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2016
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.Yassour, M., Vatanen T., Siljander H., Hämäläinen AM, Härkönen T., Ryhänen SJ, Franzosa EA, Vlamakis H., Huttenhower C., Gevers D., Lander E. S., Knip M., DIABIMMUNE Study Group, and Xavier RJ Science translational medicine, 2016/06/15, Volume 8, Issue 343, p.343ra81, (2016) Read More / View Supplemental Materials
Abstract
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector.Abudayyeh, OO, Gootenberg JS, Konermann S., Joung J., Slaymaker IM, Cox DB, Shmakov S., Makarova KS, Semenova E., Minakhin L., Severinov K., Regev A., Lander E. S., Koonin EV, and Zhang F. Science (New York, N.Y.), 2016/06/02, (2016) Read More / View Supplemental Materials
Abstract
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.Tewhey, R., Kotliar D., Park DS, Liu B., Winnicki S., Reilly SK, Andersen KG, Mikkelsen TS, Lander E. S., Schaffner SF, and Sabeti PC Cell, 2016/06/02, Volume 165, Issue 6, p.1519-29, (2016) Read More / View Supplemental Materials
Abstract
Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease.Blumenstiel, B., DeFelice M., Birsoy O., Bleyer AJ, Kmoch S., Carter TA, Gnirke A., Kidd K., Rehm HL, Ronco L., Lander E. S., Gabriel S., and Lennon NJ The Journal of molecular diagnostics : JMD, 2016/05/05, (2016) Read More / View Supplemental Materials
Abstract
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.Giannakis, M., Mu XJ, Shukla SA, Qian ZR, Cohen O., Nishihara R., Bahl S., Cao Y., Amin-Mansour A., Yamauchi M., Sukawa Y., Stewart C., Rosenberg M., Mima K., Inamura K., Nosho K., Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, et al. Cell reports, 2016/04/14, (2016) Read More / View Supplemental Materials
Abstract
Large-Scale Single Guide RNA Library Construction and Use for CRISPR-Cas9-Based Genetic Screens.Wang, T., Lander E. S., and Sabatini DM Cold Spring Harbor protocols, 2016/03/01, Volume 2016, Issue 3, p.pdb.top086892, (2016) Read More / View Supplemental Materials
Abstract
Single Guide RNA Library Design and Construction.Wang, T., Lander E. S., and Sabatini DM Cold Spring Harbor protocols, 2016/03/01, Volume 2016, Issue 3, p.pdb.prot090803, (2016) Read More / View Supplemental Materials
Abstract
Viral Packaging and Cell Culture for CRISPR-Based Screens.Wang, T., Lander E. S., and Sabatini DM Cold Spring Harbor protocols, 2016/03/01, Volume 2016, Issue 3, p.pdb.prot090811, (2016) Read More / View Supplemental Materials
Abstract
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.Yassour, M., Lim MY, Yun HS, Tickle TL, Sung J., Song YM, Lee K., Franzosa EA, Morgan XC, Gevers D., Lander E. S., Xavier RJ, Birren BW, Ko G., and Huttenhower C. Genome medicine, 2016/02/17, Volume 8, Issue 1, p.17, (2016) Read More / View Supplemental Materials
Abstract
The Heroes of CRISPR.Lander, E. S. Cell, 2016/01/14, Volume 164, Issue 1-2, p.18-28, (2016) Read More / View Supplemental Materials
Abstract
2015
Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution.Kasar, S., Kim J., Improgo R., Tiao G., Polak P., Haradhvala N., Lawrence MS, Kiezun A., Fernandes SM, Bahl S., Sougnez C., Gabriel S., Lander E. S., Kim HT, Getz G., and Brown JR Nature communications, 2015/12/07, Volume 6, p.8866, (2015) Read More / View Supplemental Materials
Abstract
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.Sanborn, AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D., Cutkosky A., Li J., Geeting KP, Gnirke A., Melnikov A., McKenna D., Stamenova EK, Lander E. S., and Aiden EL Proceedings of the National Academy of Sciences of the United States of America, 2015/10/23, (2015) Read More / View Supplemental Materials
Abstract
Mutations driving CLL and their evolution in progression and relapse.Landau, DA, Tausch E., Taylor-Weiner AN, Stewart C., Reiter JG, Bahlo J., Kluth S., Bozic I., Lawrence M., Böttcher S., Carter SL, Cibulskis K., Mertens D., Sougnez CL, Rosenberg M., Hess JM, Edelmann J., Kless S., Kneba M., Ritgen M., et al. Nature, 2015/10/22, Volume 526, Issue 7574, p.525-30, (2015) Read More / View Supplemental Materials
Abstract
Identification and characterization of essential genes in the human genome.Wang, T., Birsoy K., Hughes NW, Krupczak KM, Post Y., Wei JJ, Lander E. S., and Sabatini DM Science (New York, N.Y.), 2015/10/15, (2015) Read More / View Supplemental Materials
Abstract
Comprehensive assessment of cancer missense mutation clustering in protein structures.Kamburov, A., Lawrence MS, Polak P., Leshchiner I., Lage K., Golub T. R., Lander E. S., and Getz G. Proceedings of the National Academy of Sciences of the United States of America, 2015/10/06, Volume 112, Issue 40, p.E5486-95, (2015) Read More / View Supplemental Materials
Abstract
Reply to Lee: Downward bias in heritability estimation is not due to simplified linkage equilibrium SNP simulation.Golan, D., Rosset S., and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2015/09/28, (2015) Read More / View Supplemental Materials
Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets.Brastianos, PK, Carter SL, Santagata S., Cahill DP, Taylor-Weiner A., Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K., Ligon KL, Tabernero J., Seoane J., Martinez-Saez E., Curry WT, Dunn IF, Paek SH, Park SH, McKenna A., Chevalier A., et al. Cancer discovery, 2015/09/26, (2015) Read More / View Supplemental Materials
Abstract
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.Andersen, KG, Shapiro BJ, Matranga CB, Sealfon R., Lin AE, Moses LM, Folarin OA, Goba A., Odia I., Ehiane PE, Momoh M., England EM, Winnicki S., Branco LM, Gire SK, Phelan E., Tariyal R., Tewhey R., Omoniwa O., Fullah M., et al. Cell, 2015/08/13, Volume 162, Issue 4, p.738-50, (2015) Read More / View Supplemental Materials
Abstract
Paired exome analysis of Barrett's esophagus and adenocarcinoma.Stachler, MD, Taylor-Weiner A., Peng S., McKenna A., Loda M., Stewart C., Stojanov P., Seepo S., Lawrence MS, Lin J., Chang AC, Gabriel SB, Lander E. S., Beer DG, Getz G., Carter SL, and Bass AJ Nature genetics, 2015/07/20, (2015) Read More / View Supplemental Materials
Abstract
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
Brave New Genome.Lander, E. S. The New England journal of medicine, 2015/06/03, (2015) Read More / View Supplemental Materials
Abstract
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.McHugh, CA, Chen CK, Chow A., Surka CF, Tran C., McDonel P., Pandya-Jones A., Blanco M., Burghard C., Moradian A., Sweredoski MJ, Shishkin AA, Su J., Lander E. S., Hess S., Plath K., and Guttman M. Nature, 2015/04/27, (2015) Read More / View Supplemental Materials
Abstract
Cutting the Gordian Helix - Regulating Genomic Testing in the Era of Precision Medicine.Lander, E. S. The New England journal of medicine, 2015/02/17, (2015) Read More / View Supplemental Materials
Abstract
Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution.Im, HK, Zheng S., Amini SS, Virk SM, Mikkelsen T., Brat DJ, Grimsby J., Sougnez C., Muller F., Hu J., Sloan AE, Cohen ML, Van Meir EG, Scarpace L., Laird PW, Weinstein J. N., Lander E. S., Gabriel S., Getz G., Meyerson M., et al. Genome research, 2015/02/03, (2015) Read More / View Supplemental Materials
Abstract
Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers.Tonomura, N., Elvers I., Thomas R., Megquier K., Turner-Maier J., Howald C., Sarver AL, Swofford R., Frantz AM, Ito D., Mauceli E., Arendt M., Noh HJ, Koltookian M., Biagi T., Fryc S., Williams C., Avery AC, Kim JH, Barber L., et al. PLoS genetics, 2015/02/01, Volume 11, Issue 2, p.e1004922, (2015) Read More / View Supplemental Materials
Abstract
Systematic Cell-Based Phenotyping of Missense Alleles Empowers Rare Variant Association Studies: A Case for LDLR and Myocardial Infarction.Thormaehlen, AS, Schuberth C., Won HH, Blattmann P., Joggerst-Thomalla B., Theiss S., Asselta R., Duga S., Merlini PA, Ardissino D., Lander E. S., Gabriel S., Rader DJ, Peloso GM, Pepperkok R., Kathiresan S., and Runz H. PLoS genetics, 2015/02/01, Volume 11, Issue 2, p.e1004855, (2015) Read More / View Supplemental Materials
Abstract
RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin.Engreitz, J., Lander E. S., and Guttman M. Methods in molecular biology (Clifton, N.J.), 2015/01/01, Volume 1262, p.183-97, (2015) Read More / View Supplemental Materials
Abstract
2014
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.Perry, JA, Kiezun A., Tonzi P., Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E., Pedamallu CS, Helman E., Taylor-Weiner A., McKenna A., Deluca DS, Lawrence MS, Ambrogio L., Sougnez C., Sivachenko A., Walensky LD, Wagle N., et al. Proceedings of the National Academy of Sciences of the United States of America, 2014/12/15, (2014) Read More / View Supplemental Materials
Abstract
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.Rao, SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I., Omer AD, Lander E. S., and Aiden EL Cell, 2014/12/11, (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
Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence.Genovese, G., Kähler AK, Handsaker RE, Lindberg J., Rose SA, Bakhoum SF, Chambert K., Mick E., Neale BM, Fromer M., Purcell SM, Svantesson O., Landén M., Höglund M., Lehmann S., Gabriel SB, Moran JL, Lander E. S., Sullivan PF, Sklar P., et al. The New England journal of medicine, 2014/11/26, (2014) Read More / View Supplemental Materials
Abstract
Measuring missing heritability: Inferring the contribution of common variants.Golan, D., Lander E. S., and Rosset S. Proceedings of the National Academy of Sciences of the United States of America, 2014/11/24, (2014) Read More / View Supplemental Materials
Abstract
RNF43 is frequently mutated in colorectal and endometrial cancers.Giannakis, M., Hodis E., Jasmine Mu X., Yamauchi M., Rosenbluh J., Cibulskis K., Saksena G., Lawrence MS, Qian ZR, Nishihara R., Allen EM, Hahn WC, Gabriel SB, Lander E. S., Getz G., Ogino S., Fuchs CS, and Garraway LA Nature genetics, 2014/10/26, (2014) Read More / View Supplemental Materials
Abstract
Comprehensive variation discovery in single human genomes.Weisenfeld, NI, Yin S., Sharpe T., Lau B., Hegarty R., Holmes L., Sogoloff B., Tabbaa D., Williams L., Russ C., Nusbaum C., Lander E. S., Maccallum I., and Jaffe DB Nature genetics, 2014/10/19, (2014) Read More / View Supplemental Materials
Abstract
RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites.Engreitz, JM, Sirokman K., McDonel P., Shishkin AA, Surka C., Russell P., Grossman SR, Chow AY, Guttman M., and Lander E. S. Cell, 2014/09/25, Volume 159, Issue 1, p.188-99, (2014) Read More / View Supplemental Materials
Abstract
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.Gire, SK, Goba A., Andersen KG, Sealfon RS, Park DJ, Kanneh L., Jalloh S., Momoh M., Fullah M., Dudas G., Wohl S., Moses LM, Yozwiak NL, Winnicki S., Matranga CB, Malboeuf CM, Qu J., Gladden AD, Schaffner SF, Yang X., et al. Science (New York, N.Y.), 2014/09/12, Volume 345, Issue 6202, p.1369-72, (2014) Read More / View Supplemental Materials
Abstract
Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA.Schwartz, S., Bernstein DA, Mumbach MR, Jovanovic M., Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M., Satija R., Lander E. S., Fink G., and Regev A. Cell, 2014/09/10, (2014) Read More / View Supplemental Materials
Abstract
The genomic substrate for adaptive radiation in African cichlid fish.Brawand, D., Wagner CE, Li YI, Malinsky M., Keller I., Fan S., Simakov O., Ng AY, Lim ZW, Bezault E., Turner-Maier J., Johnson J., Alcazar R., Noh HJ, Russell P., Aken B., Alföldi J., Amemiya C., Azzouzi N., Baroiller JF, et al. Nature, 2014/09/03, (2014) Read More / View Supplemental Materials
Abstract
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.Carneiro, M., Rubin CJ, Di Palma F., Albert FW, Alföldi J., Barrio AM, Pielberg G., Rafati N., Sayyab S., Turner-Maier J., Younis S., Afonso S., Aken B., Alves JM, Barrell D., Bolet G., Boucher S., Burbano HA, Campos R., Chang JL, et al. Science (New York, N.Y.), 2014/08/29, Volume 345, Issue 6200, p.1074-9, (2014) Read More / View Supplemental Materials
Abstract
Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites.Schwartz, S., Mumbach MR, Jovanovic M., Wang T., Maciag K., Bushkin GG, Mertins P., Ter-Ovanesyan D., Habib N., Cacchiarelli D., Sanjana NE, Freinkman E., Pacold ME, Satija R., Mikkelsen TS, Hacohen N., Zhang F., Carr SA, Lander E. S., and Regev A. Cell reports, 2014/06/25, (2014) Read More / View Supplemental Materials
Abstract
Altered translation of GATA1 in Diamond-Blackfan anemia.Ludwig, LS, Gazda HT, Eng JC, Eichhorn SW, Thiru P., Ghazvinian R., George TI, Gotlib JR, Beggs AH, Sieff CA, Lodish HF, Lander E. S., and Sankaran VG Nature medicine, 2014/06/22, (2014) Read More / View Supplemental Materials
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Development and Applications of CRISPR-Cas9 for Genome Engineering.Hsu, PD, Lander E. S., and Zhang F. Cell, 2014/06/05, Volume 157, Issue 6, p.1262-1278, (2014) Read More / View Supplemental Materials
Abstract
Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.Rajasagi, M., Shukla SA, Fritsch EF, Keskin DB, Deluca D., Carmona E., Zhang W., Sougnez C., Cibulskis K., Sidney J., Stevenson K., Ritz J., Neuberg D., Brusic V., Gabriel S., Lander E. S., Getz G., Hacohen N., and Wu CJ Blood, 2014/06/02, (2014) Read More / View Supplemental Materials
Abstract
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.Van Allen, EM, Wagle N., Stojanov P., Perrin DL, Cibulskis K., Marlow S., Jane-Valbuena J., Friedrich DC, Kryukov G., Carter SL, McKenna A., Sivachenko A., Rosenberg M., Kiezun A., Voet D., Lawrence M., Lichtenstein LT, Gentry JG, Huang FW, Fostel J., et al. Nature medicine, 2014/06/01, Volume 20, Issue 6, p.682-8, (2014) Read More / View Supplemental Materials
Abstract
Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib.Wagle, N., Grabiner BC, Van Allen EM, Hodis E., Jacobus S., Choueiri TK, Gandhi L., Taplin ME, Stack EC, Signoretti S., Loda M., Shapiro GI, Sabatini DM, Lander E. S., Gabriel SB, Kantoff PW, Garraway LA, and Rosenberg JE Cancer discovery, 2014/03/27, (2014) Read More / View Supplemental Materials
Abstract
A polygenic burden of rare disruptive mutations in schizophrenia.Purcell, SM, Moran JL, Fromer M., Ruderfer D., Solovieff N., Roussos P., O'Dushlaine C., Chambert K., Bergen SE, Kähler A., Duncan L., Stahl E., Genovese G., Fernández E., Collins MO, Komiyama NH, Choudhary JS, Magnusson PK, Banks E., Shakir K., et al. Nature, 2014/02/13, Volume 506, Issue 7487, p.185-90, (2014) Read More / View Supplemental Materials
Abstract
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.Hacisuleyman, E., Goff LA, Trapnell C., Williams A., Henao-Mejia J., Sun L., McClanahan P., Hendrickson DG, Sauvageau M., Kelley DR, Morse M., Engreitz J., Lander E. S., Guttman M., Lodish HF, Flavell R., Raj A., and Rinn JL Nature structural & molecular biology, 2014/02/01, Volume 21, Issue 2, p.198-206, (2014) Read More / View Supplemental Materials
Abstract
Searching for missing heritability: Designing rare variant association studies.Zuk, O., Schaffner SF, Samocha K., Do R., Hechter E., Kathiresan S., Daly M. J., Neale BM, Sunyaev SR, and Lander E. S. Proceedings of the National Academy of Sciences of the United States of America, 2014/01/28, Volume 111, Issue 4, p.E455-64, (2014) Read More / View Supplemental Materials
Abstract
Discovery and saturation analysis of cancer genes across 21 tumour types.Lawrence, MS, Stojanov P., Mermel CH, Robinson JT, Garraway LA, Golub T. R., Meyerson M., Gabriel SB, Lander E. S., and Getz G. Nature, 2014/01/05, (2014) Read More / View Supplemental Materials
Abstract
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.Hoeppner, MP, Lundquist A., Pirun M., Meadows JR, Zamani N., Johnson J., Sundström G., Cook A., FitzGerald MG, Swofford R., Mauceli E., Moghadam BT, Greka A., Alföldi J., Abouelleil A., Aftuck L., Bessette D., Berlin A., Brown A., Gearin G., et al. PloS one, 2014/01/01, Volume 9, Issue 3, p.e91172, (2014) Read More / View Supplemental Materials
Abstract
2013
Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B.Karlsson, EK, Sigurdsson S., Ivansson E., Thomas R., Elvers I., Wright J., Howald C., Tonomura N., Perloski M., Swofford R., Biagi T., Fryc S., Anderson N., Courtay-Cahen C., Youell L., Ricketts SL, Mandlebaum S., Rivera P., von Euler H., Kisseberth WC, et al. Genome biology, 2013/12/12, Volume 14, Issue 12, p.R132, (2013) Read More / View Supplemental Materials
Abstract
High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.Schwartz, S., Agarwala SD, Mumbach MR, Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen TS, Satija R., Ruvkun G., Carr SA, Lander E. S., Fink GR, and Regev A. Cell, 2013/12/05, Volume 155, Issue 6, p.1409-21, (2013) Read More / View Supplemental Materials
Abstract
The Cancer Genome Atlas Pan-Cancer analysis project.Cancer Genome Atlas Research, Network, Genome Characterization Center, Chang K., Creighton CJ, Davis C., Donehower L., Drummond J., Wheeler D., Ally A., Balasundaram M., Birol I., Butterfield YS, Chu A., Chuah E., Chun HJ, Dhalla N., Guin R., Hirst M., Hirst C., Holt RA, et al. Nature genetics, 2013/09/26, Volume 45, Issue 10, p.1113-20, (2013) Read More / View Supplemental Materials
Mutational heterogeneity in cancer and the search for new cancer-associated genes.Lawrence, MS, Stojanov P., Polak P., Kryukov GV, Cibulskis K., Sivachenko A., Carter SL, Stewart C., Mermel CH, Roberts SA, Kiezun A., Hammerman PS, McKenna A., Drier Y., Zou L., Ramos AH, Pugh TJ, Stransky N., Helman E., Kim J., et al. Nature, 2013/07/11, Volume 499, Issue 7457, p.214-8, (2013) Read More / View Supplemental Materials
Abstract
The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome.Engreitz, JM, Pandya-Jones A., McDonel P., Shishkin A., Sirokman K., Surka C., Kadri S., Xing J., Goren A., Lander E. S., Plath K., and Guttman M. Science (New York, N.Y.), 2013/07/04, (2013) Read More / View Supplemental Materials
Abstract
Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins.Guttman, M., Russell P., Ingolia NT, Weissman JS, and Lander E. S. Cell, 2013/07/03, Volume 154, Issue 1, p.240-51, (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
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
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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
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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, McKenna A., Pedamallu CS, Ramos AH, Shefler E., Sivachenko A., Sougnez C., Stewart C., Ally A., 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., Sivachenko A., Sougnez C., Auclair D., Lawrence MS, Stojanov P., Cibulskis K., Sharifnia T., Greulich H., Banerji S., Zander T., Thompson K., Winckler W., Kwiatkowski D., 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
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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
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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
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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
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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
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
Abstract
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
Abstract
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
Abstract
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
Abstract
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