New Publications

Amplification of CRKL Induces Transformation and Epidermal Growth Factor Receptor Inhibitor Resistance in Human Non-Small Cell Lung Cancers.
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A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
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Expression of the p53 Target CDIP Correlates with Sensitivity to TNFα-Induced Apoptosis in Cancer Cells.
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Absolute quantification of somatic DNA alterations in human cancer.
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RNA-SeQC: RNA-seq metrics for quality control and process optimization.
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Scientific Publications

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2012

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Genome-wide detection and characterization of positive selection in human populations.Sabeti, PC, Varilly P., Fry B., Lohmueller J., Hostetter E., Cotsapas C., Xie X., Byrne EH, McCarroll SA, Gaudet R., Schaffner SF, Lander E. S., International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, et al. Nature, 2007/10/18, Volume 449, Issue 7164, p.913-8, (2007) Read More / View Supplemental Materials

Comment on "The consensus coding sequences of human breast and colorectal cancers".Getz, G., Höfling H., Mesirov J. P., Golub T. R., Meyerson M., Tibshirani R., and Lander E. S. Science (New York, N.Y.), 2007/09/14, Volume 317, Issue 5844, p.1500, (2007) Read More / View Supplemental Materials

Risk alleles for multiple sclerosis identified by a genomewide study.International Multiple Sclerosis Genetics, Consortium, Hafler DA, Compston A., Sawcer S., Lander E. S., Daly M. J., De Jager PL, de Bakker PI, Gabriel SB, Mirel DB, Ivinson AJ, Pericak-Vance MA, Gregory SG, Rioux JD, McCauley JL, Haines JL, Barcellos LF, Cree B., Oksenberg JR, and Hauser SL The New England journal of medicine, 2007/08/30, Volume 357, Issue 9, p.851-62, (2007) Read More / View Supplemental Materials

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

Integrative genomic approaches identify IKBKE as a breast cancer oncogene.Boehm, JS, Zhao JJ, Yao J., Kim SY, Firestein R., Dunn IF, Sjostrom SK, Garraway LA, Weremowicz S., Richardson AL, Greulich H., Stewart CJ, Mulvey LA, Shen RR, Ambrogio L., Hirozane-Kishikawa T., Hill DE, Vidal M., Meyerson M., Grenier JK, et al. Cell, 2007/06/15, Volume 129, Issue 6, p.1065-79, (2007) Read More / View Supplemental Materials

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.ENCODE Project, Consortium, Birney E., Stamatoyannopoulos JA, Dutta A., Guigó R., Gingeras TR, Margulies EH, Weng Z., Snyder M., Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S., Koch CM, Asthana S., Malhotra A., Adzhubei I., Greenbaum JA, Andrews RM, et al. Nature, 2007/06/14, Volume 447, Issue 7146, p.799-816, (2007) Read More / View Supplemental Materials

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.Margulies, EH, Cooper GM, Asimenos G., Thomas DJ, Dewey CN, Siepel A., Birney E., Keefe D., Schwartz AS, Hou M., Taylor J., Nikolaev S., Montoya-Burgos JI, Löytynoja A., Whelan S., Pardi F., Massingham T., Brown JB, Bickel P., Holmes I., et al. Genome research, 2007/06/01, Volume 17, Issue 6, p.760-74, (2007) Read More / View Supplemental Materials

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.Mikkelsen, TS, Wakefield MJ, Aken B., Amemiya CT, Chang JL, Duke S., Garber M., Gentles AJ, Goodstadt L., Heger A., Jurka J., Kamal M., Mauceli E., Searle SM, Sharpe T., Baker ML, Batzer MA, Benos PV, Belov K., Clamp M., et al. Nature, 2007/05/10, Volume 447, Issue 7141, p.167-77, (2007) Read More / View Supplemental Materials

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.Xie, X., Mikkelsen TS, Gnirke A., Lindblad-Toh K., Kellis M., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2007/04/24, Volume 104, Issue 17, p.7145-50, (2007) Read More / View Supplemental Materials

A second major histocompatibility complex susceptibility locus for multiple sclerosis.Yeo, TW, De Jager PL, Gregory SG, Barcellos LF, Walton A., Goris A., Fenoglio C., Ban M., Taylor CJ, Goodman RS, Walsh E., Wolfish CS, Horton R., Traherne J., Beck S., Trowsdale J., Caillier SJ, Ivinson AJ, Green T., Pobywajlo S., et al. Annals of neurology, 2007/03/01, Volume 61, Issue 3, p.228-36, (2007) Read More / View Supplemental Materials

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

Sleep-related epilepsy in the A/J mouse.Strohl, KP, Gallaugher L., Lynn A., Friedman L., Hill A., Singer JB, Lander E. S., and Nadeau J. Sleep, 2007/02/01, Volume 30, Issue 2, p.169-76, (2007) Read More / View Supplemental Materials

A genome-wide map of diversity in Plasmodium falciparum.Volkman, SK, Sabeti PC, DeCaprio D., Neafsey DE, Schaffner SF, Milner DA Jr, Daily JP, Sarr O., Ndiaye D., Ndir O., Mboup S., Duraisingh MT, Lukens A., Derr A., Stange-Thomann N., Waggoner S., Onofrio R., Ziaugra L., Mauceli E., Gnerre S., et al. Nature genetics, 2007/01/01, Volume 39, Issue 1, p.113-9, (2007) Read More / View Supplemental Materials

2006

A second fatty acid amide hydrolase with variable distribution among placental mammals.Wei, BQ, Mikkelsen TS, McKinney MK, Lander E. S., and Cravatt BF The Journal of biological chemistry, 2006/12/01, Volume 281, Issue 48, p.36569-78, (2006) Read More / View Supplemental Materials

Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.Bourlat, SJ, Juliusdottir T., Lowe CJ, Freeman R., Aronowicz J., Kirschner M., Lander E. S., Thorndyke M., Nakano H., Kohn AB, Heyland A., Moroz LL, Copley RR, and Telford MJ Nature, 2006/11/02, Volume 444, Issue 7115, p.85-8, (2006) Read More / View Supplemental Materials

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.Lamb, J., Crawford ED, Peck D., Modell JW, Blat IC, Wrobel MJ, Lerner J., Brunet JP, Subramanian A., Ross KN, Reich M., Hieronymus H., Wei G., Armstrong SA, Haggarty SJ, Clemons PA, Wei R., Carr SA, Lander E. S., and Golub T. R. Science (New York, N.Y.), 2006/09/29, Volume 313, Issue 5795, p.1929-35, (2006) Read More / View Supplemental Materials

Genome-scale loss-of-function screening with a lentiviral RNAi library.Root, DE, Hacohen N., Hahn WC, Lander E. S., and Sabatini DM Nature methods, 2006/09/01, Volume 3, Issue 9, p.715-9, (2006) Read More / View Supplemental Materials

A family of conserved noncoding elements derived from an ancient transposable element.Xie, X., Kamal M., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2006/08/01, Volume 103, Issue 31, p.11659-64, (2006) Read More / View Supplemental Materials

Genetic evidence for complex speciation of humans and chimpanzees.Patterson, N., Richter DJ, Gnerre S., Lander E. S., and Reich D. Nature, 2006/06/29, Volume 441, Issue 7097, p.1103-8, (2006) Read More / View Supplemental Materials

Positive natural selection in the human lineage.Sabeti, PC, Schaffner SF, Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen TS, Altshuler D., and Lander E. S. Science (New York, N.Y.), 2006/06/16, Volume 312, Issue 5780, p.1614-20, (2006) Read More / View Supplemental Materials

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

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.Zody, MC, Garber M., Adams DJ, Sharpe T., Harrow J., Lupski JR, Nicholson C., Searle SM, Wilming L., Young SK, Abouelleil A., Allen NR, Bi W., Bloom T., Borowsky ML, Bugalter BE, Butler J., Chang JL, Chen CK, Cook A., et al. Nature, 2006/04/20, Volume 440, Issue 7087, p.1045-9, (2006) Read More / View Supplemental Materials

Reactive oxygen species have a causal role in multiple forms of insulin resistance.Houstis, N., Rosen ED, and Lander E. S. Nature, 2006/04/13, Volume 440, Issue 7086, p.944-8, (2006) Read More / View Supplemental Materials

Identification and classification of conserved RNA secondary structures in the human genome.Pedersen, JS, Bejerano G., Siepel A., Rosenbloom K., Lindblad-Toh K., Lander E. S., Kent J., Miller W., and Haussler D. PLoS computational biology, 2006/04/01, Volume 2, Issue 4, p.e33, (2006) Read More / View Supplemental Materials

Analysis of the DNA sequence and duplication history of human chromosome 15.Zody, MC, Garber M., Sharpe T., Young SK, Rowen L., O'Neill K., Whittaker CA, Kamal M., Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Kodira CD, Madan A., Qin S., Yang X., Abbasi N., Abouelleil A., Arachchi HM, Baradarani L., et al. Nature, 2006/03/30, Volume 440, Issue 7084, p.671-5, (2006) Read More / View Supplemental Materials

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.Moffat, J., Grueneberg DA, Yang X., Kim SY, Kloepfer AM, Hinkle G., Piqani B., Eisenhaure TM, Luo B., Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N., Hahn WC, Lander E. S., Sabatini DM, and Root DE Cell, 2006/03/24, Volume 124, Issue 6, p.1283-98, (2006) Read More / View Supplemental Materials