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  • Showing 1-22 of 22 Results
2012
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
De novo assembly of highly diverse viral populations.Yang, X., Charlebois P., Gnerre S., Coole MG, Lennon NJ, Levin JZ, Qu J., Ryan EM, Zody MC, and Henn MR BMC genomics, 2012/09/13, Volume 13, p.475, (2012) Read More / View Supplemental Materials
Abstract
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, 2012/09/08, (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
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
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
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
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
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
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
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
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
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
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
2005
Genomics of the fungal kingdom: insights into eukaryotic biology.Galagan, JE, Henn MR, Ma LJ, Cuomo CA, and Birren B. Genome research, 2005/12/01, Volume 15, Issue 12, p.1620-31, (2005) Read More / View Supplemental Materials
Abstract
  • Showing 1-22 of 22 Results