Selected Publications
Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, Walsh M, Friedel RH, Zaslavsky E, Tsankova NM.
Nat Commun. 2018 10 01; 9(1):4020. PMID: 30275445.

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.
Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J.
Nature. 2018 08; 560(7718):319-324. PMID: 30069044.

Global delay in nascent strand DNA methylation.
Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A.
Nat Struct Mol Biol. 2018 Apr; 25(4):327-332. PMID: 29531288.

Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease.
Warren CR, O'Sullivan JF, Friesen M, Becker CE, Zhang X, Liu P, Wakabayashi Y, Morningstar JE, Shi X, Choi J, Xia F, Peters DT, Florido MHC, Tsankov AM, Duberow E, Comisar L, Shay J, Jiang X, Meissner A, Musunuru K, Kathiresan S, Daheron L, Zhu J, Gerszten RE, Deo RC, Vasan RS, O'Donnell CJ, Cowan CA.
Cell Stem Cell. 2017 04 06; 20(4):547-557.e7. PMID: 28388431.

Transcription factor binding dynamics during human ES cell differentiation.
Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A.
Nature. 2015 Feb 19; 518(7539):344-9. PMID: 25693565; PMCID: PMC4499331.

A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells.

Tsankov AM, Akopian V, Pop R, Chetty S, Gifford CA, Daheron L, Tsankova NM, Meissner A.
Nat Biotechnol. 2015 Nov; 33(11):1182-92. PMID: 26501952; PMCID: PMC4636964.

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.
Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K.
Nat Biotechnol. 2015 Nov; 33(11):1173-81. PMID: 26501951; PMCID: PMC4847940.

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells.
Paull D, Sevilla A, Zhou H, Hahn AK, Kim H, Napolitano C, Tsankov A, Shang L, Krumholz K, Jagadeesan P, Woodard CM, Sun B, Vilboux T, Zimmer M, Forero E, Moroziewicz DN, Martinez H, Malicdan MC, Weiss KA, Vensand LB, Dusenberry CR, Polus H, Sy KT, Kahler DJ, Gahl WA, Solomon SL, Chang S, Meissner A, Eggan K, Noggle SA.
Nat Methods. 2015 Sep; 12(9):885-92. PMID: 26237226.

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.
Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A.
Nat Genet. 2015 May; 47(5):469-78. PMID: 25822089; PMCID: PMC4414868.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.
Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A.
Nature. 2015 Feb 19; 518(7539):355-359. PMID: 25533951; PMCID: PMC4336237.

A comparison of non-integrating reprogramming methods.
Schlaeger TM, Daheron L, Brickler TR, Entwisle S, Chan K, Cianci A, DeVine A, Ettenger A, Fitzgerald K, Godfrey M, Gupta D, McPherson J, Malwadkar P, Gupta M, Bell B, Doi A, Jung N, Li X, Lynes MS, Brookes E, Cherry AB, Demirbas D, Tsankov AM, Zon LI, Rubin LL, Feinberg AP, Meissner A, Cowan CA, Daley GQ.
Nat Biotechnol. 2015 Jan; 33(1):58-63. PMID: 25437882.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A.
Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763; PMCID: PMC3709577.

Toward a unified physical model of nucleosome patterns flanking transcription start sites.
Möbius W, Osberg B, Tsankov AM, Rando OJ, Gerland U.
Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5719-24. PMID: 23509245; PMCID: PMC3619296.

Genome-wide identification and characterization of replication origins by deep sequencing.
Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N.
Genome Biol. 2012 Apr 24; 13(4):R27. PMID: 22531001; PMCID: PMC3446301.

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.
Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ.
Genome Res. 2011 Nov; 21(11):1851-62. PMID: 21914852; PMCID: PMC3205570.

The role of nucleosome positioning in the evolution of gene regulation.
Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ.
PLoS Biol. 2010 Jul 06; 8(7):e1000414. PMID: 20625544; PMCID: PMC2897762.

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