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2013
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, 2013/05/07, (2013) Read More / View Supplemental Materials
Abstract
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.Dulak, AM, Stojanov P., Peng S., Lawrence MS, Fox C., Stewart C., Bandla S., Imamura Y., Schumacher SE, Shefler E., McKenna A., Carter SL, Cibulskis K., Sivachenko A., Saksena G., Voet D., Ramos AH, Auclair D., Thompson K., Sougnez C., et al. Nature genetics, 2013/04/26, Volume 45, Issue 5, p.478-86, (2013) Read More / View Supplemental Materials
Abstract
Punctuated evolution of prostate cancer genomes.Baca, SC, Prandi D., Lawrence MS, Mosquera JM, Romanel A., Drier Y., Park K., Kitabayashi N., MacDonald TY, Ghandi M., Van Allen E., Kryukov GV, Sboner A., Theurillat JP, Soong TD, Nickerson E., Auclair D., Tewari A., Beltran H., Onofrio RC, et al. Cell, 2013/04/25, Volume 153, Issue 3, p.666-77, (2013) Read More / View Supplemental Materials
Abstract
Lessons from the cancer genome.Garraway, LA, and Lander E. S. Cell, 2013/03/28, Volume 153, Issue 1, p.17-37, (2013) Read More / View Supplemental Materials
Abstract
Cinnamides as selective small-molecule inhibitors of a cellular model of breast cancer stem cells.Germain, AR, Carmody LC, Nag PP, Morgan B., VerPlank L., Fernandez C., Donckele E., Feng Y., Perez JR, Dandapani S., Palmer M., Lander E. S., Gupta PB, Schreiber SL, and Munoz B. Bioorganic & medicinal chemistry letters, 2013/03/15, Volume 23, Issue 6, p.1834-8, (2013) Read More / View Supplemental Materials
Abstract
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.Kirby, A., Gnirke A., Jaffe DB, Barešová V., Pochet N., Blumenstiel B., Ye C., Aird D., Stevens C., Robinson JT, Cabili MN, Gat-Viks I., Kelliher E., Daza R., DeFelice M., Hůlková H., Sovová J., Vylet'al P., Antignac C., Guttman M., et al. Nature genetics, 2013/03/01, Volume 45, Issue 3, p.299-303, (2013) Read More / View Supplemental Materials
Abstract
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia.Landau, DA, Carter SL, Stojanov P., McKenna A., Stevenson K., Lawrence MS, Sougnez C., Stewart C., Sivachenko A., Wang L., Wan Y., Zhang W., Shukla SA, Vartanov A., Fernandes SM, Saksena G., Cibulskis K., Tesar B., Gabriel S., Hacohen N., et al. Cell, 2013/02/14, Volume 152, Issue 4, p.714-26, (2013) Read More / View Supplemental Materials
Abstract
Identifying recent adaptations in large-scale genomic data.Grossman, SR, Andersen KG, Shlyakhter I., Tabrizi S., Winnicki S., Yen A., Park DJ, Griesemer D., Karlsson EK, Wong SH, Cabili M., Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL, 1000 Genomes Project, Lander E. S., Schaffner SF, and Sabeti PC Cell, 2013/02/14, Volume 152, Issue 4, p.703-13, (2013) Read More / View Supplemental Materials
Abstract
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.Cibulskis, K., Lawrence MS, Carter SL, Sivachenko A., Jaffe D., Sougnez C., Gabriel S., Meyerson M., Lander E. S., and Getz G. Nature biotechnology, 2013/02/10, (2013) Read More / View Supplemental Materials
Abstract
The genetic landscape of high-risk neuroblastoma.Pugh, TJ, Morozova O., Attiyeh EF, Asgharzadeh S., Wei JS, Auclair D., Carter SL, Cibulskis K., Hanna M., Kiezun A., Kim J., Lawrence MS, Lichenstein L., McKenna A., Pedamallu CS, Ramos AH, Shefler E., Sivachenko A., Sougnez C., Stewart C., et al. Nature genetics, 2013/01/20, (2013) Read More / View Supplemental Materials
Abstract
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation.Costello, M., Pugh TJ, Fennell TJ, Stewart C., Lichtenstein L., Meldrim JC, Fostel JL, Friedrich DC, Perrin D., Dionne D., Kim S., Gabriel SB, Lander E. S., Fisher S., and Getz G. Nucleic acids research, 2013/01/08, (2013) Read More / View Supplemental Materials
Abstract
2012
Epidemiology. Emerging disease or diagnosis?Gire, SK, Stremlau M., Andersen KG, Schaffner SF, Bjornson Z., Rubins K., Hensley L., McCormick JB, Lander E. S., Garry RF, Happi C., and Sabeti PC Science (New York, N.Y.), 2012/11/09, Volume 338, Issue 6108, p.750-2, (2012) Read More / View Supplemental Materials
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.Drier, Y., Lawrence MS, Carter SL, Stewart C., Gabriel SB, Lander E. S., Meyerson M., Beroukhim R., and Getz G. Genome research, 2012/11/02, (2012) Read More / View Supplemental Materials
Abstract
Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number.Sankaran, VG, Ludwig LS, Sicinska E., Xu J., Bauer DE, Eng JC, Patterson HC, Metcalf RA, Natkunam Y., Orkin SH, Sicinski P., Lander E. S., and Lodish HF Genes & development, 2012/09/15, Volume 26, Issue 18, p.2075-87, (2012) Read More / View Supplemental Materials
Abstract
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.Imielinski, M., Berger AH, Hammerman PS, Hernandez B., Pugh TJ, Hodis E., Cho J., Suh J., Capelletti M., Sivachenko A., Sougnez C., Auclair D., Lawrence MS, Stojanov P., Cibulskis K., Choi K., de Waal L., Sharifnia T., Brooks A., Greulich H., et al. Cell, 2012/09/14, Volume 150, Issue 6, p.1107-20, (2012) Read More / View Supplemental Materials
Abstract
Comprehensive genomic characterization of squamous cell lung cancers.The Cancer Genome Atlas Research, Network, institution.)(Participants are arranged by area of contribution and then by, Genome sequencing centres: Broad Institute, Hammerman PS, Lawrence MS, Voet D., Jing R., Cibulskis K., Sivachenko A., Stojanov P., McKenna A., Lander E. S., Gabriel S., Getz G., Sougnez C., Imielinski M., Helman E., Hernandez B., Pho NH, Meyerson M., et al. Nature, 2012/09/09, (2012) Read More / View Supplemental Materials
Abstract
A landscape of driver mutations in melanoma.Hodis, E., Watson IR, Kryukov GV, Arold ST, Imielinski M., Theurillat JP, Nickerson E., Auclair D., Li L., Place C., Dicara D., Ramos AH, Lawrence MS, Cibulskis K., Sivachenko A., Voet D., Saksena G., Stransky N., Onofrio RC, Winckler W., et al. Cell, 2012/07/20, Volume 150, Issue 2, p.251-63, (2012) Read More / View Supplemental Materials
Abstract
Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia.Sankaran, VG, Ghazvinian R., Do R., Thiru P., Vergilio JA, Beggs AH, Sieff CA, Orkin SH, Nathan DG, Lander E. S., and Gazda HT The Journal of clinical investigation, 2012/07/02, Volume 122, Issue 7, p.2439-43, (2012) Read More / View Supplemental Materials
Abstract
Sequence analysis of mutations and translocations across breast cancer subtypes.Banerji, S., Cibulskis K., Rangel-Escareno C., Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C., Zou L., Cortes ML, Fernandez-Lopez JC, Peng S., Ardlie KG, Auclair D., Bautista-Piña V., Duke F., Francis J., Jung J., Maffuz-Aziz A., et al. Nature, 2012/06/20, Volume 486, Issue 7403, p.405-9, (2012) Read More / View Supplemental Materials
Abstract
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.Barbieri, CE, Baca SC, Lawrence MS, Demichelis F., Blattner M., Theurillat JP, White TA, Stojanov P., Van Allen E., Stransky N., Nickerson E., Chae SS, Boysen G., Auclair D., Onofrio RC, Park K., Kitabayashi N., MacDonald TY, Sheikh K., Vuong T., et al. Nature genetics, 2012/05/20, Volume 44, Issue 6, p.685-9, (2012) Read More / View Supplemental Materials
Abstract
Identification of a selective small molecule inhibitor of breast cancer stem cells.Germain, AR, Carmody LC, Morgan B., Fernandez C., Forbeck E., Lewis TA, Nag PP, Ting A., VerPlank L., Feng Y., Perez JR, Dandapani S., Palmer M., Lander E. S., Gupta PB, Schreiber SL, and Munoz B. Bioorganic & medicinal chemistry letters, 2012/05/15, Volume 22, Issue 10, p.3571-4, (2012) Read More / View Supplemental Materials
Abstract
Melanoma genome sequencing reveals frequent PREX2 mutations.Berger, MF, Hodis E., Heffernan TP, Deribe YL, Lawrence MS, Protopopov A., Ivanova E., Watson IR, Nickerson E., Ghosh P., Zhang H., Zeid R., Ren X., Cibulskis K., Sivachenko AY, Wagle N., Sucker A., Sougnez C., Onofrio R., Ambrogio L., et al. Nature, 2012/05/09, Volume 485, Issue 7399, p.502-6, (2012) Read More / View Supplemental Materials
Abstract
Absolute quantification of somatic DNA alterations in human cancer.Carter, SL, Cibulskis K., Helman E., McKenna A., Shen H., Zack T., Laird PW, Onofrio RC, Winckler W., Weir BA, Beroukhim R., Pellman D., Levine DA, Lander E. S., Meyerson M., and Getz G. Nature biotechnology, 2012/04/29, (2012) Read More / View Supplemental Materials
Abstract
The genomic basis of adaptive evolution in threespine sticklebacks.Jones, FC, Grabherr MG, Chan YF, Russell P., Mauceli E., Johnson J., Swofford R., Pirun M., Zody MC, White S., Birney E., Searle S., Schmutz J., Grimwood J., Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, et al. Nature, 2012/04/04, Volume 484, Issue 7392, p.55-61, (2012) Read More / View Supplemental Materials
Abstract
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing.Lohr, JG, Stojanov P., Lawrence MS, Auclair D., Chapuy B., Sougnez C., Cruz-Gordillo P., Knoechel B., Asmann YW, Slager SL, Novak AJ, Dogan A., Ansell SM, Link BK, Zou L., Gould J., Saksena G., Stransky N., Rangel-Escareño C., Fernandez-Lopez JC, et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/03/06, Volume 109, Issue 10, p.3879-84, (2012) Read More / View Supplemental Materials
Abstract
Chromatin-modifying enzymes as modulators of reprogramming.Onder, TT, Kara N., Cherry A., Sinha AU, Zhu N., Bernt KM, Cahan P., Marcarci BO, Unternaehrer J., Gupta PB, Lander E. S., Armstrong SA, and Daley GQ Nature, 2012/03/04, Volume 483, Issue 7391, p.598-602, (2012) Read More / View Supplemental Materials
Abstract
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.Melnikov, A., Murugan A., Zhang X., Tesileanu T., Wang L., Rogov P., Feizi S., Gnirke A., Callan CG Jr, Kinney JB, Kellis M., Lander E. S., and Mikkelsen TS Nature biotechnology, 2012/02/26, Volume 30, Issue 3, p.271-7, (2012) Read More / View Supplemental Materials
Abstract
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.Grad, YH, Lipsitch M., Feldgarden M., Arachchi HM, Cerqueira GC, FitzGerald M., Godfrey P., Haas BJ, Murphy CI, Russ C., Sykes S., Walker BJ, Wortman JR, Young S., Zeng Q., Abouelleil A., Bochicchio J., Chauvin S., Desmet T., Gujja S., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/02/21, Volume 109, Issue 8, p.3065-70, (2012) Read More / View Supplemental Materials
Abstract
The mystery of missing heritability: Genetic interactions create phantom heritability.Zuk, O., Hechter E., Sunyaev SR, and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2012/01/24, Volume 109, Issue 4, p.1193-8, (2012) Read More / View Supplemental Materials
Abstract
Assisted assembly: how to improve a de novo genome assembly by using related species.Gnerre, S., Lander E. S., Lindblad-Toh K., and Jaffe DB Genome biology, 2012/01/09, Volume 10, Issue 8, p.R88, (2012) Read More / View Supplemental Materials
Abstract
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.Neafsey, DE, Schaffner SF, Volkman SK, Park D., Montgomery P., Milner DA Jr, Lukens A., Rosen D., Daniels R., Houde N., Cortese JF, Tyndall E., Gates C., Stange-Thomann N., Sarr O., Ndiaye D., Ndir O., Mboup S., Ferreira MU, Moraes Sdo L., et al. Genome biology, 2012/01/07, Volume 9, Issue 12, p.R171, (2012) Read More / View Supplemental Materials
Abstract
2011
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia.Wang, L., Lawrence MS, Wan Y., Stojanov P., Sougnez C., Stevenson K., Werner L., Sivachenko A., Deluca DS, Zhang L., Zhang W., Vartanov AR, Fernandes SM, Goldstein NR, Folco EG, Cibulskis K., Tesar B., Sievers QL, Shefler E., Gabriel S., et al. The New England journal of medicine, 2011/12/29, Volume 365, Issue 26, p.2497-506, (2011) Read More / View Supplemental Materials
Abstract
Detecting novel associations in large data sets.Reshef, DN, Reshef YA, Finucane HK, Grossman SR, McVean G., Turnbaugh PJ, Lander E. S., Mitzenmacher M., and Sabeti PC Science (New York, N.Y.), 2011/12/16, Volume 334, Issue 6062, p.1518-24, (2011) Read More / View Supplemental Materials
Abstract
Chromosome substitution strains: a new way to study genetically complex traits.Hill, AE, Lander E. S., and Nadeau JH Methods in molecular medicine, 2011/12/08, Volume 128, p.153-72, (2011) Read More / View Supplemental Materials
Abstract
Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery.Kellis, M., Patterson N., Birren B., Berger B., and Lander E. S. Journal of computational biology : a journal of computational molecular cell biology, 2011/12/08, Volume 11, Issue 2-3, p.319-55, (2011) Read More / View Supplemental Materials
Abstract
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
A high-resolution map of human evolutionary constraint using 29 mammals.Lindblad-Toh, K., Garber M., Zuk O., Lin MF, Parker BJ, Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., Ward LD, Lowe CB, Holloway AK, Clamp M., Gnerre S., Alföldi J., Beal K., Chang J., Clawson H., Cuff J., et al. Nature, 2011/10/12, Volume 478, Issue 7370, p.476-82, (2011) Read More / View Supplemental Materials
Abstract
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.Bass, AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y., Cibulskis K., Sougnez C., Voet D., Saksena G., Sivachenko A., Jing R., Parkin M., Pugh T., Verhaak RG, Stransky N., Boutin AT, Barretina J., Solit DB, Vakiani E., Shao W., et al. Nature genetics, 2011/09/04, Volume 43, Issue 10, p.964-8, (2011) Read More / View Supplemental Materials
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The genome of the green anole lizard and a comparative analysis with birds and mammals.Alföldi, J., Di Palma F., Grabherr M., Williams C., Kong L., Mauceli E., Russell P., Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S., Shedlock AM, Botka C., Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D., et al. Nature, 2011/08/31, Volume 477, Issue 7366, p.587-91, (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
The mutational landscape of head and neck squamous cell carcinoma.Stransky, N., Egloff AM, Tward AD, Kostic AD, Cibulskis K., Sivachenko A., Kryukov GV, Lawrence MS, Sougnez C., McKenna A., Shefler E., Ramos AH, Stojanov P., Carter SL, Voet D., Cortés ML, Auclair D., Berger MF, Saksena G., Guiducci C., et al. Science (New York, N.Y.), 2011/08/26, Volume 333, Issue 6046, p.1157-60, (2011) Read More / View Supplemental Materials
Abstract
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells.Gupta, PB, Fillmore CM, Jiang G., Shapira SD, Tao K., Kuperwasser C., and Lander E. S. Cell, 2011/08/19, Volume 146, Issue 4, p.633-44, (2011) Read More / View Supplemental Materials
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Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer.Cheung, HW, Cowley GS, Weir BA, Boehm JS, Rusin S., Scott JA, East A., Ali LD, Lizotte PH, Wong TC, Jiang G., Hsiao J., Mermel CH, Getz G., Barretina J., Gopal S., Tamayo P., Gould J., Tsherniak A., Stransky N., et al. Proceedings of the National Academy of Sciences of the United States of America, 2011/07/26, Volume 108, Issue 30, p.12372-7, (2011) Read More / View Supplemental Materials
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QnAs with Eric S. Lander. Interview by Prashant Nair.Lander, E. S. Proceedings of the National Academy of Sciences of the United States of America, 2011/07/12, Volume 108, Issue 28, p.11319, (2011) Read More / View Supplemental Materials
Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.Van Tyne, D., Park DJ, Schaffner SF, Neafsey DE, Angelino E., Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA Jr, Johnson CA, Shlyakhter I., Grossman SR, Becker JS, Yamins D., Karlsson EK, Ndiaye D., Sarr O., Mboup S., et al. PLoS genetics, 2011/04/01, Volume 7, Issue 4, p.e1001383, (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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Genome-sequencing anniversary. The accelerator.Lander, E. S. Science (New York, N.Y.), 2011/02/25, Volume 331, Issue 6020, p.1024, (2011) Read More / View Supplemental Materials
The genomic complexity of primary human prostate cancer.Berger, MF, Lawrence MS, Demichelis F., Drier Y., Cibulskis K., Sivachenko AY, Sboner A., Esgueva R., Pflueger D., Sougnez C., Onofrio R., Carter SL, Park K., Habegger L., Ambrogio L., Fennell T., Parkin M., Saksena G., Voet D., Ramos AH, et al. Nature, 2011/02/10, Volume 470, Issue 7333, p.214-20, (2011) Read More / View Supplemental Materials
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Initial impact of the sequencing of the human genome.Lander, E. S. Nature, 2011/02/10, Volume 470, Issue 7333, p.187-97, (2011) Read More / View Supplemental Materials
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Genetic predisposition directs breast cancer phenotype by dictating progenitor cell fate.Proia, TA, Keller PJ, Gupta PB, Klebba I., Jones AD, Sedic M., Gilmore H., Tung N., Naber SP, Schnitt S., Lander E. S., and Kuperwasser C. Cell stem cell, 2011/02/04, Volume 8, Issue 2, p.149-63, (2011) Read More / View Supplemental Materials
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data.Gnerre, S., Maccallum I., Przybylski D., Ribeiro FJ, Burton JN, Walker BJ, Sharpe T., Hall G., Shea TP, Sykes S., Berlin AM, Aird D., Costello M., Daza R., Williams L., Nicol R., Gnirke A., Nusbaum C., Lander E. S., and Jaffe DB Proceedings of the National Academy of Sciences of the United States of America, 2011/01/25, Volume 108, Issue 4, p.1513-8, (2011) Read More / View Supplemental Materials
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MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13.Sankaran, VG, Menne TF, Šćepanović D., Vergilio JA, Ji P., Kim J., Thiru P., Orkin SH, Lander E. S., and Lodish HF Proceedings of the National Academy of Sciences of the United States of America, 2011/01/25, Volume 108, Issue 4, p.1519-24, (2011) Read More / View Supplemental Materials
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Integrative genomics viewer.Robinson, JT, Thorvaldsdóttir H., Winckler W., Guttman M., Lander E. S., Getz G., and Mesirov J. P. Nature biotechnology, 2011/01/01, Volume 29, Issue 1, p.24-6, (2011) Read More / View Supplemental Materials
2010
Estrogen expands breast cancer stem-like cells through paracrine FGF/Tbx3 signaling.Fillmore, CM, Gupta PB, Rudnick JA, Caballero S., Keller PJ, Lander E. S., and Kuperwasser C. Proceedings of the National Academy of Sciences of the United States of America, 2010/12/14, Volume 107, Issue 50, p.21737-42, (2010) Read More / View Supplemental Materials
Abstract
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells.Loewer, S., Cabili MN, Guttman M., Loh YH, Thomas K., Park IH, Garber M., Curran M., Onder T., Agarwal S., Manos PD, Datta S., Lander E. S., Schlaeger TM, Daley GQ, and Rinn JL Nature genetics, 2010/12/01, Volume 42, Issue 12, p.1113-7, (2010) Read More / View Supplemental Materials
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SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes.Neafsey, DE, Lawniczak MK, Park DJ, Redmond SN, Coulibaly MB, Traoré SF, Sagnon N., Costantini C., Johnson C., Wiegand RC, Collins FH, Lander E. S., Wirth DF, Kafatos FC, Besansky NJ, Christophides GK, and Muskavitch MA Science (New York, N.Y.), 2010/10/22, Volume 330, Issue 6003, p.514-7, (2010) Read More / View Supplemental Materials
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Prepare and inspire.Lander, E. S., and Gates SJ Jr Science (New York, N.Y.), 2010/10/08, Volume 330, Issue 6001, p.151, (2010) Read More / View Supplemental Materials
Comparative epigenomic analysis of murine and human adipogenesis.Mikkelsen, TS, Xu Z., Zhang X., Wang L., Gimble JM, Lander E. S., and Rosen ED Cell, 2010/10/01, Volume 143, Issue 1, p.156-69, (2010) Read More / View Supplemental Materials
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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
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Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes.Taube, JH, Herschkowitz JI, Komurov K., Zhou AY, Gupta S., Yang J., Hartwell K., Onder TT, Gupta PB, Evans KW, Hollier BG, Ram PT, Lander E. S., Rosen JM, Weinberg R. A., and Mani SA Proceedings of the National Academy of Sciences of the United States of America, 2010/08/31, Volume 107, Issue 35, p.15449-54, (2010) Read More / View Supplemental Materials
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A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.Huarte, M., Guttman M., Feldser D., Garber M., Koziol MJ, Kenzelmann-Broz D., Khalil AM, Zuk O., Amit I., Rabani M., Attardi LD, Regev A., Lander E. S., Jacks T., and Rinn JL Cell, 2010/08/06, Volume 142, Issue 3, p.409-19, (2010) Read More / View Supplemental Materials
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Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy.Barretina, J., Taylor BS, Banerji S., Ramos AH, Lagos-Quintana M., Decarolis PL, Shah K., Socci ND, Weir BA, Ho A., Chiang DY, Reva B., Mermel CH, Getz G., Antipin Y., Beroukhim R., Major JE, Hatton C., Nicoletti R., Hanna M., et al. Nature genetics, 2010/08/01, Volume 42, Issue 8, p.715-21, (2010) Read More / View Supplemental Materials
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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
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A draft sequence of the Neandertal genome.Green, RE, Krause J., Briggs AW, Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T., Alkan C., Prüfer K., Meyer M., Burbano HA, Good JM, et al. Science (New York, N.Y.), 2010/05/07, Volume 328, Issue 5979, p.710-22, (2010) Read More / View Supplemental Materials
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Hi-C: a method to study the three-dimensional architecture of genomes.van Berkum, NL, Lieberman-Aiden E., Williams L., Imakaev M., Gnirke A., Mirny LA, Dekker J., and Lander E. S. Journal of visualized experiments : JoVE, 2010/05/06, Issue 39, (2010) Read More / View Supplemental Materials
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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.Guttman, M., Garber M., Levin JZ, Donaghey J., Robinson J., Adiconis X., Fan L., Koziol MJ, Gnirke A., Nusbaum C., Rinn JL, Lander E. S., and Regev A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.503-10, (2010) Read More / View Supplemental Materials
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International network of cancer genome projects.International Cancer Genome, Consortium, Hudson T. J., Anderson W., Artez A., Barker AD, Bell C., Bernabé RR, Bhan MK, Calvo F., Eerola I., Gerhard DS, Guttmacher A., Guyer M., Hemsley FM, Jennings JL, Kerr D., Klatt P., Kolar P., Kusada J., Lane DP, et al. Nature, 2010/04/15, Volume 464, Issue 7291, p.993-8, (2010) Read More / View Supplemental Materials
Abstract
Genetic resistance to diet-induced obesity in chromosome substitution strains of mice.Burrage, LC, Baskin-Hill AE, Sinasac DS, Singer JB, Croniger CM, Kirby A., Kulbokas E. J., Daly M. J., Lander E. S., Broman KW, and Nadeau JH Mammalian genome : official journal of the International Mammalian Genome Society, 2010/04/01, Volume 21, Issue 3-4, p.115-29, (2010) Read More / View Supplemental Materials
Abstract
Integrative analysis of the melanoma transcriptome.Berger, MF, Levin JZ, Vijayendran K., Sivachenko A., Adiconis X., Maguire J., Johnson LA, Robinson J., Verhaak RG, Sougnez C., Onofrio RC, Ziaugra L., Cibulskis K., Laine E., Barretina J., Winckler W., Fisher DE, Getz G., Meyerson M., Jaffe DB, et al. Genome research, 2010/04/01, Volume 20, Issue 4, p.413-27, (2010) Read More / View Supplemental Materials
Abstract
The landscape of somatic copy-number alteration across human cancers.Beroukhim, R., Mermel CH, Porter D., Wei G., Raychaudhuri S., Donovan J., Barretina J., Boehm JS, Dobson J., Urashima M., Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L., Greulich H., Reich M., Winckler W., Lawrence MS, Weir BA, et al. Nature, 2010/02/18, Volume 463, Issue 7283, p.899-905, (2010) Read More / View Supplemental Materials
Abstract
A composite of multiple signals distinguishes causal variants in regions of positive selection.Grossman, SR, Shylakhter I., Karlsson EK, Byrne EH, Morales S., Frieden G., Hostetter E., Angelino E., Garber M., Zuk O., Lander E. S., Schaffner SF, and Sabeti PC Science (New York, N.Y.), 2010/02/12, Volume 327, Issue 5967, p.883-6, (2010) Read More / View Supplemental Materials
Abstract
CK1epsilon is required for breast cancers dependent on beta-catenin activity.Kim, SY, Dunn IF, Firestein R., Gupta P., Wardwell L., Repich K., Schinzel AC, Wittner B., Silver SJ, Root DE, Boehm JS, Ramaswamy S., Lander E. S., and Hahn WC PloS one, 2010/02/01, Volume 5, Issue 2, p.e8979, (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
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.Markljung, E., Jiang L., Jaffe JD, Mikkelsen TS, Wallerman O., Larhammar M., Zhang X., Wang L., Saenz-Vash V., Gnirke A., Lindroth AM, Barrés R., Yan J., Strömberg S., De S., Pontén F., Lander E. S., Carr SA, Zierath JR, Kullander K., et al. PLoS biology, 2009/12/01, Volume 7, Issue 12, p.e1000256, (2009) Read More / View Supplemental Materials
Abstract
Genome sequence, comparative analysis, and population genetics of the domestic horse.Wade, CM, Giulotto E., Sigurdsson S., Zoli M., Gnerre S., Imsland F., Lear TL, Adelson DL, Bailey E., Bellone RR, Blöcker H., Distl O., Edgar RC, Garber M., Leeb T., Mauceli E., MacLeod JN, Penedo MC, Raison JM, Sharpe T., et al. Science (New York, N.Y.), 2009/11/06, Volume 326, Issue 5954, p.865-7, (2009) Read More / View Supplemental Materials
Abstract
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.Barbie, DA, Tamayo P., Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P., Meylan E., Scholl C., Fröhling S., Chan EM, Sos ML, Michel K., Mermel C., Silver SJ, Weir BA, Reiling JH, Sheng Q., Gupta PB, et al. Nature, 2009/11/05, Volume 462, Issue 7269, p.108-12, (2009) Read More / View Supplemental Materials
Abstract
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Lieberman-Aiden, E., van Berkum NL, Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R., Bernstein B., Bender MA, Groudine M., Gnirke A., Stamatoyannopoulos J., Mirny LA, Lander E. S., and Dekker J. Science (New York, N.Y.), 2009/10/09, Volume 326, Issue 5950, p.289-93, (2009) Read More / View Supplemental Materials
Abstract
Identification of selective inhibitors of cancer stem cells by high-throughput screening.Gupta, PB, Onder TT, Jiang G., Tao K., Kuperwasser C., Weinberg R. A., and Lander E. S. Cell, 2009/08/21, Volume 138, Issue 4, p.645-59, (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
AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer.Vasudevan, KM, Barbie DA, Davies MA, Rabinovsky R., McNear CJ, Kim JJ, Hennessy BT, Tseng H., Pochanard P., Kim SY, Dunn IF, Schinzel AC, Sandy P., Hoersch S., Sheng Q., Gupta PB, Boehm JS, Reiling JH, Silver S., Lu Y., et al. Cancer cell, 2009/07/07, Volume 16, Issue 1, p.21-32, (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
Abstract
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.Gnirke, A., Melnikov A., Maguire J., Rogov P., LeProust EM, Brockman W., Fennell T., Giannoukos G., Fisher S., Russ C., Gabriel S., Jaffe DB, Lander E. S., and Nusbaum C. Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.182-9, (2009) Read More / View Supplemental Materials
Abstract
High-resolution mapping of copy-number alterations with massively parallel sequencing.Chiang, DY, Getz G., Jaffe DB, O'Kelly MJ, Zhao X., Carter SL, Russ C., Nusbaum C., Meyerson M., and Lander E. S. Nature methods, 2009/01/01, Volume 6, Issue 1, p.99-103, (2009) Read More / View Supplemental Materials
Abstract
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.Nusbaum, C., Ohsumi TK, Gomez J., Aquadro J., Victor TC, Warren RM, Hung DT, Birren BW, Lander E. S., and Jaffe DB Nature methods, 2009/01/01, Volume 6, Issue 1, p.67-9, (2009) Read More / View Supplemental Materials
Abstract
2008
Highly parallel identification of essential genes in cancer cells.Luo, B., Cheung HW, Subramanian A., Sharifnia T., Okamoto M., Yang X., Hinkle G., Boehm JS, Beroukhim R., Weir BA, Mermel C., Barbie DA, Awad T., Zhou X., Nguyen T., Piqani B., Li C., Golub T. R., Meyerson M., Hacohen N., et al. Proceedings of the National Academy of Sciences of the United States of America, 2008/12/23, Volume 105, Issue 51, p.20380-5, (2008) Read More / View Supplemental Materials
Abstract
Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis.Shao, H., Burrage LC, Sinasac DS, Hill AE, Ernest SR, O'Brien W., Courtland HW, Jepsen KJ, Kirby A., Kulbokas E. J., Daly M. J., Broman KW, Lander E. S., and Nadeau JH Proceedings of the National Academy of Sciences of the United States of America, 2008/12/16, Volume 105, Issue 50, p.19910-4, (2008) Read More / View Supplemental Materials
Abstract
Sequencing the nuclear genome of the extinct woolly mammoth.Miller, W., Drautz DI, Ratan A., Pusey B., Qi J., Lesk AM, Tomsho LP, Packard MD, Zhao F., Sher A., Tikhonov A., Raney B., Patterson N., Lindblad-Toh K., Lander E. S., Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S., et al. Nature, 2008/11/20, Volume 456, Issue 7220, p.387-90, (2008) Read More / View Supplemental Materials
Abstract
Genetic mapping in human disease.Altshuler, D., Daly M. J., and Lander E. S. Science (New York, N.Y.), 2008/11/07, Volume 322, Issue 5903, p.881-8, (2008) Read More / View Supplemental Materials
Abstract
Somatic mutations affect key pathways in lung adenocarcinoma.Ding, L., Getz G., Wheeler DA, Mardis ER, McLellan MD, Cibulskis K., Sougnez C., Greulich H., Muzny DM, Morgan MB, Fulton L., Fulton RS, Zhang Q., Wendl MC, Lawrence MS, Larson DE, Chen K., Dooling DJ, Sabo A., Hawes AC, et al. Nature, 2008/10/23, Volume 455, Issue 7216, p.1069-75, (2008) Read More / View Supplemental Materials
Abstract
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
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
Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways.Onder, TT, Gupta PB, Mani SA, Yang J., Lander E. S., and Weinberg R. A. Cancer research, 2008/05/15, Volume 68, Issue 10, p.3645-54, (2008) Read More / View Supplemental Materials
Abstract
ALLPATHS: de novo assembly of whole-genome shotgun microreads.Butler, J., Maccallum I., Kleber M., Shlyakhter IA, Belmonte MK, Lander E. S., Nusbaum C., and Jaffe DB Genome research, 2008/05/01, Volume 18, Issue 5, p.810-20, (2008) Read More / View Supplemental Materials
Abstract
Quality scores and SNP detection in sequencing-by-synthesis systems.Brockman, W., Alvarez P., Young S., Garber M., Giannoukos G., Lee WL, Russ C., Lander E. S., Nusbaum C., and Jaffe DB Genome research, 2008/05/01, Volume 18, Issue 5, p.763-70, (2008) Read More / View Supplemental Materials
Abstract
2007
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.Beroukhim, R., Getz G., Nghiemphu L., Barretina J., Hsueh T., Linhart D., Vivanco I., Lee JC, Huang JH, Alexander S., Du J., Kau T., Thomas RK, Shah K., Soto H., Perner S., Prensner J., Debiasi RM, Demichelis F., Hatton C., et al. Proceedings of the National Academy of Sciences of the United States of America, 2007/12/11, Volume 104, Issue 50, p.20007-12, (2007) Read More / View Supplemental Materials
Abstract
Characterizing the cancer genome in lung adenocarcinoma.Weir, BA, Woo MS, Getz G., Perner S., Ding L., Beroukhim R., Lin WM, Province MA, Kraja A., Johnson LA, Shah K., Sato M., Thomas RK, Barletta JA, Borecki IB, Broderick S., Chang AC, Chiang DY, Chirieac LR, Cho J., et al. Nature, 2007/12/06, Volume 450, Issue 7171, p.893-8, (2007) Read More / View Supplemental Materials
Abstract
Distinguishing protein-coding and noncoding genes in the human genome.Clamp, M., Fry B., Kamal M., Xie X., Cuff J., Lin MF, Kellis M., Lindblad-Toh K., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2007/12/04, Volume 104, Issue 49, p.19428-33, (2007) Read More / View Supplemental Materials
Abstract
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.Miller, W., Rosenbloom K., Hardison RC, Hou M., Taylor J., Raney B., Burhans R., King DC, Baertsch R., Blankenberg D., Kosakovsky Pond SL, Nekrutenko A., Giardine B., Harris RS, Tyekucheva S., Diekhans M., Pringle TH, Murphy WJ, Lesk A., Weinstock GM, et al. Genome research, 2007/12/01, Volume 17, Issue 12, p.1797-808, (2007) Read More / View Supplemental Materials
Abstract
Efficient mapping of mendelian traits in dogs through genome-wide association.Karlsson, EK, Baranowska I., Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N., Biagi TM, Patterson N., Pielberg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov J. P., von Euler H., Kämpe O., Hedhammar A., Lander E. S., Andersson G., Andersson L., and Lindblad-Toh K. Nature genetics, 2007/11/01, Volume 39, Issue 11, p.1321-8, (2007) Read More / View Supplemental Materials
Abstract
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