Publications from the MSC, GSCID and GCID

2015

Evolution and Spread of Ebola Virus in Liberia, 2014-2015.Ladner, JT, Wiley MR, Mate S., Dudas G., Prieto K., Lovett S., Nagle ER, Beitzel B., Gilbert ML, Fakoli L., Diclaro JW 2nd, Schoepp RJ, Fair J., Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A., Sanchez-Lockhart M., Bolay FK, et al. Cell host & microbe, 2015/12/09, Volume 18, Issue 6, p.659-69, (2015) Read More / View Supplemental Materials
Abstract
50 Years of Emmonsia Disease in Humans: The Dramatic Emergence of a Cluster of Novel Fungal Pathogens.Schwartz, IS, Kenyon C., Feng P., Govender NP, Dukik K., Sigler L., Jiang Y., Stielow JB, Muñoz JF, Cuomo CA, Botha A., Stchigel AM, and de Hoog GS PLoS pathogens, 2015/11/01, Volume 11, Issue 11, p.e1005198, (2015) Read More / View Supplemental Materials
Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine.Neafsey, DE, Juraska M., Bedford T., Benkeser D., Valim C., Griggs A., Lievens M., Abdulla S., Adjei S., Agbenyega T., Agnandji ST, Aide P., Anderson S., Ansong D., Aponte JJ, Asante KP, Bejon P., Birkett AJ, Bruls M., Connolly KM, et al. The New England journal of medicine, 2015/10/21, (2015) Read More / View Supplemental Materials
Abstract
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.Muñoz, JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J., Sullivan TD, Marty AJ, Carmen JC, Chen Z., Ding L., Gujja S., Magrini V., Misas E., Mitreva M., Priest M., Saif S., Whiston EA, Young S., Zeng Q., Goldman WE, et al. PLoS genetics, 2015/10/01, Volume 11, Issue 10, p.e1005493, (2015) Read More / View Supplemental Materials
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Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt.Pelleau, S., Moss EL, Dhingra SK, Volney B., Casteras J., Gabryszewski SJ, Volkman SK, Wirth DF, Legrand E., Fidock DA, Neafsey DE, and Musset L. Proceedings of the National Academy of Sciences of the United States of America, 2015/09/15, Volume 112, Issue 37, p.11672-7, (2015) Read More / View Supplemental Materials
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Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.Cohen, KA, Abeel T., Manson McGuire A., Desjardins CA, Munsamy V., Shea TP, Walker BJ, Bantubani N., Almeida DV, Alvarado L., Chapman SB, Mvelase NR, Duffy EY, FitzGerald MG, Govender P., Gujja S., Hamilton S., Howarth C., Larimer JD, Maharaj K., et al. PLoS medicine, 2015/09/01, Volume 12, Issue 9, p.e1001880, (2015) Read More / View Supplemental Materials
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Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.Farrer, RA, Desjardins CA, Sakthikumar S., Gujja S., Saif S., Zeng Q., Chen Y., Voelz K., Heitman J., May RC, Fisher MC, and Cuomo CA mBio, 2015/09/01, Volume 6, Issue 5, (2015) Read More / View Supplemental Materials
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Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells.Sefik, E., Geva-Zatorsky N., Oh S., Konnikova L., Zemmour D., McGuire AM, Burzyn D., Ortiz-Lopez A., Lobera M., Yang J., Ghosh S., Earl A., Snapper SB, Jupp R., Kasper D., Mathis D., and Benoist C. Science (New York, N.Y.), 2015/08/13, (2015) Read More / View Supplemental Materials
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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
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Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.Woo, YH, Ansari H., Otto TD, Klinger CM, Kolisko M., Michálek J., Saxena A., Shanmugam D., Tayyrov A., Veluchamy A., Ali S., Bernal A., del Campo J., Cihlář J., Gornik SG, Hajdušková E., Horák A., Janouškovec J., Katris NJ, Mast FD, et al. eLife, 2015/07/15, Volume 4, p.e06974, (2015) Read More / View Supplemental Materials
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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.Park, DJ, Dudas G., Wohl S., Goba A., Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J., Gire SK, Jalloh S., Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Gbakie M., et al. Cell, 2015/06/18, Volume 161, Issue 7, p.1516-26, (2015) Read More / View Supplemental Materials
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Fatal nosocomial MDR TB identified through routine genetic analysis and whole-genome sequencing.Williams, OM, Abeel T., Casali N., Cohen K., Pym AS, Mungall SB, Desjardins CA, Banerjee A., Drobniewski F., Earl AM, and Cooke GS Emerging infectious diseases, 2015/06/01, Volume 21, Issue 6, p.1082-4, (2015) Read More / View Supplemental Materials
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.Desjardins, CA, Sanscrainte ND, Goldberg JM, Heiman D., Young S., Zeng Q., Madhani HD, Becnel JJ, and Cuomo CA Nature communications, 2015/05/13, Volume 6, p.7121, (2015) Read More / View Supplemental Materials
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16S community profiling identifies proton pump inhibitor related differences in gastric, lung, and oropharyngeal microflora.Rosen, R., Hu L., Amirault J., Khatwa U., Ward DV, and Onderdonk A. The Journal of pediatrics, 2015/04/01, Volume 166, Issue 4, p.917-23, (2015) Read More / View Supplemental Materials
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Genetic and phenotypic intra-species variation in Candida albicans.Hirakawa, MP, Martinez DA, Sakthikumar S., Anderson MZ, Berlin A., Gujja S., Zeng Q., Zisson E., Wang JM, Greenberg JM, Berman J., Bennett RJ, and Cuomo CA Genome research, 2015/03/01, Volume 25, Issue 3, p.413-25, (2015) Read More / View Supplemental Materials
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Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa.Stremlau, MH, Andersen KG, Folarin OA, Grove JN, Odia I., Ehiane PE, Omoniwa O., Omoregie O., Jiang PP, Yozwiak NL, Matranga CB, Yang X., Gire SK, Winnicki S., Tariyal R., Schaffner SF, Okokhere PO, Okogbenin S., Akpede GO, Asogun DA, et al. PLoS neglected tropical diseases, 2015/03/01, Volume 9, Issue 3, p.e0003631, (2015) Read More / View Supplemental Materials
Abstract
Data sharing: Make outbreak research open access.Yozwiak, NL, Schaffner SF, and Sabeti PC Nature, 2015/02/26, Volume 518, Issue 7540, p.477-9, (2015) Read More / View Supplemental Materials
GB virus C coinfections in west African Ebola patients.Lauck, M., Bailey AL, Andersen KG, and Sabeti PC Journal of virology, 2015/02/01, Volume 89, Issue 4, p.2425-9, (2015) Read More / View Supplemental Materials
Abstract
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.Sizova, MV, Chilaka A., Earl AM, Doerfert SN, Muller PA, Torralba M., McCorrison JM, Durkin AS, Nelson KE, and Epstein SS Standards in genomic sciences, 2015/01/01, Volume 10, p.37, (2015) Read More / View Supplemental Materials
Abstract
Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants.Taft, DH, Ambalavanan N., Schibler KR, Yu Z., Newburg DS, Deshmukh H., Ward DV, and Morrow AL PloS one, 2015/01/01, Volume 10, Issue 6, p.e0130604, (2015) Read More / View Supplemental Materials
Abstract

2014

Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis.Muñoz, JF, Gallo JE, Misas E., Priest M., Imamovic A., Young S., Zeng Q., Clay OK, McEwen JG, and Cuomo CA PLoS neglected tropical diseases, 2014/12/01, Volume 8, Issue 12, p.e3348, (2014) Read More / View Supplemental Materials
Abstract
Clinical illness and outcomes in patients with Ebola in Sierra Leone.Schieffelin, JS, Shaffer JG, Goba A., Gbakie M., Gire SK, Colubri A., Sealfon RS, Kanneh L., Moigboi A., Momoh M., Fullah M., Moses LM, Brown BL, Andersen KG, Winnicki S., Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D., et al. The New England journal of medicine, 2014/11/27, Volume 371, Issue 22, p.2092-100, (2014) Read More / View Supplemental Materials
Abstract
Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster.Valentino, MD, McGuire AM, Earl AM, and Gilmore MS Nature communications, 2014/11/12, Volume 5, p.5411, (2014) Read More / View Supplemental Materials
Abstract
Evolution of invasion in a diverse set of fusobacterium species.Manson McGuire, A., Cochrane K., Griggs AD, Haas BJ, Abeel T., Zeng Q., Birren BW, Allen-Vercoe E., and Earl AM mBio, 2014/11/04, Volume 5, Issue 6, (2014) Read More / View Supplemental Materials
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The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences.Touchon, M., Yoon EJ, Krizova L., Cerqueira GC, Murphy C., Feldgarden M., Wortman J., Clermont D., Lambert T., Grillot-Courvalin C., Nemec A., and Courvalin P. Genome biology and evolution, 2014/10/13, Volume 6, Issue 10, p.2866-82, (2014) Read More / View Supplemental Materials
Abstract
Genome Sequence of the Microsporidian Species Nematocida sp1 Strain ERTm6 (ATCC PRA-372).Bakowski, MA, Priest M., Young S., Cuomo CA, and Troemel ER Genome announcements, 2014/09/18, Volume 2, Issue 5, (2014) Read More / View Supplemental Materials
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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
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Draft genome sequences of six enterohepatic helicobacter species isolated from humans and one from rhesus macaques.Shen, Z., Sheh A., Young SK, Abouelliel A., Ward DV, Earl AM, and Fox JG Genome announcements, 2014/09/11, Volume 2, Issue 5, (2014) Read More / View Supplemental Materials
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Selection of unique Escherichia coli clones by random amplified polymorphic DNA (RAPD): Evaluation by whole genome sequencing.Nielsen, KL, Godfrey PA, Stegger M., and Feldgarden M. Journal of microbiological methods, 2014/08/01, Volume 103, p.101-3, (2014) Read More / View Supplemental Materials
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Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.Sizova, MV, Muller PA, Stancyk D., Panikov NS, Mandalakis M., Hazen A., Hohmann T., Doerfert SN, Fowle W., Earl AM, Nelson KE, and Epstein SS International journal of systematic and evolutionary microbiology, 2014/08/01, Volume 64, Issue Pt 8, p.2642-9, (2014) Read More / View Supplemental Materials
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Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter.Greenwood, C., Morrow AL, Lagomarcino AJ, Altaye M., Taft DH, Yu Z., Newburg DS, Ward DV, and Schibler KR The Journal of pediatrics, 2014/07/01, Volume 165, Issue 1, p.23-9, (2014) Read More / View Supplemental Materials
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Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut.Coyne, MJ, Zitomersky NL, McGuire AM, Earl AM, and Comstock LE mBio, 2014/06/17, Volume 5, Issue 3, (2014) Read More / View Supplemental Materials
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Relating the metatranscriptome and metagenome of the human gut.Franzosa, EA, Morgan XC, Segata N., Waldron L., Reyes J., Earl AM, Giannoukos G., Ciulla D., Gevers D., Izard J., Garrett WS, Chan AT, and Huttenhower C. Proceedings of the National Academy of Sciences of the United States of America, 2014/06/03, Volume 111, Issue 22, p.E2329-38, (2014) Read More / View Supplemental Materials
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Ubiquitin-mediated response to microsporidia and virus infection in C. elegans.Bakowski, MA, Desjardins CA, Smelkinson MG, Dunbar TL, Lopez-Moyado IF, Rifkin SA, Cuomo CA, and Troemel ER PLoS pathogens, 2014/06/01, Volume 10, Issue 6, p.e1004200, (2014) Read More / View Supplemental Materials
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Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.Janbon, G., Ormerod KL, Paulet D., Byrnes EJ 3rd, Yadav V., Chatterjee G., Mullapudi N., Hon CC, Billmyre RB, Brunel F., Bahn YS, Chen W., Chen Y., Goldberg J., Gujja S., Jones S., Kodira CD, Marra M., Mieczkowski PA, Schein JE, et al. PLoS genetics, 2014/04/01, Volume 10, Issue 4, p.e1004261, (2014) Read More / View Supplemental Materials
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Staphylococcal enterotoxin P predicts bacteremia in hospitalized patients colonized with methicillin-resistant Staphylococcus aureus.Calderwood, MS, Desjardins CA, Sakoulas G., Nicol R., Cosimi LA, Feldgarden M., Onderdonk AB, Birren BW, Platt R., Huang SS, and CDC Prevention Epicenters Program The Journal of infectious diseases, 2014/02/15, Volume 209, Issue 4, p.571-7, (2014) Read More / View Supplemental Materials
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Intestinal microbiota of preterm infants differ over time and between hospitals.Taft, DH, Ambalavanan N., Schibler KR, Yu Z., Newburg DS, Ward DV, and Morrow AL Microbiome, 2014/01/01, Volume 2, p.36, (2014) Read More / View Supplemental Materials
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Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.Walker, BJ, Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo CA, Zeng Q., Wortman J., Young SK, and Earl AM PloS one, 2014/01/01, Volume 9, Issue 11, p.e112963, (2014) Read More / View Supplemental Materials
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16S rRNA gene survey of microbial communities in Winogradsky columns.Ward, DV, and Birren B. PloS one, 2014/01/01, Volume 9, Issue 8, p.e104134, (2014) Read More / View Supplemental Materials
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Identification of 50 class D β-lactamases and 65 Acinetobacter-derived cephalosporinases in Acinetobacter spp.Périchon, B., Goussard S., Walewski V., Krizova L., Cerqueira G., Murphy C., Feldgarden M., Wortman J., Clermont D., Nemec A., and Courvalin P. Antimicrobial agents and chemotherapy, 2014/01/01, Volume 58, Issue 2, p.936-49, (2014) Read More / View Supplemental Materials
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Standardized metadata for human pathogen/vector genomic sequences.Dugan, VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I., Ward DV, Yao A., Zheng J., Barrett T., Birren B., Brinkac L., Bruno VM, Caler E., Chapman S., et al. PloS one, 2014/01/01, Volume 9, Issue 6, p.e99979, (2014) Read More / View Supplemental Materials
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Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.Matranga, CB, Andersen KG, Winnicki S., Busby M., Gladden AD, Tewhey R., Stremlau M., Berlin A., Gire SK, England E., Moses LM, Mikkelsen TS, Odia I., Ehiane PE, Folarin O., Goba A., Kahn SH, Grant DS, Honko A., Hensley L., et al. Genome biology, 2014/01/01, Volume 15, Issue 11, p.519, (2014) Read More / View Supplemental Materials
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2013

High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides.Lebreton, F., Valentino MD, Duncan LB, Zeng Q., Manson McGuire A., Earl AM, and Gilmore MS Genome announcements, 2013/12/26, Volume 1, Issue 6, (2013) Read More / View Supplemental Materials
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Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato.Van der Auwera, GA, Feldgarden M., Kolter R., and Mahillon J. Genome announcements, 2013/10/03, Volume 1, Issue 5, (2013) Read More / View Supplemental Materials
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Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains.Lebreton, F., McGuire AM, Godfrey P., Griggs A., Cheng L., Saif S., Young S., Zeng Q., Wortman J., Birren B., Earl AM, and Gilmore MS mBio, 2013/08/20, Volume 4, Issue 4, (2013) Read More / View Supplemental Materials
Abstract
Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling.Marty, AJ, Wüthrich M., Carmen JC, Sullivan TD, Klein BS, Cuomo CA, and Gauthier GM Fungal genetics and biology : FG & B, 2013/07/01, Volume 56, p.1-8, (2013) Read More / View Supplemental Materials
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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, 2013/05/01, Volume 45, Issue 5, p.495-500, (2013) Read More / View Supplemental Materials
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Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.Pombert, JF, Xu J., Smith DR, Heiman D., Young S., Cuomo CA, Weiss LM, and Keeling PJ Eukaryotic cell, 2013/04/01, Volume 12, Issue 4, p.503-11, (2013) Read More / View Supplemental Materials
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Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.Malboeuf, CM, Yang X., Charlebois P., Qu J., Berlin AM, Casali M., Pesko KN, Boutwell CL, Devincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, and Levin JZ Nucleic acids research, 2013/01/07, Volume 41, Issue 1, p.e13, (2013) Read More / View Supplemental Materials
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Identification of the mating-type (MAT) locus that controls sexual reproduction of Blastomyces dermatitidis.Li, W., Sullivan TD, Walton E., Averette AF, Sakthikumar S., Cuomo CA, Klein BS, and Heitman J. Eukaryotic cell, 2013/01/01, Volume 12, Issue 1, p.109-17, (2013) Read More / View Supplemental Materials
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Evolutionary dynamics of the accessory genome of Listeria monocytogenes.den Bakker, HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q., Young SK, Kodira CD, Yandava C., Hepburn TA, Haas BJ, Birren BW, and Wiedmann M. PloS one, 2013/01/01, Volume 8, Issue 6, p.e67511, (2013) Read More / View Supplemental Materials
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2012

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.Cuomo, CA, Desjardins CA, Bakowski MA, Goldberg J., Ma AT, Becnel JJ, Didier ES, Fan L., Heiman DI, Levin JZ, Young S., Zeng Q., and Troemel ER Genome research, 2012/12/01, Volume 22, Issue 12, p.2478-88, (2012) Read More / View Supplemental Materials
Abstract
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
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, 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
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Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus.McAdam, PR, Templeton KE, Edwards GF, Holden MT, Feil EJ, Aanensen DM, Spratt BG, Parkhill J., Godfrey PA, Feldgarden M., Rambaut A., and Robinson DA Proceedings of the National Academy of Sciences of the United States of America, 2012/06/05, Volume 109, Issue 23, p.9107-12, (2012) Read More / View Supplemental Materials
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Draft genome sequences of Staphylococcus aureus sequence type 34 (ST34) and ST42 hybrids.Thomas, JC, Godfrey PA, Feldgarden M., and Robinson DA Journal of bacteriology, 2012/05/01, Volume 194, Issue 10, p.2740-1, (2012) Read More / View Supplemental Materials
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Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.McGuire, AM, Weiner B., Park ST, Wapinski I., Raman S., Dolganov G., Peterson M., Zucker J., Abeel T., White J., Sisk P., Stolte C., Koehrsen M., Yamamoto RT, Iacobelli-Martinez M., Kidd MJ, Maer AM, Schoolnik GK, Regev A., and Galagan J. BMC genomics, 2012/03/28, Volume 13, p.120, (2012) Read More / View Supplemental Materials
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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
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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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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.Aird, D., Ross MG, Chen WS, Danielsson M., Fennell T., Russ C., Jaffe DB, Nusbaum C., and Gnirke A. Genome biology, 2012/01/09, Volume 12, Issue 2, p.R18, (2012) Read More / View Supplemental Materials
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The success of acinetobacter species; genetic, metabolic and virulence attributes.Peleg, AY, de Breij A., Adams MD, Cerqueira GM, Mocali S., Nibbering PH, Earl AM, Ward DV, Paterson DL, Seifert H., and Dijkshoorn L. PloS one, 2012/01/01, Volume 7, Issue 10, p.e46984, (2012) Read More / View Supplemental Materials
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Evaluation of 16S rDNA-based community profiling for human microbiome research.Jumpstart Consortium Human Microbiome Project Data Generation Working, Group PloS one, 2012/01/01, Volume 7, Issue 6, p.e39315, (2012) Read More / View Supplemental Materials
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Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States.Kos, VN, Desjardins CA, Griggs A., Cerqueira G., Holden MT, Godfrey P., Palmer KL, Wortman J., Feldgarden M., Haas BJ, Birren B., and Gilmore MS mBio, 2012/01/01, Volume 3, Issue 3, (2012) Read More / View Supplemental Materials
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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.Giannoukos, G., Ciulla DM, Huang K., Haas BJ, Izard J., Levin JZ, Livny J., Earl AM, Gevers D., Ward DV, Nusbaum C., Birren BW, and Gnirke A. Genome biology, 2012/01/01, Volume 13, Issue 3, p.R23, (2012) Read More / View Supplemental Materials
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The "most wanted" taxa from the human microbiome for whole genome sequencing.Fodor, AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y., Hepburn T., Hu P., Sodergren E., Liolios K., Huot-Creasy H., Birren BW, and Earl AM PloS one, 2012/01/01, Volume 7, Issue 7, p.e41294, (2012) Read More / View Supplemental Materials
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Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus.Palmer, KL, Godfrey P., Griggs A., Kos VN, Zucker J., Desjardins C., Cerqueira G., Gevers D., Walker S., Wortman J., Feldgarden M., Haas B., Birren B., and Gilmore MS mBio, 2012/01/01, Volume 3, Issue 1, p.e00318-11, (2012) Read More / View Supplemental Materials
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2011

High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).Earl, AM, Desjardins CA, FitzGerald MG, Arachchi HM, Zeng Q., Mehta T., Griggs A., Birren BW, Toney NC, Carr J., Posey J., and Butler WR Standards in genomic sciences, 2011/12/31, Volume 5, Issue 3, p.389-97, (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
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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
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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
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
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
Next-generation sequencing for HLA typing of class I loci.Erlich, RL, Jia X., Anderson S., Banks E., Gao X., Carrington M., Gupta N., DePristo MA, Henn MR, Lennon NJ, and de Bakker PI BMC genomics, 2011/01/18, Volume 12, p.42, (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

2010

Comprehensive comparative analysis of strand-specific RNA sequencing methods.Levin, JZ, Yassour M., Adiconis X., Nusbaum C., Thompson DA, Friedman N., Gnirke A., and Regev A. Nature methods, 2010/09/01, Volume 7, Issue 9, p.709-15, (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
Abstract
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.Lennon, NJ, Lintner RE, Anderson S., Alvarez P., Barry A., Brockman W., Daza R., Erlich RL, Giannoukos G., Green L., Hollinger A., Hoover CA, Jaffe DB, Juhn F., McCarthy D., Perrin D., Ponchner K., Powers TL, Rizzolo K., Robbins D., et al. Genome biology, 2010/02/05, Volume 11, Issue 2, p.R15, (2010) Read More / View Supplemental Materials
Abstract

2009

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production.Colijn, C., Brandes A., Zucker J., Lun DS, Weiner B., Farhat MR, Cheng TY, Moody DB, Murray M., and Galagan JE PLoS computational biology, 2009/08/01, Volume 5, Issue 8, p.e1000489, (2009) Read More / View Supplemental Materials
Abstract
Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.Champion, MD, Zeng Q., Nix EB, Nano FE, Keim P., Kodira CD, Borowsky M., Young S., Koehrsen M., Engels R., Pearson M., Howarth C., Larson L., White J., Alvarado L., Forsman M., Bearden SW, Sjöstedt A., Titball R., Michell SL, et al. PLoS pathogens, 2009/05/01, Volume 5, Issue 5, p.e1000459, (2009) Read More / View Supplemental Materials
Abstract
High-resolution mapping of copy-number alterations with massively parallel sequencing.Chiang, DY, Getz G., Jaffe DB, O'Kelly MJ, Zhao X., Carter SL, Russ C., Nusbaum C., Meyerson M., and Lander E. S. Nature methods, 2009/01/01, Volume 6, Issue 1, p.99-103, (2009) Read More / View Supplemental Materials
Abstract
Closing gaps in the human genome using sequencing by synthesis.Garber, M., Zody MC, Arachchi HM, Berlin A., Gnerre S., Green LM, Lennon N., and Nusbaum C. Genome biology, 2009/01/01, Volume 10, Issue 6, p.R60, (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

Comparative evolutionary genomics of human malaria parasites.Carlton, JM, Escalante AA, Neafsey D., and Volkman SK Trends in parasitology, 2008/12/01, Volume 24, Issue 12, p.545-50, (2008) Read More / View Supplemental Materials
Abstract
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
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.Orsi, RH, Borowsky ML, Auer PL, Young SK, Nusbaum C., Galagan JE, Birren BW, Ivy RA, Sun Q., Graves LM, Swaminathan B., and Wiedmann M. BMC genomics, 2008/11/13, Volume 9, p.539, (2008) Read More / View Supplemental Materials
Abstract
A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking.Daniels, R., Volkman SK, Milner DA, Mahesh N., Neafsey DE, Park DJ, Rosen D., Angelino E., Sabeti PC, Wirth DF, and Wiegand RC Malaria journal, 2008/10/29, Volume 7, p.223, (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
Generating and testing molecular hypotheses in the dermatophytes.White, TC, Oliver BG, Gräser Y., and Henn MR Eukaryotic cell, 2008/08/01, Volume 7, Issue 8, p.1238-45, (2008) Read More / View Supplemental Materials
Conserved secondary structures in Aspergillus.McGuire, AM, and Galagan JE PloS one, 2008/07/30, Volume 3, Issue 7, p.e2812, (2008) Read More / View Supplemental Materials
Abstract
ALLPATHS: de novo assembly of whole-genome shotgun microreads.Butler, J., Maccallum I., Kleber M., Shlyakhter IA, Belmonte MK, Lander E. S., Nusbaum C., and Jaffe DB Genome research, 2008/05/01, Volume 18, Issue 5, p.810-20, (2008) Read More / View Supplemental Materials
Abstract
Quality scores and SNP detection in sequencing-by-synthesis systems.Brockman, W., Alvarez P., Young S., Garber M., Giannoukos G., Lee WL, Russ C., Lander E. S., Nusbaum C., and Jaffe DB Genome research, 2008/05/01, Volume 18, Issue 5, p.763-70, (2008) Read More / View Supplemental Materials
Abstract
Dynamics of Pseudomonas aeruginosa genome evolution.Mathee, K., Narasimhan G., Valdes C., Qiu X., Matewish JM, Koehrsen M., Rokas A., Yandava CN, Engels R., Zeng E., Olavarietta R., Doud M., Smith RS, Montgomery P., White JR, Godfrey PA, Kodira C., Birren B., Galagan JE, and Lory S. Proceedings of the National Academy of Sciences of the United States of America, 2008/02/26, Volume 105, Issue 8, p.3100-5, (2008) 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, 2008/01/01, Volume 9, Issue 12, p.R171, (2008) Read More / View Supplemental Materials
Abstract
Short-term temporal variability in airborne bacterial and fungal populations.Fierer, N., Liu Z., Knight R., and Henn M. Applied and environmental microbiology, 2008/01/01, Volume 74, Issue 1, p.200-7, (2008) Read More / View Supplemental Materials
Abstract
Cross-kingdom patterns of alternative splicing and splice recognition.McGuire, AM, Pearson MD, Neafsey DE, and Galagan JE Genome biology, 2008/01/01, Volume 9, Issue 3, p.R50, (2008) Read More / View Supplemental Materials
Abstract

2007

Conrad: gene prediction using conditional random fields.DeCaprio, D., Vinson JP, Pearson MD, Montgomery P., Doherty M., and Galagan JE Genome research, 2007/09/01, Volume 17, Issue 9, p.1389-98, (2007) Read More / View Supplemental Materials
Abstract
Dual modes of natural selection on upstream open reading frames.Neafsey, DE, and Galagan JE Molecular biology and evolution, 2007/08/01, Volume 24, Issue 8, p.1744-51, (2007) Read More / View Supplemental Materials
Abstract
Positive selection for unpreferred codon usage in eukaryotic genomes.Neafsey, DE, and Galagan JE BMC evolutionary biology, 2007/07/18, Volume 7, p.119, (2007) Read More / View Supplemental Materials
Abstract