Now showing items 21-40 of 49

    • Genome-Wide SNP Genotyping Highlights the Role of Natural Selection in Plasmodium Falciparum Population Divergence 

      Wirth, Dyann F.; Sabeti, Pardis C.; Lander, Eric S.; Birren, Bruce W.; Hartl, Daniel; Wiegand, Roger; Chitnis, Chetan E.; Dash, Aditya P.; do Lago Moraes, Sandra; Ferreira, Marcelo U.; Mboup, Soulyemane; Ndir, Omar; Ndiaye, Daouda; Ousmane, Sarr; Stange-Thomann, Nicole; Gates, Casey; Tyndall, Erin; Cortese, Joseph F.; Houde, Nathan; Daniels, Rachel; Rosen, David; Lukens, Amanda; Milner, Danny; Montgomery, Philip; Park, Daniel; Volkman, Sarah K.; Schaffner, Stephen F.; Neafsey, Daniel (BioMed Central, 2008)
      Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun ...
    • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

      Rheinbay, Esther; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Nusbaum, Chad; Xie, Xiaohui; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Koseki, Haruhiko; van Steensel, Bas; Ku, Manching; Koche, Richard Patrick; Mendenhall, Eric M; Presser, Aviva; Chi, Andrew S.; Cowan, Chad A.; Lander, Eric Steven; Bernstein, Bradley E. (Public Library of Science, 2008)
      In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...
    • Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 

      Grad, Yonatan Hagai; Lipsitch, Marc; Feldgarden, M.; Arachchi, H. M.; Cerqueira, G. C.; Fitzgerald, Michael L.; Godfrey, P.; Haas, Brandon Russell; Murphy, C. I.; Russ, C.; Sykes, Sean; Walker, B. J.; Wortman, J. R.; Young, Sarah; Zeng, Q.; Abouelleil, A.; Bochicchio, J.; Chauvin, S.; DeSmet, T.; Gujja, S.; Mccowan, Caryn Alissa; Montmayeur, A.; Steelman, S.; Frimodt-Moller, J.; Petersen, A. M.; Struve, C.; Krogfelt, K. A.; Bingen, E.; Weill, F.-X.; Lander, Eric Steven; Nusbaum, C.; Birren, B. W.; Hung, Deborah Tan; Hanage, William P. (Proceedings of the National Academy of Sciences, 2012)
      The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia ...
    • The genomic substrate for adaptive radiation in African cichlid fish 

      Brawand, David; Wagner, Catherine E.; Li, Yang I.; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y.; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L.; Conte, Matthew A.; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F.; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S.; Haerty, Wilfried; Harris, Rayna M.; Hofmann, Hans A.; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B.; Lara, Marcia; Lee, Alison P.; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J.; Przybylski, Dariusz; Rakotomanga, Michaelle; Renn, Suzy C. P.; Ribeiro, Filipe J.; Ron, Micha; Salzburger, Walter; Sanchez-Pulido, Luis; Santos, M. Emilia; Searle, Steve; Sharpe, Ted; Swofford, Ross; Tan, Frederick J.; Williams, Louise; Young, Sarah; Yin, Shuangye; Okada, Norihiro; Kocher, Thomas D.; Miska, Eric A.; Lander, Eric S.; Venkatesh, Byrappa; Fernald, Russell D.; Meyer, Axel; Ponting, Chris P.; Streelman, J. Todd; Lindblad-Toh, Kerstin; Seehausen, Ole; Di Palma, Federica (2014)
      Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes ...
    • Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak 

      Gire, Stephen; Goba, A.; Andersen, Kristian G; Sealfon, R. S. G.; Park, D. J.; Kanneh, L.; Jalloh, S.; Momoh, M.; Fullah, M.; Dudas, G.; Wohl, Shirlee; Moses, L. M.; Yozwiak, Nathan; Winnicki, Sarah M.; Matranga, C. B.; Malboeuf, C. M.; Qu, J.; Gladden, Adrianne Deanna; Schaffner, Stephen; Yang, X.; Jiang, P.-P.; Nekoui, M.; Colubri, Andres; Coomber, M. R.; Fonnie, M.; Moigboi, A.; Gbakie, M.; Kamara, F. K.; Tucker, V.; Konuwa, E.; Saffa, S.; Sellu, J.; Jalloh, A. A.; Kovoma, A.; Koninga, J.; Mustapha, I.; Kargbo, K.; Foday, M.; Yillah, M.; Kanneh, F.; Robert, W.; Massally, J. L. B.; Chapman, S. B.; Bochicchio, J.; Murphy, C.; Nusbaum, C.; Young, S.; Birren, B. W.; Grant, D. S.; Scheiffelin, J. S.; Lander, Eric Steven; Happi, Christian Tientcha; Gevao, S. M.; Gnirke, A.; Rambaut, A.; Garry, R. F.; Khan, S. H.; Sabeti, Pardis Christine (American Association for the Advancement of Science (AAAS), 2014)
      In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid ...
    • Identification and Classification of Conserved RNA Secondary Structures in the Human Genome 

      Pedersen, Jakob Skou; Bejerano, Gill; Siepel, Adam; Rosenbloom, Kate; Lindblad-Toh, Kerstin; Lander, Eric Steven; Kent, Jim; Webb, Miller; Haussler, David (Public Library of Science, 2006)
      The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative ...
    • Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum 

      Van Tyne, Daria Natalie; Park, Daniel John; Schaffner, Stephen; Neafsey, Daniel Edward; Angelino, Elaine Lee; Cortese, Joseph F.; Barnes, Kayla G.; Rosen, David M.; Lukens, Amanda Kathleen; Daniels, Rachel Fath; Milner, Danny Arnold; Johnson, Charles A.; Shlyakhter, Ilya; Grossman, Sharon Rachel; Becker, Justin S.; Yamins, Daniel Louis Kanef; Karlsson, Elinor Kathryn; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Happi, Christian Tientcha; Furlotte, Nicholas A.; Eskin, Eleazar; Kang, Hyun Min; Hartl, Daniel L.; Birren, Bruce W.; Wiegand, Roger C.; Lander, Eric Steven; Wirth, Dyann Fergus; Cooke, Sarah Volkman; Sabeti, Pardis Christine (Public Library of Science, 2011)
      The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis ...
    • Identification of a Selective Small Molecule Inhibitor of Breast Cancer Stem Cells 

      Germain, Andrew R.; Carmody, Leigh C.; Morgan, Barbara; Fernandez, Cristina; Forbeck, Erin; Lewis, Timothy A.; Nag, Partha P.; Ting, Amal; VerPlank, Lynn; Feng, Yuxiong; Perez, Jose R.; Dandapani, Sivaraman; Palmer, Michelle; Lander, Eric Steven; Gupta, Piyush B.; Schreiber, Stuart L.; Munoz, Benito (Elsevier BV, 2012)
      A high-throughput screen (HTS) with the National Institute of Health–Molecular Libraries Small Molecule Repository (NIH–MLSMR) compound collection identified a class of acyl hydrazones to be selectively lethal to breast ...
    • Identifying Recent Adaptations in Large-Scale Genomic Data 

      Grossman, Shamai Aaron; Andersen, Kristian G; Shlyakhter, Ilya; Tabrizi, Shervin; Winnicki, Sarah M.; Yen, Angela; Park, Daniel J.; Griesemer, Dustin Shahab; Karlsson, Elinor Kathryn; Wong, Sunny H.; Cabili, Moran; Adegbola, Richard A.; Bamezai, Rameshwar N.K.; Hill, Adrian V.S.; Vannberg, Fredrik O.; Rinn, John L; Lander, Eric Steven; Schaffner, Stephen; Sabeti, Pardis Christine (Elsevier BV, 2013)
      Summary: Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from ...
    • An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts 

      Hoeppner, Marc P.; Lundquist, Andrew; Pirun, Mono; Meadows, Jennifer R. S.; Zamani, Neda; Johnson, Jeremy; Sundström, Görel; Cook, April; FitzGerald, Michael G.; Swofford, Ross; Mauceli, Evan; Moghadam, Behrooz Torabi; Greka, Anna; Alföldi, Jessica; Abouelleil, Amr; Aftuck, Lynne; Bessette, Daniel; Berlin, Aaron; Brown, Adam; Gearin, Gary; Lui, Annie; Macdonald, J. Pendexter; Priest, Margaret; Shea, Terrance; Turner-Maier, Jason; Zimmer, Andrew; Lander, Eric S.; di Palma, Federica; Lindblad-Toh, Kerstin; Grabherr, Manfred G. (Public Library of Science, 2014)
      The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the ...
    • Large-Scale Chemical–genetics Yields New M. Tuberculosis Inhibitor Classes 

      LaVerriere, Emily; Meyer, Elisabeth; Kawate, Tomohiko; Gomez, James; Gardner, Michelle; Cigarroa Kennedy, Sofia; Wakabayashi, Shoko; Watson, Christopher; Fitzgerald, Michael; Johnson, Eachan; Office, Emma; Stanley, Mary; Audette, Rebecca; Bandyopadhyay, Nirmalya; Betancourt, Natalia; Delano, Kayla; Da Silva, Israel; Davis, Joshua; Gallo, Christina; Golas, Aaron; Guinn, Kristine; Korn, Rebecca; McConnell, Jennifer; Moss, Caitlin; Murphy, Kenan; Nietupski, Raymond; Papavinasasundaram, Kadamba; Pinkham, Jessica; Pino, Paula; Proulx, Megan; Ruecker, Nadine; Song, Naomi; Thompson, Matthew; Trujillo, Carolina; Metcalf-Wallach, Joshua; Ioerger, Thomas; Lander, Eric; Hubbard, Brian; Serrano-Wu, Michael; Ehrt, Sabine; Rubin, Eric; Sassetti, Christopher; Schnappinger, Dirk; Hung, Deborah (Springer Science and Business Media LLC, 2019-06-19)
      New antibiotics are needed to combat rising resistance, with new Mycobacterium tuberculosis (Mtb) drugs of highest priority. Conventional whole-cell and biochemical antibiotic screens have failed. We developed a novel ...
    • Local regulation of gene expression by lncRNA promoters, transcription and splicing 

      Engreitz, Jesse M.; Haines, Jenna E.; Perez, Elizabeth M.; Munson, Glen; Chen, Jenny; Kane, Michael; McDonel, Patrick E.; Guttman, Mitchell; Lander, Eric Steven (Springer Nature, 2016)
      Mammalian genomes are pervasively transcribed1, to produce thousands of long non-coding RNAs (lncRNAs). A few of these lncRNAs have been shown to recruit regulatory complexes through RNA–protein interactions to influence ...
    • A Map of Human Genome Variation from Population Scale Sequencing 

      Altshuler, David Matthew; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Lee, Charles; Mills, Ryan Edward; Shi, Xinghua; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; Nemesh, James C.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya (Nature Publishing Group, 2010)
      The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...
    • Mapping Copy Number Variation by Population Scale Genome Sequencing 

      Mills, Ryan Edward; Handsaker, Robert E; Korn, Joshua; Nemesh, James; Shi, Xinghua; Lee, Charles; McCarroll, Steven A.; Altshuler, David Matthew; Gabriel, Stacey B.; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya; DePristo, Mark A.; Wilkinson, Jane (Nature Publishing Group, 2011)
      Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of ...
    • Melanoma genome sequencing reveals frequent PREX2 mutations 

      Berger, Michael F.; Hodis, Eran; Heffernan, Timothy P.; Deribe, Yonathan Lissanu; Lawrence, Michael S.; Protopopov, Alexei; Ivanova, Elena; Watson, Ian R.; Nickerson, Elizabeth; Ghosh, Papia; Zhang, Hailei; Zeid, Rhamy; Ren, Xiaojia; Cibulskis, Kristian; Sivachenko, Andrey Y.; Wagle, Nikhil; Sucker, Antje; Sougnez, Carrie; Onofrio, Robert; Ambrogio, Lauren; Auclair, Daniel; Fennell, Timothy; Carter, Scott L.; Drier, Yotam; Stojanov, Petar; Singer, Meredith A.; Voet, Douglas; Jing, Rui; Saksena, Gordon; Barretina, Jordi; Ramos, Alex H.; Pugh, Trevor J.; Stransky, Nicolas; Parkin, Melissa; Winckler, Wendy; Mahan, Scott; Ardlie, Kristin; Baldwin, Jennifer; Wargo, Jennifer; Schadendorf, Dirk; Meyerson, Matthew; Gabriel, Stacey B.; Golub, Todd R.; Wagner, Stephan N.; Lander, Eric S.; Getz, Gad; Chin, Lynda; Garraway, Levi A. (2012)
      Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life1. To obtain a comprehensive genomic view of melanoma, we sequenced the ...
    • Mutational heterogeneity in cancer and the search for new cancer genes 

      Lawrence, Michael S.; Stojanov, Petar; Polak, Paz; Kryukov, Gregory V.; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Stewart, Chip; Mermel, Craig H.; Roberts, Steven A.; Kiezun, Adam; Hammerman, Peter S.; McKenna, Aaron; Drier, Yotam; Zou, Lihua; Ramos, Alex H.; Pugh, Trevor J.; Stransky, Nicolas; Helman, Elena; Kim, Jaegil; Sougnez, Carrie; Ambrogio, Lauren; Nickerson, Elizabeth; Shefler, Erica; Cortés, Maria L.; Auclair, Daniel; Saksena, Gordon; Voet, Douglas; Noble, Michael; DiCara, Daniel; Lin, Pei; Lichtenstein, Lee; Heiman, David I.; Fennell, Timothy; Imielinski, Marcin; Hernandez, Bryan; Hodis, Eran; Baca, Sylvan; Dulak, Austin M.; Lohr, Jens; Landau, Dan-Avi; Wu, Catherine J.; Melendez-Zajgla, Jorge; Hidalgo-Miranda, Alfredo; Koren, Amnon; McCarroll, Steven A.; Mora, Jaume; Crompton, Brian; Onofrio, Robert; Parkin, Melissa; Winckler, Wendy; Ardlie, Kristin; Gabriel, Stacey B.; Roberts, Charles W. M.; Biegel, Jaclyn A.; Stegmaier, Kimberly; Bass, Adam J.; Garraway, Levi A.; Meyerson, Matthew; Golub, Todd R.; Gordenin, Dmitry A.; Sunyaev, Shamil; Lander, Eric S.; Getz, Gad (2014)
      Major international projects are now underway aimed at creating a comprehensive catalog of all genes responsible for the initiation and progression of cancer. These studies involve sequencing of matched tumor–normal samples ...
    • Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing 

      Kirby, Andrew; Gnirke, Andreas; Jaffe, David B.; Barešová, Veronika; Pochet, Nathalie; Blumenstiel, Brendan; Ye, Chun; Aird, Daniel; Stevens, Christine; Robinson, James T.; Cabili, Moran N.; Gat-Viks, Irit; Kelliher, Edward; Daza, Riza; DeFelice, Matthew; Hůlková, Helena; Sovová, Jana; Vylet’al, Petr; Antignac, Corinne; Guttman, Mitchell; Handsaker, Robert E.; Perrin, Danielle; Steelman, Scott; Sigurdsson, Snaevar; Scheinman, Steven J.; Sougnez, Carrie; Cibulskis, Kristian; Parkin, Melissa; Green, Todd; Rossin, Elizabeth; Zody, Michael C.; Xavier, Ramnik J.; Pollak, Martin R.; Alper, Seth L.; Lindblad-Toh, Kerstin; Gabriel, Stacey; Hart, P. Suzanne; Regev, Aviv; Nusbaum, Chad; Kmoch, Stanislav; Bleyer, Anthony J.; Lander, Eric S.; Daly, Mark J. (2014)
      While genetic lesions responsible for some Mendelian disorders can be rapidly discovered through massively parallel sequencing (MPS) of whole genomes or exomes, not all diseases readily yield to such efforts. We describe ...
    • De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds 

      Dudchenko, Olga; Batra, Sanjit S.; Omer, Arina D.; Nyquist, Sarah K.; Hoeger, Marie; Durand, Neva C.; Shamim, Muhammad S.; Machol, Ido; Lander, Eric Steven; Aiden, Aviva; Aiden, Erez Lieberman (American Association for the Advancement of Science (AAAS), 2017)
      The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft ...
    • The SARS-CoV-2 RNA–protein Interactome in Infected Human Cells 

      Schmidt, Nora; Lareau, Caleb; Keshishian, Hasmik; Ganskih, Sabina; Schneider, Cornelius; Hennig, Thomas; Melanson, Randy; Werner, Simone; Wei, Yuanjie; Zimmer, Matthias; Ade, Jens; Kirschner, Luisa; Zielinski, Sebastian; Dölken, Lars; Lander, Eric; Caliskan, Neva; Fischer, Utz; Vogel, Jörg; Carr, Steven A.; Bodem, Jochen; Munschauer, Mathias (Springer Science and Business Media LLC, 2020-12-21)
      Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense ...
    • A Second Major Histocompatibility Complex Susceptibility Locus for Multiple Sclerosis 

      Yeo, Tai Wai; Gregory, Simon G; Barcellos, Lisa F; Walton, Amie; Goris, An; Fenoglio, Chiara; Ban, Maria; Taylor, Craig J; Goodman, Reyna S; Walsh, Emily; Wolfish, Cara S; Horton, Roger; Traherne, James; Beck, Stephan; Trowsdale, John; Caillier, Stacy J; Green, Todd; Pobywajlo, Susan; Pericak-Vance, Margaret A; Haines, Jonathan L; Oksenberg, Jorge R; Hauser, Stephen L; Compston, Alastair; Rioux, John D; Sawcer, Stephen; De Jager, Philip Lawrence; Ivinson, Adrian J.; Lander, Eric Steven; Daly, Mark Joseph; Hafler, David A. (Wiley Subscription Services, Inc., A Wiley Company, 2007)
      Objective: Variation in the major histocompatibility complex (MHC) on chromosome 6p21 is known to influence susceptibility to multiple sclerosis with the strongest effect originating from the HLA-DRB1 gene in the class II ...