Scientific Publications

Search by Keyword(s)
Found 31 results

Filters: Author is Zody, MC  [Clear All Filters]

Search Results

  • Showing 1-31 of 31 Results
2014
Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.Li, JZ, Chapman B., Charlebois P., Hofmann O., Weiner B., Porter AJ, Samuel R., Vardhanabhuti S., Zheng L., Eron J., Taiwo B., Zody MC, Henn MR, Kuritzkes DR, Hide W., ACTG A5262 Study Team, Wilson CC, Berzins BI, Acosta EP, Bastow B., et al. PloS one, 2014/01/01, Volume 9, Issue 3, p.e90485, (2014) Read More / View Supplemental Materials
Abstract
2013
ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.Liu, C., Yang X., Duffy B., Mohanakumar T., Mitra RD, Zody MC, and Pfeifer JD Nucleic acids research, 2013/06/08, (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
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
Structural haplotypes and recent evolution of the human 17q21.31 region.Boettger, LM, Handsaker RE, Zody MC, and McCarroll SA Nature genetics, 2012/07/01, (2012) Read More / View Supplemental Materials
Abstract
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
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
Exploiting nucleotide composition to engineer promoters.Grabherr, MG, Pontiller J., Mauceli E., Ernst W., Baumann M., Biagi T., Swofford R., Russell P., Zody MC, Di Palma F., Lindblad-Toh K., and Grabherr RM PloS one, 2012/01/09, Volume 6, Issue 5, p.e20136, (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 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
2009
Genome sequence, comparative analysis, and population genetics of the domestic horse.Wade, CM, Giulotto E., Sigurdsson S., Zoli M., Gnerre S., Imsland F., Lear TL, Adelson DL, Bailey E., Bellone RR, Blöcker H., Distl O., Edgar RC, Garber M., Leeb T., Mauceli E., MacLeod JN, Penedo MC, Raison JM, Sharpe T., et al. Science (New York, N.Y.), 2009/11/06, Volume 326, Issue 5954, p.865-7, (2009) Read More / View Supplemental Materials
Abstract
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.Haas, BJ, Kamoun S., Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M., Kodira CD, Raffaele S., Torto-Alalibo T., Bozkurt TO, Ah-Fong AM, Alvarado L., Anderson VL, Armstrong MR, Avrova A., Baxter L., Beynon J., Boevink PC, Bollmann SR, et al. Nature, 2009/09/17, Volume 461, Issue 7262, p.393-8, (2009) Read More / View Supplemental Materials
Abstract
Identifying novel constrained elements by exploiting biased substitution patterns.Garber, M., Guttman M., Clamp M., Zody MC, Friedman N., and Xie X. Bioinformatics (Oxford, England), 2009/06/15, Volume 25, Issue 12, p.i54-62, (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
2008
Somatic mutations affect key pathways in lung adenocarcinoma.Ding, L., Getz G., Wheeler DA, Mardis ER, McLellan MD, Cibulskis K., Sougnez C., Greulich H., Muzny DM, Morgan MB, Fulton L., Fulton RS, Zhang Q., Wendl MC, Lawrence MS, Larson DE, Chen K., Dooling DJ, Sabo A., Hawes AC, et al. Nature, 2008/10/23, Volume 455, Issue 7216, p.1069-75, (2008) Read More / View Supplemental Materials
Abstract
Evolutionary toggling of the MAPT 17q21.31 inversion region.Zody, MC, Jiang Z., Fung HC, Antonacci F., Hillier LW, Cardone MF, Graves TA, Kidd JM, Cheng Z., Abouelleil A., Chen L., Wallis J., Glasscock J., Wilson RK, Reily AD, Duckworth J., Ventura M., Hardy J., Warren WC, and Eichler EE Nature genetics, 2008/09/01, Volume 40, Issue 9, p.1076-83, (2008) Read More / View Supplemental Materials
Abstract
Drug-sensitive FGFR2 mutations in endometrial carcinoma.Dutt, A., Salvesen HB, Chen TH, Ramos AH, Onofrio RC, Hatton C., Nicoletti R., Winckler W., Grewal R., Hanna M., Wyhs N., Ziaugra L., Richter DJ, Trovik J., Engelsen IB, Stefansson IM, Fennell T., Cibulskis K., Zody MC, Akslen LA, et al. Proceedings of the National Academy of Sciences of the United States of America, 2008/06/24, Volume 105, Issue 25, p.8713-7, (2008) Read More / View Supplemental Materials
Abstract
2007
Efficient mapping of mendelian traits in dogs through genome-wide association.Karlsson, EK, Baranowska I., Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N., Biagi TM, Patterson N., Pielberg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov J. P., von Euler H., Kämpe O., Hedhammar A., Lander E. S., Andersson G., Andersson L., and Lindblad-Toh K. Nature genetics, 2007/11/01, Volume 39, Issue 11, p.1321-8, (2007) Read More / View Supplemental Materials
Abstract
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.ENCODE Project, Consortium, Birney E., Stamatoyannopoulos JA, Dutta A., Guigó R., Gingeras TR, Margulies EH, Weng Z., Snyder M., Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S., Koch CM, Asthana S., Malhotra A., Adzhubei I., Greenbaum JA, Andrews RM, et al. Nature, 2007/06/14, Volume 447, Issue 7146, p.799-816, (2007) Read More / View Supplemental Materials
Abstract
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.Mikkelsen, TS, Wakefield MJ, Aken B., Amemiya CT, Chang JL, Duke S., Garber M., Gentles AJ, Goodstadt L., Heger A., Jurka J., Kamal M., Mauceli E., Searle SM, Sharpe T., Baker ML, Batzer MA, Benos PV, Belov K., Clamp M., et al. Nature, 2007/05/10, Volume 447, Issue 7141, p.167-77, (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
Abstract
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
Abstract
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
Abstract
2005
Genome sequence, comparative analysis and haplotype structure of the domestic dog.Lindblad-Toh, K., Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M., Clamp M., Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E., Xie X., Breen M., Wayne RK, Ostrander EA, Ponting CP, Galibert F., Smith DR, de Jong PJ, Kirkness E., et al. Nature, 2005/12/08, Volume 438, Issue 7069, p.803-19, (2005) Read More / View Supplemental Materials
Abstract
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
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.Jaillon, O., Aury JM, Brunet F., Petit JL, Stange-Thomann N., Mauceli E., Bouneau L., Fischer C., Ozouf-Costaz C., Bernot A., Nicaud S., Jaffe D., Fisher S., Lutfalla G., Dossat C., Segurens B., Dasilva C., Salanoubat M., Levy M., Boudet N., et al. Nature, 2004/10/21, Volume 431, Issue 7011, p.946-57, (2004) Read More / View Supplemental Materials
Abstract
  • Showing 1-31 of 31 Results