

Cancer Cell. 2014 Nov 10;26(5):668-681. doi: 10.1016/j.ccell.2014.10.004. Epub 2014 Oct 30.


Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.

Ziller MJ, Hansen KD, Meissner A, Aryee MJ.

Nat Methods. 2015 Mar;12(3):230-2, 1 p following 232. doi: 10.1038/nmeth.3152. Epub 2014 Nov 2.


Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.

Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK.

Nat Biotechnol. 2014 Jun;32(6):569-76. doi: 10.1038/nbt.2908. Epub 2014 Apr 25.


GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease.

Liu Y, Li X, Aryee MJ, Ekström TJ, Padyukov L, Klareskog L, Vandiver A, Moore AZ, Tanaka T, Ferrucci L, Fallin MD, Feinberg AP.

Am J Hum Genet. 2014 Apr 3;94(4):485-95. doi: 10.1016/j.ajhg.2014.02.011. Epub 2014 Mar 20.


Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.


Identification of direction in gene networks from expression and methylation.

Simcha DM, Younes L, Aryee MJ, Geman D.

BMC Syst Biol. 2013 Nov 1;7:118. doi: 10.1186/1752-0509-7-118.


Global causes of diarrheal disease mortality in children <5 years of age: a systematic review.

Lanata CF, Fischer-Walker CL, Olascoaga AC, Torres CX, Aryee MJ, Black RE; Child Health Epidemiology Reference Group of the World Health Organization and UNICEF.

PLoS One. 2013 Sep 4;8(9):e72788. doi: 10.1371/journal.pone.0072788. eCollection 2013. Review.


A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression.

Guintivano J, Aryee MJ, Kaminsky ZA.

Epigenetics. 2013 Mar;8(3):290-302. doi: 10.4161/epi.23924. Epub 2013 Feb 20.


DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.

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.

Sci Transl Med. 2013 Jan 23;5(169):169ra10. doi: 10.1126/scitranslmed.3005211.


Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.

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.

Nat Biotechnol. 2013 Feb;31(2):142-7. doi: 10.1038/nbt.2487. Epub 2013 Jan 20.


Reversible switching between epigenetic states in honeybee behavioral subcastes.

Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP.

Nat Neurosci. 2012 Oct;15(10):1371-3. doi: 10.1038/nn.3218. Epub 2012 Sep 16.


Genome-wide DNA methylation scan in major depressive disorder.

Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, Murakami P, Lessard A, Yolken RH, Feinberg AP, Potash JB; GenRED Consortium.

PLoS One. 2012;7(4):e34451. doi: 10.1371/journal.pone.0034451. Epub 2012 Apr 12.


Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review.

Fischer Walker CL, Perin J, Aryee MJ, Boschi-Pinto C, Black RE.

BMC Public Health. 2012 Mar 21;12:220. doi: 10.1186/1471-2458-12-220. Review.


DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.

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.

Int J Epidemiol. 2012 Feb;41(1):188-99. doi: 10.1093/ije/dyr237.


A DNA hypermethylation module for the stem/progenitor cell signature of cancer.

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.

Genome Res. 2012 May;22(5):837-49. doi: 10.1101/gr.131169.111. Epub 2012 Mar 5.


Expression, immunogenicity, histopathology, and potency of a mosquito-based malaria transmission-blocking recombinant vaccine.

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.

Infect Immun. 2012 Apr;80(4):1606-14. doi: 10.1128/IAI.06212-11. Epub 2012 Feb 6.


nEASE: a method for gene ontology subclassification of high-throughput gene expression data.

Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C.

Bioinformatics. 2012 Mar 1;28(5):726-8. doi: 10.1093/bioinformatics/bts011. Epub 2012 Jan 13.


Estimating diarrhea mortality among young children in low and middle income countries.

Walker CL, Aryee MJ, Boschi-Pinto C, Black RE.

PLoS One. 2012;7(1):e29151. doi: 10.1371/journal.pone.0029151. Epub 2012 Jan 3.


Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells.

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.

Nat Biotechnol. 2011 Nov 27;29(12):1117-9. doi: 10.1038/nbt.2052. Erratum in: Nat Biotechnol. 2012 Jan;30(1):112.


Adaptation of the CHARM DNA methylation platform for the rat genome reveals novel brain region-specific differences.

Lee RS, Tamashiro KL, Aryee MJ, Murakami P, Seifuddin F, Herb B, Huo Y, Rongione M, Feinberg AP, Moran TH, Potash JB.

Epigenetics. 2011 Nov;6(11):1378-90. doi: 10.4161/epi.6.11.18072. Epub 2011 Nov 1.


Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences.

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.

BMC Genomics. 2011 Jun 13;12:313. doi: 10.1186/1471-2164-12-313.


Alterations in nucleolar structure and gene expression programs in prostatic neoplasia are driven by the MYC oncogene.

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.

Am J Pathol. 2011 Apr;178(4):1824-34. doi: 10.1016/j.ajpath.2010.12.040.


Subset quantile normalization using negative control features.

Wu Z, Aryee MJ.

J Comput Biol. 2010 Oct;17(10):1385-95.


Accurate genome-scale percentage DNA methylation estimates from microarray data.

Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, Irizarry RA.

Biostatistics. 2011 Apr;12(2):197-210. doi: 10.1093/biostatistics/kxq055. Epub 2010 Sep 21.


Personalized epigenomic signatures that are stable over time and covary with body mass index.

Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, Eiriksdottir G, Harris TB, Launer L, Gudnason V, Fallin MD.

Sci Transl Med. 2010 Sep 15;2(49):49ra67. doi: 10.1126/scitranslmed.3001262. Erratum in: Sci Transl Med. 2011 Jan 12;3(65):65er1.


Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

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.

Nature. 2010 Sep 16;467(7313):338-42. doi: 10.1038/nature09367. Epub 2010 Aug 15.


Epigenetic memory in induced pluripotent stem cells.

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.

Nature. 2010 Sep 16;467(7313):285-90. doi: 10.1038/nature09342.

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