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profileAlexander Meissner, Ph.D., Ph.D.

TitleProfessor of Stem Cell and Regenerative Biology
InstitutionFaculty of Arts & Sciences
DepartmentStem Cell and Regenerative Biology
AddressMeissner Lab
Bauer Laboratory, Room 208
7 Divinity Ave
Cambridge MA 02138
Phone617/495-8801
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Collapse Research 
Collapse research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
DP3DK111898     (MEISSNER, ALEXANDER)Sep 30, 2016 - Jun 30, 2021
NIH/NIDDK
Deciphering the molecular basis of T1D in human cells using functional genomics
Role: Co-Principal Investigator

R01HD078679     (MCCARREY, JOHN R)Sep 1, 2014 - May 31, 2019
NIH/NICHD
Epimutations in Offspring Produced by Assisted Reproductive Technologies (ART)
Role: Co-Principal Investigator

R01DA036898     (MEISSNER, ALEXANDER)Sep 30, 2013 - May 31, 2018
NIH/NIDA
Generation and characterization of tools for target-specific de novo DNA methylat
Role: Principal Investigator

P01GM099117     (MEISSNER, ALEXANDER)Aug 1, 2011 - Mar 31, 2022
NIH/NIGMS
Dissecting the establishment and regulation of human pluripotency
Role: Principal Investigator

RC1AA019317     (FEIG, LARRY)Sep 30, 2009 - Aug 31, 2011
NIH/NIAAA
Epigenetics behind long-term and transgenerational effects of adolescent behavior
Role: Co-Principal Investigator

Collapse Bibliographic 
Collapse selected publications
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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  1. 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 MH, 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. Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease. Cell Stem Cell. 2017 Apr 06; 20(4):547-557.e7. PMID: 28388431.
    View in: PubMed
  2. Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell. 2017 May 04; 20(5):706-719.e7. PMID: 28366588.
    View in: PubMed
  3. Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2017 Feb 23; 168(5):944-945. PMID: 28235203.
    View in: PubMed
  4. Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep. 2016 Dec 20; 17(12):3395-3406. PMID: 28009305.
    View in: PubMed
  5. Ziller MJ, Stamenova EK, Gu H, Gnirke A, Meissner A. Targeted bisulfite sequencing of the dynamic DNA methylome. Epigenetics Chromatin. 2016; 9:55. PMID: 27980681.
    View in: PubMed
  6. Yu VW, Yusuf RZ, Oki T, Wu J, Saez B, Wang X, Cook C, Baryawno N, Ziller MJ, Lee E, Gu H, Meissner A, Lin CP, Kharchenko PV, Scadden DT. Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells. Cell. 2016 11 17; 167(5):1310-1322.e17. PMID: 27863245.
    View in: PubMed
  7. Kottakis F, Nicolay BN, Roumane A, Karnik R, Gu H, Nagle JM, Boukhali M, Hayward MC, Li YY, Chen T, Liesa M, Hammerman PS, Wong KK, Hayes DN, Shirihai OS, Dyson NJ, Haas W, Meissner A, Bardeesy N. LKB1 loss links serine metabolism to DNA methylation and tumorigenesis. Nature. 2016 11 17; 539(7629):390-395. PMID: 27799657.
    View in: PubMed
  8. Aguilar CA, Pop R, Shcherbina A, Watts A, Matheny RW, Cacchiarelli D, Han WM, Shin E, Nakhai SA, Jang YC, Carrigan CT, Gifford CA, Kottke MA, Cesana M, Lee J, Urso ML, Meissner A. Transcriptional and Chromatin Dynamics of Muscle Regeneration after Severe Trauma. Stem Cell Reports. 2016 Nov 08; 7(5):983-997. PMID: 27773702.
    View in: PubMed
  9. Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Information recovery from low coverage whole-genome bisulfite sequencing. Nat Commun. 2016 Jun 27; 7:11306. PMID: 27346250; PMCID: PMC4931220.
  10. Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Saturation analysis for whole-genome bisulfite sequencing data. Nat Biotechnol. 2016 Jun 27. PMID: 27347755.
    View in: PubMed
  11. Smith ZD, Sindhu C, Meissner A. Molecular features of cellular reprogramming and development. Nat Rev Mol Cell Biol. 2016 Mar; 17(3):139-54. PMID: 26883001.
    View in: PubMed
  12. Shea JM, Serra RW, Carone BR, Shulha HP, Kucukural A, Ziller MJ, Vallaster MP, Gu H, Tapper AR, Gardner PD, Meissner A, Garber M, Rando OJ. Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome. Dev Cell. 2015 Dec 21; 35(6):750-8. PMID: 26702833; PMCID: PMC4691283 [Available on 12/21/16].
  13. 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. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 2015 Nov; 33(11):1173-81. PMID: 26501951; PMCID: PMC4847940.
  14. Tsankov AM, Akopian V, Pop R, Chetty S, Gifford CA, Daheron L, Tsankova NM, Meissner A. A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells. Nat Biotechnol. 2015 Nov; 33(11):1182-92. PMID: 26501952; PMCID: PMC4636964.
  15. Aguilar CA, Shcherbina A, Ricke DO, Pop R, Carrigan CT, Gifford CA, Urso ML, Kottke MA, Meissner A. In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing. Sci Rep. 2015 Sep 18; 5:13885. PMID: 26381351; PMCID: PMC4585378.
  16. Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep. 2015 Sep 01; 12(9):1456-70. PMID: 26299972.
    View in: PubMed
  17. 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. Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells. Nat Methods. 2015 Sep; 12(9):885-92. PMID: 26237226.
    View in: PubMed
  18. Li W, Cavelti-Weder C, Zhang Y, Clement K, Donovan S, Gonzalez G, Zhu J, Stemann M, Xu K, Hashimoto T, Yamada T, Nakanishi M, Zhang Y, Zeng S, Gifford D, Meissner A, Weir G, Zhou Q. Corrigendum: Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells. Nat Biotechnol. 2015 Aug; 33(8):882. PMID: 26252147.
    View in: PubMed
  19. Galonska C, Ziller MJ, Karnik R, Meissner A. Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming. Cell Stem Cell. 2015 Oct 01; 17(4):462-70. PMID: 26235340; PMCID: PMC4592414 [Available on 10/01/16].
  20. Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 2015 Jul 16; 162(2):412-24. PMID: 26186193; PMCID: PMC4511597.
  21. Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Müller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT. Corrigendum: DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun. 2015 Jul 07; 6:7740. PMID: 26151124.
    View in: PubMed
  22. Yang J, Yu L, Gaiteri C, Srivastava GP, Chibnik LB, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA. Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies. Int J Biochem Cell Biol. 2015 Oct; 67:58-64. PMID: 26003740; PMCID: PMC4564337 [Available on 10/01/16].
  23. 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. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015 May; 47(5):469-78. PMID: 25822089; PMCID: PMC4414868.
  24. Edri R, Yaffe Y, Ziller MJ, Mutukula N, Volkman R, David E, Jacob-Hirsch J, Malcov H, Levy C, Rechavi G, Gat-Viks I, Meissner A, Elkabetz Y. Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors. Nat Commun. 2015 Mar 23; 6:6500. PMID: 25799239; PMCID: PMC4383005.
  25. Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A. Transcription factor binding dynamics during human ES cell differentiation. Nature. 2015 Feb 19; 518(7539):344-9. PMID: 25693565; PMCID: PMC4499331.
  26. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
  27. French A, Bravery C, Smith J, Chandra A, Archibald P, Gold JD, Artzi N, Kim HW, Barker RW, Meissner A, Wu JC, Knowles JC, Williams D, García-Cardeña G, Sipp D, Oh S, Loring JF, Rao MS, Reeve B, Wall I, Carr AJ, Bure K, Stacey G, Karp JM, Snyder EY, Brindley DA. Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards. Stem Cells Transl Med. 2015 Mar; 4(3):217-23. PMID: 25650438; PMCID: PMC4339854.
  28. Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, Moses HL, Barcellos-Hoff MH, Jackson-Grusby L, Meissner A, Polyak K. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports. 2015 Feb 10; 4(2):297-311. PMID: 25619437; PMCID: PMC4325231.
  29. Pour M, Pilzer I, Rosner R, Smith ZD, Meissner A, Nachman I. Epigenetic predisposition to reprogramming fates in somatic cells. EMBO Rep. 2015 Mar; 16(3):370-8. PMID: 25600117; PMCID: PMC4364876.
  30. Meissner A. (Epi)genomics approaches and their applications. Methods. 2015 Jan 15; 72:1-2. PMID: 25597875.
    View in: PubMed
  31. Yu L, Chibnik LB, Srivastava GP, Pochet N, Yang J, Xu J, Kozubek J, Obholzer N, Leurgans SE, Schneider JA, Meissner A, De Jager PL, Bennett DA. Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease. JAMA Neurol. 2015 Jan; 72(1):15-24. PMID: 25365775; PMCID: PMC4344367.
  32. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-9. PMID: 25533951; PMCID: PMC4336237.
  33. Pasque V, Tchieu J, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, Papp B, Bonora G, Patel S, Ho R, Schmidt R, McKee R, Sado T, Tada T, Meissner A, Plath K. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell. 2014 Dec 18; 159(7):1681-97. PMID: 25525883; PMCID: PMC4282187 [Available on 12/18/15].
  34. Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell. 2014 Dec 08; 26(6):813-25. PMID: 25490447; PMCID: PMC4302418 [Available on 12/08/15].
  35. 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. A comparison of non-integrating reprogramming methods. Nat Biotechnol. 2015 Jan; 33(1):58-63. PMID: 25437882; PMCID: PMC4329913.
  36. Tobi EW, Goeman JJ, Monajemi R, Gu H, Putter H, Zhang Y, Slieker RC, Stok AP, Thijssen PE, Müller F, van Zwet EW, Bock C, Meissner A, Lumey LH, Eline Slagboom P, Heijmans BT. DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun. 2014 Nov 26; 5:5592. PMID: 25424739; PMCID: PMC4246417.
  37. Li W, Cavelti-Weder C, Zhang Y, Zhang Y, Clement K, Donovan S, Gonzalez G, Zhu J, Stemann M, Xu K, Hashimoto T, Yamada T, Nakanishi M, Zhang Y, Zeng S, Gifford D, Meissner A, Weir G, Zhou Q. Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells. Nat Biotechnol. 2014 Dec; 32(12):1223-30. PMID: 25402613.
    View in: PubMed
  38. Ichida JK, W JT, Williams LA, Carter AC, Shi Y, Moura MT, Ziller M, Singh S, Amabile G, Bock C, Umezawa A, Rubin LL, Bradner JE, Akutsu H, Meissner A, Eggan K. Erratum: Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Nov 13; 10(12):1074. PMID: 25393494.
    View in: PubMed
  39. Ichida JK, W JT, Williams LA, Carter AC, Shi Y, Moura MT, Ziller M, Singh S, Amabile G, Bock C, Umezawa A, Rubin LL, Bradner JE, Akutsu H, Meissner A, Eggan K. Erratum: Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Nov 13; 10(12):1074. PMID: 25393496.
    View in: PubMed
  40. 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; PMCID: PMC4344394.
  41. De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014 Sep; 17(9):1156-63. PMID: 25129075; PMCID: PMC4292795.
  42. Smith ZD, Chan MM, Humm KC, Karnik R, Mekhoubad S, Regev A, Eggan K, Meissner A. DNA methylation dynamics of the human preimplantation embryo. Nature. 2014 Jul 31; 511(7511):611-5. PMID: 25079558; PMCID: PMC4178976.
  43. Ichida JK, TCW J, T C W J, Williams LA, Carter AC, Shi Y, Moura MT, Ziller M, Singh S, Amabile G, Bock C, Umezawa A, Rubin LL, Bradner JE, Akutsu H, Meissner A, Eggan K. Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol. 2014 Aug; 10(8):632-9. PMID: 24952596; PMCID: PMC4310751.
  44. Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Göttgens B, Darlington GJ, Li W, Goodell MA. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell. 2014 May 01; 14(5):673-88. PMID: 24792119; PMCID: PMC4070311.
  45. Galonska C, Smith ZD, Meissner A. In Vivo and in vitro dynamics of undifferentiated embryonic cell transcription factor 1. Stem Cell Reports. 2014 Mar 11; 2(3):245-52. PMID: 24672748; PMCID: PMC3964277.
  46. Kats LM, Reschke M, Taulli R, Pozdnyakova O, Burgess K, Bhargava P, Straley K, Karnik R, Meissner A, Small D, Su SM, Yen K, Zhang J, Pandolfi PP. Proto-oncogenic role of mutant IDH2 in leukemia initiation and maintenance. Cell Stem Cell. 2014 Mar 06; 14(3):329-41. PMID: 24440599; PMCID: PMC4380188.
  47. Federation AJ, Bradner JE, Meissner A. The use of small molecules in somatic-cell reprogramming. Trends Cell Biol. 2014 Mar; 24(3):179-87. PMID: 24183602; PMCID: PMC3943685.
  48. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. PMID: 24076989.
    View in: PubMed
  49. Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013 Aug 22; 500(7463):477-81. PMID: 23925113; PMCID: PMC3821869.
  50. Karnik R, Meissner A. Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Cell Stem Cell. 2013 Jul 03; 13(1):14-21. PMID: 23827707; PMCID: PMC3750740.
  51. Kearns NA, Genga RM, Ziller M, Kapinas K, Peters H, Brehm MA, Meissner A, Maehr R. Generation of organized anterior foregut epithelia from pluripotent stem cells using small molecules. Stem Cell Res. 2013 Nov; 11(3):1003-12. PMID: 23917481.
    View in: PubMed
  52. Zhang RR, Cui QY, Murai K, Lim YC, Smith ZD, Jin S, Ye P, Rosa L, Lee YK, Wu HP, Liu W, Xu ZM, Yang L, Ding YQ, Tang F, Meissner A, Ding C, Shi Y, Xu GL. Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell. 2013 Aug 01; 13(2):237-45. PMID: 23770080; PMCID: PMC4474382.
  53. Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N. Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. Stem Cell Reports. 2013; 1(1):79-89. PMID: 24052944; PMCID: PMC3757747.
  54. 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. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763; PMCID: PMC3709577.
  55. Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell. 2013 Apr 04; 12(4):413-25. PMID: 23415915.
    View in: PubMed
  56. Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013 Mar; 14(3):204-20. PMID: 23400093.
    View in: PubMed
  57. Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31; 152(3):642-54. PMID: 23333102; PMCID: PMC3563935.
  58. Ogino S, Lochhead P, Chan AT, Nishihara R, Cho E, Wolpin BM, Meyerhardt JA, Meissner A, Schernhammer ES, Fuchs CS, Giovannucci E. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease. Mod Pathol. 2013 Apr; 26(4):465-84. PMID: 23307060; PMCID: PMC3637979.
  59. Smith ZD, Meissner A. The simplest explanation: passive DNA demethylation in PGCs. EMBO J. 2013 Feb 06; 32(3):318-21. PMID: 23299938; PMCID: PMC3567498.
  60. Meissner A. What can epigenomics do for you? Genome Biol. 2012 Oct 23; 13(10):420. PMID: 23095436; PMCID: PMC3491409.
  61. Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 2012 Oct 03; 13(10):R92. PMID: 23034176; PMCID: PMC3491420.
  62. Sindhu C, Samavarchi-Tehrani P, Meissner A. Transcription factor-mediated epigenetic reprogramming. J Biol Chem. 2012 Sep 07; 287(37):30922-31. PMID: 22952239; PMCID: PMC3438925.
  63. Gifford CA, Meissner A. Epigenetic obstacles encountered by transcription factors: reprogramming against all odds. Curr Opin Genet Dev. 2012 Oct; 22(5):409-15. PMID: 22922161; PMCID: PMC3490009.
  64. Chan MM, Smith ZD, Egli D, Regev A, Meissner A. Mouse ooplasm confers context-specific reprogramming capacity. Nat Genet. 2012 Sep; 44(9):978-80. PMID: 22902786; PMCID: PMC3432711.
  65. Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell. 2012 Aug 24; 47(4):633-47. PMID: 22841485; PMCID: PMC3428428.
  66. Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, Jenuwein T, Xu G, Leonhardt H, Wolf V, Walter J. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 2012 Jun; 8(6):e1002750. PMID: 22761581; PMCID: PMC3386304.
  67. Mekhoubad S, Bock C, de Boer AS, Kiskinis E, Meissner A, Eggan K. Erosion of dosage compensation impacts human iPSC disease modeling. Cell Stem Cell. 2012 May 04; 10(5):595-609. PMID: 22560080; PMCID: PMC3603710.
  68. Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012 Jun; 22(6):1128-38. PMID: 22466170; PMCID: PMC3371717.
  69. Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012 Mar 28; 484(7394):339-44. PMID: 22456710; PMCID: PMC3331945.
  70. Akopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics. Genome Biol. 2012 Feb 24; 13(2):313. PMID: 22364154; PMCID: PMC3334565.
  71. Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011 Dec; 7(12):e1002389. PMID: 22174693; PMCID: PMC3234221.
  72. Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W. RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics. 2012 Feb 01; 28(3):430-2. PMID: 22155871; PMCID: PMC3268241.
  73. Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2011 Dec 04; 44(1):23-31. PMID: 22138693; PMCID: PMC3637952.
  74. Shearstone JR, Pop R, Bock C, Boyle P, Meissner A, Socolovsky M. Global DNA demethylation during mouse erythropoiesis in vivo. Science. 2011 Nov 11; 334(6057):799-802. PMID: 22076376; PMCID: PMC3230325.
  75. Xu H, Yi BA, Wu H, Bock C, Gu H, Lui KO, Park JH, Shao Y, Riley AK, Domian IJ, Hu E, Willette R, Lepore J, Meissner A, Wang Z, Chien KR. Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature. Cell Res. 2012 Jan; 22(1):142-54. PMID: 22064699; PMCID: PMC3351933.
  76. Meissner A. Guiding DNA methylation. Cell Stem Cell. 2011 Nov 04; 9(5):388-90. PMID: 22056134.
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  77. Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 02; 9(3):272-81. PMID: 21885022; PMCID: PMC3167236.
  78. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011 Aug 28; 477(7364):295-300. PMID: 21874018; PMCID: PMC3175327.
  79. Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011 Jun 10; 145(6):875-89. PMID: 21663792.
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  80. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011 Apr; 6(4):468-81. PMID: 21412275.
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  81. Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell. 2011 Feb 04; 144(3):439-52. PMID: 21295703; PMCID: PMC3063454.
  82. Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 2011 Jan 07; 8(1):96-105. PMID: 21211784; PMCID: PMC3220622.
  83. Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010 Dec 23; 143(7):1084-96. PMID: 21183072; PMCID: PMC3039484.
  84. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. PMID: 20944595; PMCID: PMC3607281.
  85. Meissner A. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol. 2010 Oct; 28(10):1079-88. PMID: 20944600.
    View in: PubMed
  86. Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010 Nov 05; 7(5):618-30. PMID: 20888316; PMCID: PMC3656821.
  87. Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010 Oct; 28(10):1106-14. PMID: 20852634; PMCID: PMC3066564.
  88. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
  89. Artyomov MN, Meissner A, Chakraborty AK. A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency. PLoS Comput Biol. 2010 May 13; 6(5):e1000785. PMID: 20485562; PMCID: PMC2869311.
  90. Smith ZD, Nachman I, Regev A, Meissner A. Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nat Biotechnol. 2010 May; 28(5):521-6. PMID: 20436460; PMCID: PMC2908494.
  91. Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010 Feb; 7(2):133-6. PMID: 20062050; PMCID: PMC2860480.
  92. Tomazou EM, Meissner A. Epigenetic regulation of pluripotency. Adv Exp Med Biol. 2010; 695:26-40. PMID: 21222197.
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  93. Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 09; 326(5950):257-63. PMID: 19729616; PMCID: PMC2879337.
  94. Meissner A. Alexander Meissner: learning the reprogramming code. J Cell Biol. 2009 Aug 24; 186(4):450-1. PMID: 19704017; PMCID: PMC2733751.
  95. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes. Methods. 2009 Jul; 48(3):226-32. PMID: 19442738; PMCID: PMC2864123.
  96. Han DW, Do JT, Araúzo-Bravo MJ, Lee SH, Meissner A, Lee HT, Jaenisch R, Schöler HR. Epigenetic hierarchy governing Nestin expression. Stem Cells. 2009 May; 27(5):1088-97. PMID: 19415779.
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  97. Amabile G, Meissner A. Induced pluripotent stem cells: current progress and potential for regenerative medicine. Trends Mol Med. 2009 Feb; 15(2):59-68. PMID: 19162546.
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  98. Meissner A, Eminli S, Jaenisch R. Derivation and manipulation of murine embryonic stem cells. Methods Mol Biol. 2009; 482:3-19. PMID: 19089346.
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  99. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 07; 454(7205):766-70. PMID: 18600261; PMCID: PMC2896277.
  100. Markoulaki S, Meissner A, Jaenisch R. Somatic cell nuclear transfer and derivation of embryonic stem cells in the mouse. Methods. 2008 Jun; 45(2):101-14. PMID: 18593608.
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  101. Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008 Jul 03; 454(7200):49-55. PMID: 18509334; PMCID: PMC2754827.
  102. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell. 2008 Feb 07; 2(2):160-9. PMID: 18371437; PMCID: PMC3070208.
  103. Wernig M, Meissner A, Cassady JP, Jaenisch R. c-Myc is dispensable for direct reprogramming of mouse fibroblasts. Cell Stem Cell. 2008 Jan 10; 2(1):10-2. PMID: 18371415.
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  104. Hanna J, Wernig M, Markoulaki S, Sun CW, Meissner A, Cassady JP, Beard C, Brambrink T, Wu LC, Townes TM, Jaenisch R. Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science. 2007 Dec 21; 318(5858):1920-3. PMID: 18063756.
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  105. Linhart HG, Lin H, Yamada Y, Moran E, Steine EJ, Gokhale S, Lo G, Cantu E, Ehrich M, He T, Meissner A, Jaenisch R. Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev. 2007 Dec 01; 21(23):3110-22. PMID: 18056424; PMCID: PMC2081977.
  106. Meissner A, Wernig M, Jaenisch R. Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. Nat Biotechnol. 2007 Oct; 25(10):1177-81. PMID: 17724450.
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  107. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 02; 448(7153):553-60. PMID: 17603471; PMCID: PMC2921165.
  108. Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007 Jul 19; 448(7151):318-24. PMID: 17554336.
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  109. Shaw AT, Meissner A, Dowdle JA, Crowley D, Magendantz M, Ouyang C, Parisi T, Rajagopal J, Blank LJ, Bronson RT, Stone JR, Tuveson DA, Jaenisch R, Jacks T. Sprouty-2 regulates oncogenic K-ras in lung development and tumorigenesis. Genes Dev. 2007 Mar 15; 21(6):694-707. PMID: 17369402; PMCID: PMC1820943.
  110. Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 2007 Feb 23; 128(4):669-81. PMID: 17320505.
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  111. Meissner A, Jaenisch R. Mammalian nuclear transfer. Dev Dyn. 2006 Sep; 235(9):2460-9. PMID: 16881069.
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  112. Blelloch R, Wang Z, Meissner A, Pollard S, Smith A, Jaenisch R. Reprogramming efficiency following somatic cell nuclear transfer is influenced by the differentiation and methylation state of the donor nucleus. Stem Cells. 2006 Sep; 24(9):2007-13. PMID: 16709876; PMCID: PMC3000431.
  113. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21; 125(2):315-26. PMID: 16630819.
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  114. Lin H, Yamada Y, Nguyen S, Linhart H, Jackson-Grusby L, Meissner A, Meletis K, Lo G, Jaenisch R. Suppression of intestinal neoplasia by deletion of Dnmt3b. Mol Cell Biol. 2006 Apr; 26(8):2976-83. PMID: 16581773; PMCID: PMC1446955.
  115. Meissner A, Jaenisch R. Generation of nuclear transfer-derived pluripotent ES cells from cloned Cdx2-deficient blastocysts. Nature. 2006 Jan 12; 439(7073):212-5. PMID: 16227971.
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  116. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18):5868-77. PMID: 16224102; PMCID: PMC1258174.
  117. Yamada Y, Jackson-Grusby L, Linhart H, Meissner A, Eden A, Lin H, Jaenisch R. Opposing effects of DNA hypomethylation on intestinal and liver carcinogenesis. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13580-5. PMID: 16174748; PMCID: PMC1224663.
  118. Ventura A, Meissner A, Dillon CP, McManus M, Sharp PA, Van Parijs L, Jaenisch R, Jacks T. Cre-lox-regulated conditional RNA interference from transgenes. Proc Natl Acad Sci U S A. 2004 Jul 13; 101(28):10380-5. PMID: 15240889; PMCID: PMC478580.
  119. Chen WG, Chang Q, Lin Y, Meissner A, West AE, Griffith EC, Jaenisch R, Greenberg ME. Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science. 2003 Oct 31; 302(5646):885-9. PMID: 14593183.
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