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2014
Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells.Suvà, ML, Rheinbay E., Gillespie SM, Patel AP, Wakimoto H., Rabkin SD, Riggi N., Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N., Kasif S., Beik S., Kadri S., Tirosh I., Wortman I., Shalek AK, et al. Cell, 2014/04/09, (2014) Read More / View Supplemental Materials
Abstract
An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.Knoechel, B., Roderick JE, Williamson KE, Zhu J., Lohr JG, Cotton MJ, Gillespie SM, Fernandez D., Ku M., Wang H., Piccioni F., Silver SJ, Jain M., Pearson D., Kluk MJ, Ott CJ, Shultz LD, Brehm MA, Greiner DL, Gutierrez A., et al. Nature genetics, 2014/03/02, (2014) Read More / View Supplemental Materials
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2013
Locus-specific editing of histone modifications at endogenous enhancers.Mendenhall, EM, Williamson KE, Reyon D., Zou JY, Ram O., Joung JK, and Bernstein BE Nature biotechnology, 2013/09/08, (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
In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.Sander, JD, Ramirez CL, Linder SJ, Pattanayak V., Shoresh N., Ku M., Foden JA, Reyon D., Bernstein BE, Liu DR, and Joung JK Nucleic acids research, 2013/08/14, (2013) Read More / View Supplemental Materials
Abstract
An aberrant transcription factor network essential for wnt signaling and stem cell maintenance in glioblastoma.Rheinbay, E., Suvà ML, Gillespie SM, Wakimoto H., Patel AP, Shahid M., Oksuz O., Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S., Chi AS, and Bernstein BE Cell reports, 2013/05/30, Volume 3, Issue 5, p.1567-79, (2013) Read More / View Supplemental Materials
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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
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
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2012
H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.Ku, M., Jaffe JD, Koche RP, Rheinbay E., Endoh M., Koseki H., Carr SA, and Bernstein BE Genome biology, 2012/10/03, Volume 13, Issue 10, p.R85, (2012) Read More / View Supplemental Materials
Abstract
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.Garber, M., Yosef N., Goren A., Raychowdhury R., Thielke A., Guttman M., Robinson J., Minie B., Chevrier N., Itzhaki Z., Blecher-Gonen R., Bornstein C., Amann-Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., et al. Molecular cell, 2012/09/14, Volume 47, Issue 5, p.810-22, (2012) Read More / View Supplemental Materials
Abstract
ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.Abdel-Wahab, O., Adli M., LaFave LM, Gao J., Hricik T., Shih AH, Pandey S., Patel JP, Chung YR, Koche R., Perna F., Zhao X., Taylor JE, Park CY, Carroll M., Melnick A., Nimer SD, Jaffe JD, Aifantis I., Bernstein BE, et al. Cancer cell, 2012/08/14, Volume 22, Issue 2, p.180-93, (2012) Read More / View Supplemental Materials
Abstract
A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma.Rheinbay, E., Louis DN, Bernstein BE, and Suvà ML Cancer cell, 2012/03/20, Volume 21, Issue 3, p.329-31, (2012) Read More / View Supplemental Materials
Abstract
2011
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.Ram, O., Goren A., Amit I., Shoresh N., Yosef N., Ernst J., Kellis M., Gymrek M., Issner R., Coyne M., Durham T., Zhang X., Donaghey J., Epstein CB, Regev A., and Bernstein BE Cell, 2011/12/23, Volume 147, Issue 7, p.1628-39, (2011) Read More / View Supplemental Materials
Abstract
Global nucleosome occupancy in yeast.Bernstein, BE, Liu CL, Humphrey EL, Perlstein EO, and Schreiber SL Genome biology, 2011/12/08, Volume 5, Issue 9, p.R62, (2011) Read More / View Supplemental Materials
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Large-scale discovery and validation of functional elements in the human genome.Bernstein, BE, and Kellis M. Genome biology, 2011/12/08, Volume 6, Issue 3, p.312, (2011) Read More / View Supplemental Materials
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The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications.Bernstein, BE, Humphrey EL, Liu CL, and Schreiber SL Methods in enzymology, 2011/12/08, Volume 376, p.349-60, (2011) Read More / View Supplemental Materials
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
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Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.Adli, M., and Bernstein BE Nature protocols, 2011/09/29, Volume 6, Issue 10, p.1656-68, (2011) Read More / View Supplemental Materials
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Mapping and analysis of chromatin state dynamics in nine human cell types.Ernst, J., Kheradpour P., Mikkelsen TS, Shoresh N., Ward LD, Epstein CB, Zhang X., Wang L., Issner R., Coyne M., Ku M., Durham T., Kellis M., and Bernstein BE Nature, 2011/05/05, Volume 473, Issue 7345, p.43-9, (2011) Read More / View Supplemental Materials
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Initial genome sequencing and analysis of multiple myeloma.Chapman, MA, Lawrence MS, Keats JJ, Cibulskis K., Sougnez C., Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M., Anderson KC, Ardlie KG, Auclair D., Baker A., Bergsagel PL, Bernstein BE, Drier Y., Fonseca R., Gabriel SB, Hofmeister CC, et al. Nature, 2011/03/24, Volume 471, Issue 7339, p.467-72, (2011) Read More / View Supplemental Materials
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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
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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
Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network.Aiden, AP, Rivera MN, Rheinbay E., Ku M., Coffman EJ, Truong TT, Vargas SO, Lander E. S., Haber DA, and Bernstein BE Cell stem cell, 2010/06/04, Volume 6, Issue 6, p.591-602, (2010) Read More / View Supplemental Materials
Abstract
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.Goren, A., Ozsolak F., Shoresh N., Ku M., Adli M., Hart C., Gymrek M., Zuk O., Regev A., Milos PM, and Bernstein BE Nature methods, 2010/01/01, Volume 7, Issue 1, p.47-9, (2010) Read More / View Supplemental Materials
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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
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.Khalil, AM, Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein BE, van Oudenaarden A., Regev A., Lander E. S., and Rinn JL Proceedings of the National Academy of Sciences of the United States of America, 2009/07/14, Volume 106, Issue 28, p.11667-72, (2009) Read More / View Supplemental Materials
Abstract
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.Guttman, M., Amit I., Garber M., French C., Lin MF, Feldser D., Huarte M., Zuk O., Carey BW, Cassady JP, Cabili MN, Jaenisch R., Mikkelsen TS, Jacks T., Hacohen N., Bernstein BE, Kellis M., Regev A., Rinn JL, and Lander E. S. Nature, 2009/03/12, Volume 458, Issue 7235, p.223-7, (2009) Read More / View Supplemental Materials
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2008
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.Ku, M., Koche RP, Rheinbay E., Mendenhall EM, Endoh M., Mikkelsen TS, Presser A., Nusbaum C., Xie X., Chi AS, Adli M., Kasif S., Ptaszek LM, Cowan CA, Lander E. S., Koseki H., and Bernstein BE PLoS genetics, 2008/10/01, Volume 4, Issue 10, p.e1000242, (2008) Read More / View Supplemental Materials
Abstract
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
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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
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase.Liu, CL, Bernstein BE, and Schreiber SL CSH protocols, 2008/05/01, Volume 2008, p.pdb.prot5002, (2008) Read More / View Supplemental Materials
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Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription.Liu, CL, Bernstein BE, and Schreiber SL CSH protocols, 2008/05/01, Volume 2008, p.pdb.prot5003, (2008) Read More / View Supplemental Materials
Abstract
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification.Liu, CL, Bernstein BE, and Schreiber SL CSH protocols, 2008/05/01, Volume 2008, p.pdb.prot5004, (2008) Read More / View Supplemental Materials
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Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview.Liu, CL, Bernstein BE, and Schreiber SL CSH protocols, 2008/05/01, Volume 2008, p.pdb.top42, (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
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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
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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
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2005
Genomic maps and comparative analysis of histone modifications in human and mouse.Bernstein, BE, Kamal M., Lindblad-Toh K., Bekiranov S., Bailey DK, Huebert DJ, McMahon S., Karlsson EK, Kulbokas EJ 3rd, Gingeras TR, Schreiber SL, and Lander E. S. Cell, 2005/01/28, Volume 120, Issue 2, p.169-81, (2005) Read More / View Supplemental Materials
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2004
Rpd3p relocation mediates a transcriptional response to rapamycin in yeast.Humphrey, EL, Shamji AF, Bernstein BE, and Schreiber SL Chemistry & biology, 2004/03/01, Volume 11, Issue 3, p.295-9, (2004) Read More / View Supplemental Materials
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  • Showing 1-39 of 39 Results