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2013
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.Desjardins, CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J., Ribeiro JM, Saif S., Levin JZ, Fan L., Zeng Q., Russ C., Wortman JR, Fink DL, Birren BW, and Nutman TB Nature genetics, 2013/04/26, Volume 45, Issue 5, p.495-500, (2013) Read More / View Supplemental Materials
Abstract
2012
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?Haas, BJ, Chin M., Nusbaum C., Birren BW, and Livny J. BMC genomics, 2012/12/27, Volume 13, p.734, (2012) Read More / View Supplemental Materials
Abstract
Whole Genome Pyrosequencing of Rare Hepatitis C Virus Genotypes Enhances Subtype Classification and Identification of Naturally Occurring Drug Resistance Variants.Newman, RM, Kuntzen T., Weiner B., Berical A., Charlebois P., Kuiken C., Murphy DG, Simmonds P., Bennett P., Lennon NJ, Birren BW, Zody MC, Allen TM, and Henn MR The Journal of infectious diseases, 2012/11/06, (2012) Read More / View Supplemental Materials
Abstract
The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum.Neafsey, DE, Galinsky K., Jiang RH, Young L., Sykes SM, Saif S., Gujja S., Goldberg JM, Young S., Zeng Q., Chapman SB, Dash AP, Anvikar AR, Sutton PL, Birren BW, Escalante AA, Barnwell JW, and Carlton JM Nature genetics, 2012/09/01, Volume 44, Issue 9, p.1046-50, (2012) Read More / View Supplemental Materials
Abstract
The human microbiome project: a community resource for the healthy human microbiome.Gevers, D., Knight R., Petrosino JF, Huang K., McGuire AL, Birren BW, Nelson KE, White O., Methé BA, and Huttenhower C. PLoS biology, 2012/08/01, Volume 10, Issue 8, p.e1001377, (2012) Read More / View Supplemental Materials
Abstract
Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.Macalalad, AR, Zody MC, Charlebois P., Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, and Henn MR PLoS computational biology, 2012/03/01, Volume 8, Issue 3, p.e1002417, (2012) Read More / View Supplemental Materials
Abstract
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection.Henn, MR, Boutwell CL, Charlebois P., Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S., Zody MC, Erlich RL, Green LM, Berical A., Wang Y., Casali M., Streeck H., Bloom AK, Dudek T., Tully D., et al. PLoS pathogens, 2012/03/01, Volume 8, Issue 3, p.e1002529, (2012) Read More / View Supplemental Materials
Abstract
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.Grad, YH, Lipsitch M., Feldgarden M., Arachchi HM, Cerqueira GC, FitzGerald M., Godfrey P., Haas BJ, Murphy CI, Russ C., Sykes S., Walker BJ, Wortman JR, Young S., Zeng Q., Abouelleil A., Bochicchio J., Chauvin S., Desmet T., Gujja S., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/02/21, Volume 109, Issue 8, p.3065-70, (2012) Read More / View Supplemental Materials
Abstract
The fungal genome initiative and lessons learned from genome sequencing.Cuomo, CA, and Birren BW Methods in enzymology, 2012/01/09, Volume 470, p.833-55, (2012) Read More / View Supplemental Materials
Abstract
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.Neafsey, DE, Schaffner SF, Volkman SK, Park D., Montgomery P., Milner DA Jr, Lukens A., Rosen D., Daniels R., Houde N., Cortese JF, Tyndall E., Gates C., Stange-Thomann N., Sarr O., Ndiaye D., Ndir O., Mboup S., Ferreira MU, Moraes Sdo L., et al. Genome biology, 2012/01/07, Volume 9, Issue 12, p.R171, (2012) Read More / View Supplemental Materials
Abstract
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.D'Souza, CA, Kronstad JW, Taylor G., Warren R., Yuen M., Hu G., Jung WH, Sham A., Kidd SE, Tangen K., Lee N., Zeilmaker T., Sawkins J., McVicker G., Shah S., Gnerre S., Griggs A., Zeng Q., Bartlett K., Li W., et al. mBio, 2012/01/06, Volume 2, Issue 1, p.e00342-10, (2012) Read More / View Supplemental Materials
Abstract
Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection.Martinez, DA, Oliver BG, Gräser Y., Goldberg JM, Li W., Martinez-Rossi NM, Monod M., Shelest E., Barton RC, Birch E., Brakhage AA, Chen Z., Gurr SJ, Heiman D., Heitman J., Kosti I., Rossi A., Saif S., Samalova M., Saunders CW, et al. mBio, 2012/01/01, Volume 3, Issue 5, (2012) Read More / View Supplemental Materials
Abstract
High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.Thai, KT, Henn MR, Zody MC, Tricou V., Nguyet NM, Charlebois P., Lennon NJ, Green L., de Vries PJ, Hien TT, Farrar J., van Doorn HR, de Jong MD, Birren BW, Holmes EC, and Simmons CP Journal of virology, 2012/01/01, Volume 86, Issue 2, p.835-43, (2012) Read More / View Supplemental Materials
Abstract
2011
Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.Ohainle, M., Balmaseda A., Macalalad AR, Tellez Y., Zody MC, Saborío S., Nuñez A., Lennon NJ, Birren BW, Gordon A., Henn MR, and Harris E. Science translational medicine, 2011/12/21, Volume 3, Issue 114, p.114ra128, (2011) Read More / View Supplemental Materials
Abstract
A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation.Schmidt, DJ, Pickett BE, Camacho D., Comach G., Xhaja K., Lennon NJ, Rizzolo K., de Bosch N., Becerra A., Nogueira ML, Mondini A., da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R., Gehrke L., Lefkowitz EJ, Birren BW, Henn MR, et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2011/12/01, Volume 11, Issue 8, p.2011-9, (2011) Read More / View Supplemental Materials
Abstract
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.Kostic, AD, Gevers D., Pedamallu CS, Michaud M., Duke F., Earl AM, Ojesina AI, Jung J., Bass AJ, Tabernero J., Baselga J., Liu C., Shivdasani RA, Ogino S., Birren BW, Huttenhower C., Garrett WS, and Meyerson M. Genome research, 2011/10/18, (2011) Read More / View Supplemental Materials
Abstract
Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis.Desjardins, CA, Champion MD, Holder JW, Muszewska A., Goldberg J., Bailão AM, Brigido MM, Ferreira ME, Garcia AM, Grynberg M., Gujja S., Heiman DI, Henn MR, Kodira CD, León-Narváez H., Longo LV, Ma LJ, Malavazi I., Matsuo AL, Morais FV, et al. PLoS genetics, 2011/10/01, Volume 7, Issue 10, p.e1002345, (2011) Read More / View Supplemental Materials
Abstract
Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development.Holder, JW, Ulrich JC, DeBono AC, Godfrey PA, Desjardins CA, Zucker J., Zeng Q., Leach AL, Ghiviriga I., Dancel C., Abeel T., Gevers D., Kodira CD, Desany B., Affourtit JP, Birren BW, and Sinskey AJ PLoS genetics, 2011/09/01, Volume 7, Issue 9, p.e1002219, (2011) Read More / View Supplemental Materials
Abstract
Molecular evolution of West Nile virus in a northern temperate region: Connecticut, USA 1999-2008.Armstrong, PM, Vossbrinck CR, Andreadis TG, Anderson JF, Pesko KN, Newman RM, Lennon NJ, Birren BW, Ebel GD, and Henn MR Virology, 2011/08/15, Volume 417, Issue 1, p.203-10, (2011) Read More / View Supplemental Materials
Abstract
Hybrid selection for sequencing pathogen genomes from clinical samples.Melnikov, A., Galinsky K., Rogov P., Fennell T., Van Tyne D., Russ C., Daniels R., Barnes KG, Bochicchio J., Ndiaye D., Sene PD, Wirth DF, Nusbaum C., Volkman SK, Birren BW, Gnirke A., and Neafsey DE Genome biology, 2011/08/11, Volume 12, Issue 8, p.R73, (2011) Read More / View Supplemental Materials
Abstract
Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.Duong, V., Simmons C., Gavotte L., Viari A., Ong S., Chantha N., Lennon NJ, Birren BW, Vong S., Farrar JJ, Henn MR, Deubel V., Frutos R., and Buchy P. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2011/07/02, (2011) Read More / View Supplemental Materials
Abstract
Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.Raghwani, J., Rambaut A., Holmes EC, Hang VT, Hien TT, Farrar J., Wills B., Lennon NJ, Birren BW, Henn MR, and Simmons CP PLoS pathogens, 2011/06/01, Volume 7, Issue 6, p.e1002064, (2011) Read More / View Supplemental Materials
Abstract
Full-length transcriptome assembly from RNA-Seq data without a reference genome.Grabherr, MG, Haas BJ, Yassour M., Levin JZ, Thompson DA, Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Di Palma F., Birren BW, Nusbaum C., Lindblad-Toh K., Friedman N., et al. Nature biotechnology, 2011/05/15, Volume 29, Issue 7, p.644-52, (2011) Read More / View Supplemental Materials
Abstract
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.Yilmaz, P., Kottmann R., Field D., Knight R., Cole JR, Amaral-Zettler L., Gilbert JA, Karsch-Mizrachi I., Johnston A., Cochrane G., Vaughan R., Hunter C., Park J., Morrison N., Rocca-Serra P., Sterk P., Arumugam M., Bailey M., Baumgartner L., Birren BW, et al. Nature biotechnology, 2011/05/01, Volume 29, Issue 5, p.415-20, (2011) Read More / View Supplemental Materials
Abstract
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
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.Haas, BJ, Gevers D., Earl AM, Feldgarden M., Ward DV, Giannoukos G., Ciulla D., Tabbaa D., Highlander SK, Sodergren E., Methé B., DeSantis TZ, Human Microbiome Consortium, Petrosino JF, Knight R., and Birren BW Genome research, 2011/03/01, Volume 21, Issue 3, p.494-504, (2011) Read More / View Supplemental Materials
Abstract
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes.Yu, Q., Ryan EM, Allen TM, Birren BW, Henn MR, and Lennon NJ Bioinformatics (Oxford, England), 2011/01/15, Volume 27, Issue 2, p.266-7, (2011) Read More / View Supplemental Materials
Abstract
Endurance, refuge, and reemergence of dengue virus type 2, Puerto Rico, 1986-2007.McElroy, KL, Santiago GA, Lennon NJ, Birren BW, Henn MR, and Muñoz-Jordán JL Emerging infectious diseases, 2011/01/01, Volume 17, Issue 1, p.64-71, (2011) Read More / View Supplemental Materials
Abstract
2010
The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults.Hoang, LT, Lynn DJ, Henn M., Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT, Mai LN, Farrar JJ, Hibberd ML, and Simmons CP Journal of virology, 2010/12/01, Volume 84, Issue 24, p.12982-94, (2010) Read More / View Supplemental Materials
Abstract
Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia.Vu, TT, Holmes EC, Duong V., Nguyen TQ, Tran TH, Quail M., Churcher C., Parkhill J., Cardosa J., Farrar J., Wills B., Lennon NJ, Birren BW, Buchy P., Henn MR, and Simmons CP PLoS neglected tropical diseases, 2010/07/20, Volume 4, Issue 7, p.e757, (2010) Read More / View Supplemental Materials
Abstract
Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control.Neafsey, DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E., Hung CY, McMahan C., White J., Sykes S., Heiman D., Young S., Zeng Q., Abouelleil A., Aftuck L., Bessette D., Brown A., FitzGerald M., Lui A., Macdonald JP, et al. Genome research, 2010/07/01, Volume 20, Issue 7, p.938-46, (2010) Read More / View Supplemental Materials
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A catalog of reference genomes from the human microbiome.Human Microbiome Jumpstart Reference Strains, Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M., Sodergren E., Chinwalla AT, Feldgarden M., Gevers D., Haas BJ, Madupu R., Ward DV, Birren BW, Gibbs RA, Methe B., Petrosino JF, et al. Science (New York, N.Y.), 2010/05/21, Volume 328, Issue 5981, p.994-9, (2010) Read More / View Supplemental Materials
Abstract
Analysis of high-throughput sequencing and annotation strategies for phage genomes.Henn, MR, Sullivan MB, Stange-Thomann N., Osburne MS, Berlin AM, Kelly L., Yandava C., Kodira C., Zeng Q., Weiand M., Sparrow T., Saif S., Giannoukos G., Young SK, Nusbaum C., Birren BW, and Chisholm SW PloS one, 2010/02/05, Volume 5, Issue 2, p.e9083, (2010) Read More / View Supplemental Materials
Abstract
2009
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.Ma, LJ, Ibrahim AS, Skory C., Grabherr MG, Burger G., Butler M., Elias M., Idnurm A., Lang BF, Sone T., Abe A., Calvo SE, Corrochano LM, Engels R., Fu J., Hansberg W., Kim JM, Kodira CD, Koehrsen MJ, Liu B., et al. PLoS genetics, 2009/07/01, Volume 5, Issue 7, p.e1000549, (2009) Read More / View Supplemental Materials
Abstract
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.Nusbaum, C., Ohsumi TK, Gomez J., Aquadro J., Victor TC, Warren RM, Hung DT, Birren BW, Lander E. S., and Jaffe DB Nature methods, 2009/01/01, Volume 6, Issue 1, p.67-9, (2009) Read More / View Supplemental Materials
Abstract
2008
Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients.Kuntzen, T., Timm J., Berical A., Lennon N., Berlin AM, Young SK, Lee B., Heckerman D., Carlson J., Reyor LL, Kleyman M., McMahon CM, Birch C., Schulze Zur Wiesch J., Ledlie T., Koehrsen M., Kodira C., Roberts AD, Lauer GM, Rosen HR, et al. Hepatology (Baltimore, Md.), 2008/12/01, Volume 48, Issue 6, p.1769-78, (2008) Read More / View Supplemental Materials
Abstract
A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame.Kuntzen, T., Berical A., Ndjomou J., Bennett P., Schneidewind A., Lennon N., Birren BW, Kuiken C., Henn MR, Simmonds P., and Allen TM Journal of medical virology, 2008/08/01, Volume 80, Issue 8, p.1370-8, (2008) Read More / View Supplemental Materials
Abstract
2007
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
Abstract
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.Cuomo, CA, Güldener U., Xu JR, Trail F., Turgeon BG, Di Pietro A., Walton JD, Ma LJ, Baker SE, Rep M., Adam G., Antoniw J., Baldwin T., Calvo S., Chang YL, DeCaprio D., Gale LR, Gnerre S., Goswami RS, Hammond-Kosack K., et al. Science (New York, N.Y.), 2007/09/07, Volume 317, Issue 5843, p.1400-2, (2007) Read More / View Supplemental Materials
Abstract
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
Abstract
2006
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
Abstract
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
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Human chromosome 11 DNA sequence and analysis including novel gene identification.Taylor, TD, Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., Lloyd C., Itoh T., Takeda T., Kim DW, She X., Barlow KF, Bloom T., Bruford E., Chang JL, Cuomo CA, Eichler E., FitzGerald MG, Jaffe DB, LaButti K., et al. Nature, 2006/03/23, Volume 440, Issue 7083, p.497-500, (2006) Read More / View Supplemental Materials
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DNA sequence and analysis of human chromosome 8.Nusbaum, C., Mikkelsen TS, Zody MC, Asakawa S., Taudien S., Garber M., Kodira CD, Schueler MG, Shimizu A., Whittaker CA, Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Yang X., Allen NR, Anderson S., Asakawa T., Blechschmidt K., Bloom T., et al. Nature, 2006/01/19, Volume 439, Issue 7074, p.331-5, (2006) Read More / View Supplemental Materials
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2005
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.Galagan, JE, Calvo SE, Cuomo C., Ma LJ, Wortman JR, Batzoglou S., Lee SI, Baştürkmen M., Spevak CC, Clutterbuck J., Kapitonov V., Jurka J., Scazzocchio C., Farman M., Butler J., Purcell S., Harris S., Braus GH, Draht O., Busch S., et al. Nature, 2005/12/22, Volume 438, Issue 7071, p.1105-15, (2005) Read More / View Supplemental Materials
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DNA sequence and analysis of human chromosome 18.Nusbaum, C., Zody MC, Borowsky ML, Kamal M., Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K., FitzGerald MG, Yang X., Abouelleil A., Allen NR, Anderson S., Bloom T., Bugalter B., Butler J., Cook A., DeCaprio D., et al. Nature, 2005/09/22, Volume 437, Issue 7058, p.551-5, (2005) Read More / View Supplemental Materials
Abstract
2004
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Kellis, M., Birren BW, and Lander E. S. Nature, 2004/04/08, Volume 428, Issue 6983, p.617-24, (2004) Read More / View Supplemental Materials
Abstract
  • Showing 1-47 of 47 Results