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2015
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.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 E. S., and Mikkelsen TS Cell, 2015/07/16, Volume 162, Issue 2, p.412-24, (2015) Read More / View Supplemental Materials
Abstract
Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies.Yang, J., Yu L., Gaiteri C., Srivastava GP, Chibnik LB, Leurgans SE, Schneider JA, Meissner A., De Jager PL, and Bennett DA The international journal of biochemistry & cell biology, 2015/05/21, (2015) Read More / View Supplemental Materials
Abstract
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., and Meissner A. Nature genetics, 2015/03/30, (2015) Read More / View Supplemental Materials
Abstract
Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors.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., and Elkabetz Y. Nature communications, 2015/03/23, Volume 6, p.6500, (2015) Read More / View Supplemental Materials
Abstract
Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity.Dahlberg, A., Woo S., Delaney C., Boyle P., Gnirke A., Bock C., Bernstein BE, Meissner A., Gottardo R., and Bernstein ID Leukemia, 2015/03/06, (2015) Read More / View Supplemental Materials
Integrative analysis of 111 reference human epigenomes.Roadmap Epigenomics, Consortium, 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, et al. Nature, 2015/02/19, Volume 518, Issue 7539, p.317-30, (2015) Read More / View Supplemental Materials
Abstract
Transcription factor binding dynamics during human ES cell differentiation.Tsankov, AM, Gu H., Akopian V., Ziller MJ, Donaghey J., Amit I., Gnirke A., and Meissner A. Nature, 2015/02/19, Volume 518, Issue 7539, p.344-9, (2015) Read More / View Supplemental Materials
Abstract
Enabling Consistency in Pluripotent Stem Cell-Derived Products for Research and Development and Clinical Applications Through Material Standards.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., et al. Stem cells translational medicine, 2015/02/03, (2015) Read More / View Supplemental Materials
Abstract
Age- and Pregnancy-Associated DNA Methylation Changes in Mammary Epithelial Cells.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., and Polyak K. Stem cell reports, 2015/01/21, (2015) Read More / View Supplemental Materials
Abstract
(Epi)Genomics approaches and their applications.Meissner, A. Methods (San Diego, Calif.), 2015/01/15, Volume 72, p.1-2, (2015) Read More / View Supplemental Materials
2014
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., Cacchiarelli D., Tsankov AM, Epstein C., Rinn JL, Mikkelsen TS, Kohlbacher O., Gnirke A., Bernstein BE, Elkabetz Y., et al. Nature, 2014/12/24, (2014) Read More / View Supplemental Materials
Abstract
X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency.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., and Plath K. Cell, 2014/12/18, Volume 159, Issue 7, p.1681-97, (2014) Read More / View Supplemental Materials
Abstract
Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.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 E. S., Brown JR, et al. Cancer cell, 2014/12/08, Volume 26, Issue 6, p.813-25, (2014) Read More / View Supplemental Materials
Abstract
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., et al. Nature biotechnology, 2014/12/01, (2014) Read More / View Supplemental Materials
Abstract
DNA methylation signatures link prenatal famine exposure to growth and metabolism.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., and Heijmans BT Nature communications, 2014/11/26, Volume 5, p.5592, (2014) Read More / View Supplemental Materials
Abstract
Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells.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., and Zhou Q. Nature biotechnology, 2014/11/17, (2014) Read More / View Supplemental Materials
Abstract
Association of Brain DNA Methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 With Pathological Diagnosis of Alzheimer Disease.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, and Bennett DA JAMA neurology, 2014/11/03, (2014) Read More / View Supplemental Materials
Abstract
Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.Ziller, MJ, Hansen KD, Meissner A., and Aryee MJ Nature methods, 2014/11/02, (2014) Read More / View Supplemental Materials
Abstract
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.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., et al. Nature neuroscience, 2014/09/01, Volume 17, Issue 9, p.1156-1163, (2014) Read More / View Supplemental Materials
Abstract
Notch inhibition allows oncogene-independent generation of iPS cells.Ichida, JK, 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., and Eggan K. Nature chemical biology, 2014/08/01, Volume 10, Issue 8, p.632-9, (2014) Read More / View Supplemental Materials
Abstract
DNA methylation dynamics of the human preimplantation embryo.Smith, ZD, Chan MM, Humm KC, Karnik R., Mekhoubad S., Regev A., Eggan K., and Meissner A. Nature, 2014/07/31, Volume 511, Issue 7511, p.611-5, (2014) Read More / View Supplemental Materials
Abstract
Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal.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., and Goodell MA Cell stem cell, 2014/05/01, Volume 14, Issue 5, p.673-88, (2014) Read More / View Supplemental Materials
Abstract
In Vivo and in vitro dynamics of undifferentiated embryonic cell transcription factor 1.Galonska, C., Smith ZD, and Meissner A. Stem cell reports, 2014/03/11, Volume 2, Issue 3, p.245-52, (2014) Read More / View Supplemental Materials
Abstract
Proto-Oncogenic Role of Mutant IDH2 in Leukemia Initiation and Maintenance.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., and Pandolfi PP Cell stem cell, 2014/01/15, (2014) Read More / View Supplemental Materials
Abstract
2013
The use of small molecules in somatic-cell reprogramming.Federation, AJ, Bradner JE, and Meissner A. Trends in cell biology, 2013/10/30, (2013) Read More / View Supplemental Materials
Abstract
Charting a dynamic DNA methylation landscape of the human genome.Ziller, MJ, Gu H., Müller F., Donaghey J., Tsai LT, Kohlbacher O., De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A., and Meissner A. Nature, 2013/08/22, Volume 500, Issue 7463, p.477-81, (2013) Read More / View Supplemental Materials
Abstract
Browsing (Epi)genomes: A Guide to Data Resources and Epigenome Browsers for Stem Cell Researchers.Karnik, R., and Meissner A. Cell stem cell, 2013/07/03, Volume 13, Issue 1, p.14-21, (2013) Read More / View Supplemental Materials
Abstract
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., et al. Cell, 2013/05/23, Volume 153, Issue 5, p.1149-63, (2013) Read More / View Supplemental Materials
Abstract
DNA methylation: roles in mammalian development.Smith, ZD, and Meissner A. Nature reviews. Genetics, 2013/02/12, Volume 14, Issue 3, p.204-20, (2013) Read More / View Supplemental Materials
Abstract
The simplest explanation: passive DNA demethylation in PGCs.Smith, ZD, and Meissner A. The EMBO journal, 2013/02/06, Volume 32, Issue 3, p.318-21, (2013) Read More / View Supplemental Materials
Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues.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., and Bernstein BE Cell, 2013/01/31, Volume 152, Issue 3, p.642-54, (2013) Read More / View Supplemental Materials
Abstract
2012
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.Boyle, P., Clement K., Gu H., Smith ZD, Ziller M., Fostel JL, Holmes L., Meldrim J., Kelley F., Gnirke A., and Meissner A. Genome biology, 2012/10/03, Volume 13, Issue 10, p.R92, (2012) Read More / View Supplemental Materials
Abstract
Transcription Factor-mediated Epigenetic Reprogramming.Sindhu, C., Samavarchi-Tehrani P., and Meissner A. The Journal of biological chemistry, 2012/09/07, Volume 287, Issue 37, p.30922-31, (2012) Read More / View Supplemental Materials
Abstract
Mouse ooplasm confers context-specific reprogramming capacity.Chan, MM, Smith ZD, Egli D., Regev A., and Meissner A. Nature genetics, 2012/09/01, Volume 44, Issue 9, p.978-80, (2012) Read More / View Supplemental Materials
Abstract
DNA Methylation Dynamics during In Vivo Differentiation of Blood and Skin Stem Cells.Bock, C., Beerman I., Lien WH, Smith ZD, Gu H., Boyle P., Gnirke A., Fuchs E., Rossi DJ, and Meissner A. Molecular cell, 2012/08/24, Volume 47, Issue 4, p.633-47, (2012) Read More / View Supplemental Materials
Abstract
Epigenetic obstacles encountered by transcription factors: reprogramming against all odds.Gifford, CA, and Meissner A. Current opinion in genetics & development, 2012/08/23, (2012) Read More / View Supplemental Materials
Abstract
A unique regulatory phase of DNA methylation in the early mammalian embryo.Smith, ZD, Chan MM, Mikkelsen TS, Gu H., Gnirke A., Regev A., and Meissner A. Nature, 2012/03/28, Volume 484, Issue 7394, p.339-44, (2012) Read More / View Supplemental Materials
Abstract
2011
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.Meissner, A., Gnirke A., Bell GW, Ramsahoye B., Lander E. S., and Jaenisch R. Nucleic acids research, 2011/12/08, Volume 33, Issue 18, p.5868-77, (2011) Read More / View Supplemental Materials
Abstract
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.Ziller, MJ, Müller F., Liao J., Zhang Y., Gu H., Bock C., Boyle P., Epstein CB, Bernstein BE, Lengauer T., Gnirke A., and Meissner A. PLoS genetics, 2011/12/01, Volume 7, Issue 12, p.e1002389, (2011) Read More / View Supplemental Materials
Abstract
Guiding DNA methylation.Meissner, A. Cell stem cell, 2011/11/04, Volume 9, Issue 5, p.388-90, (2011) Read More / View Supplemental Materials
Abstract
lincRNAs act in the circuitry controlling pluripotency and differentiation.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, and Lander E. S. Nature, 2011/08/28, Volume 477, Issue 7364, p.295-300, (2011) Read More / View Supplemental Materials
Abstract
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.Gu, H., Smith ZD, Bock C., Boyle P., Gnirke A., and Meissner A. Nature protocols, 2011/04/01, Volume 6, Issue 4, p.468-81, (2011) Read More / View Supplemental Materials
Abstract
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.Bock, C., Kiskinis E., Verstappen G., Gu H., Boulting G., Smith ZD, Ziller M., Croft GF, Amoroso MW, Oakley DH, Gnirke A., Eggan K., and Meissner A. Cell, 2011/02/04, Volume 144, Issue 3, p.439-52, (2011) Read More / View Supplemental Materials
Abstract
Reprogramming factor expression initiates widespread targeted chromatin remodeling.Koche, RP, Smith ZD, Adli M., Gu H., Ku M., Gnirke A., Bernstein BE, and Meissner A. Cell stem cell, 2011/01/07, Volume 8, Issue 1, p.96-105, (2011) Read More / View Supplemental Materials
Abstract
2010
The NIH Roadmap Epigenomics Mapping Consortium.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 E. S., Mikkelsen TS, and Thomson JA Nature biotechnology, 2010/10/01, Volume 28, Issue 10, p.1045-8, (2010) Read More / View Supplemental Materials
Abstract
Quantitative comparison of genome-wide DNA methylation mapping technologies.Bock, C., Tomazou EM, Brinkman AB, Müller F., Simmer F., Gu H., Jäger N., Gnirke A., Stunnenberg HG, and Meissner A. Nature biotechnology, 2010/10/01, Volume 28, Issue 10, p.1106-14, (2010) Read More / View Supplemental Materials
Abstract
Dynamic single-cell imaging of direct reprogramming reveals an early specifying event.Smith, ZD, Nachman I., Regev A., and Meissner A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.521-6, (2010) Read More / View Supplemental Materials
Abstract
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.Gu, H., Bock C., Mikkelsen TS, Jäger N., Smith ZD, Tomazou E., Gnirke A., Lander E. S., and Meissner A. Nature methods, 2010/02/01, Volume 7, Issue 2, p.133-6, (2010) Read More / View Supplemental Materials
Abstract
2009
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.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, et al. Science (New York, N.Y.), 2009/10/09, Volume 326, Issue 5950, p.257-63, (2009) Read More / View Supplemental Materials
Abstract
2008
Genome-scale DNA methylation maps of pluripotent and differentiated cells.Meissner, A., Mikkelsen TS, Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein BE, Nusbaum C., Jaffe DB, Gnirke A., Jaenisch R., and Lander E. S. Nature, 2008/08/07, Volume 454, Issue 7205, p.766-70, (2008) Read More / View Supplemental Materials
Abstract
Dissecting direct reprogramming through integrative genomic analysis.Mikkelsen, TS, Hanna J., Zhang X., Ku M., Wernig M., Schorderet P., Bernstein BE, Jaenisch R., Lander E. S., and Meissner A. Nature, 2008/07/03, Volume 454, Issue 7200, p.49-55, (2008) Read More / View Supplemental Materials
Abstract
2007
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.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., et al. Nature, 2007/08/02, Volume 448, Issue 7153, p.553-60, (2007) Read More / View Supplemental Materials
Abstract
The mammalian epigenome.Bernstein, BE, Meissner A., and Lander E. S. Cell, 2007/02/23, Volume 128, Issue 4, p.669-81, (2007) Read More / View Supplemental Materials
Abstract
2006
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.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, and Lander E. S. Cell, 2006/04/21, Volume 125, Issue 2, p.315-26, (2006) Read More / View Supplemental Materials
Abstract
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