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2013
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
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
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.Garber, M., Yosef N., Goren A., Raychowdhury R., Thielke A., Guttman M., Robinson J., Minie B., Chevrier N., Itzhaki Z., Blecher-Gonen R., Bornstein C., Amann-Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., et al. Molecular cell, 2012/09/14, Volume 47, Issue 5, p.810-22, (2012) Read More / View Supplemental Materials
Abstract
Finished bacterial genomes from shotgun sequence data.Ribeiro, F., Przybylski D., Yin S., Sharpe T., Gnerre S., Abouelleil A., Berlin AM, Montmayeur A., Shea TP, Walker BJ, Young SK, Russ C., Maccallum I., Nusbaum C., and Jaffe DB Genome research, 2012/07/24, (2012) Read More / View Supplemental Materials
Abstract
Paired-end sequencing of Fosmid libraries by Illumina.Williams, LJ, Tabbaa DG, Li N., Berlin AM, Shea TP, Maccallum I., Lawrence MS, Drier Y., Getz G., Young SK, Jaffe DB, Nusbaum C., and Gnirke A. Genome research, 2012/07/17, (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
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
Abstract
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.Fisher, S., Barry A., Abreu J., Minie B., Nolan J., Delorey TM, Young G., Fennell TJ, Allen A., Ambrogio L., Berlin AM, Blumenstiel B., Cibulskis K., Friedrich D., Johnson R., Juhn F., Reilly B., Shammas R., Stalker J., Sykes SM, et al. Genome biology, 2012/01/09, Volume 12, Issue 1, p.R1, (2012) Read More / View Supplemental Materials
Abstract
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.Yassour, M., Pfiffner J., Levin JZ, Adiconis X., Gnirke A., Nusbaum C., Thompson DA, Friedman N., and Regev A. Genome biology, 2012/01/09, Volume 11, Issue 8, p.R87, (2012) Read More / View Supplemental Materials
Abstract
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.Levin, JZ, Berger MF, Adiconis X., Rogov P., Melnikov A., Fennell T., Nusbaum C., Garraway LA, and Gnirke A. Genome biology, 2012/01/09, Volume 10, Issue 10, p.R115, (2012) Read More / View Supplemental Materials
Abstract
2011
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
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
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
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.Rabani, M., Levin JZ, Fan L., Adiconis X., Raychowdhury R., Garber M., Gnirke A., Nusbaum C., Hacohen N., Friedman N., Amit I., and Regev A. Nature biotechnology, 2011/05/01, Volume 29, Issue 5, p.436-42, (2011) Read More / View Supplemental Materials
Abstract
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.Gnerre, S., Maccallum I., Przybylski D., Ribeiro FJ, Burton JN, Walker BJ, Sharpe T., Hall G., Shea TP, Sykes S., Berlin AM, Aird D., Costello M., Daza R., Williams L., Nicol R., Gnirke A., Nusbaum C., Lander E. S., and Jaffe DB Proceedings of the National Academy of Sciences of the United States of America, 2011/01/25, Volume 108, Issue 4, p.1513-8, (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
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
A draft sequence of the Neandertal genome.Green, RE, Krause J., Briggs AW, Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T., Alkan C., Prüfer K., Meyer M., Burbano HA, Good JM, et al. Science (New York, N.Y.), 2010/05/07, Volume 328, Issue 5979, p.710-22, (2010) Read More / View Supplemental Materials
Abstract
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.Guttman, M., Garber M., Levin JZ, Donaghey J., Robinson J., Adiconis X., Fan L., Koziol MJ, Gnirke A., Nusbaum C., Rinn JL, Lander E. S., and Regev A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.503-10, (2010) Read More / View Supplemental Materials
Abstract
Integrative analysis of the melanoma transcriptome.Berger, MF, Levin JZ, Vijayendran K., Sivachenko A., Adiconis X., Maguire J., Johnson LA, Robinson J., Verhaak RG, Sougnez C., Onofrio RC, Ziaugra L., Cibulskis K., Laine E., Barretina J., Winckler W., Fisher DE, Getz G., Meyerson M., Jaffe DB, et al. Genome research, 2010/04/01, Volume 20, Issue 4, p.413-27, (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
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2009
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
Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA.Geml, J., Laursen GA, Timling I., McFarland JM, Booth MG, Lennon N., Nusbaum C., and Taylor DL Molecular ecology, 2009/05/01, Volume 18, Issue 10, p.2213-27, (2009) Read More / View Supplemental Materials
Abstract
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.Gnirke, A., Melnikov A., Maguire J., Rogov P., LeProust EM, Brockman W., Fennell T., Giannoukos G., Fisher S., Russ C., Gabriel S., Jaffe DB, Lander E. S., and Nusbaum C. Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.182-9, (2009) Read More / View Supplemental Materials
Abstract
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.Maccallum, I., Przybylski D., Gnerre S., Burton J., Shlyakhter I., Gnirke A., Malek J., McKernan K., Ranade S., Shea TP, Williams L., Young S., Nusbaum C., and Jaffe DB Genome biology, 2009/01/01, Volume 10, Issue 10, p.R103, (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
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
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
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.Ku, M., Koche RP, Rheinbay E., Mendenhall EM, Endoh M., Mikkelsen TS, Presser A., Nusbaum C., Xie X., Chi AS, Adli M., Kasif S., Ptaszek LM, Cowan CA, Lander E. S., Koseki H., and Bernstein BE PLoS genetics, 2008/10/01, Volume 4, Issue 10, p.e1000242, (2008) Read More / View Supplemental Materials
Abstract
Genome-scale DNA methylation maps of pluripotent and differentiated cells.Meissner, A., Mikkelsen TS, Gu H., Wernig M., Hanna J., Sivachenko A., Zhang X., Bernstein BE, Nusbaum C., Jaffe DB, Gnirke A., Jaenisch R., and Lander E. S. Nature, 2008/08/07, Volume 454, Issue 7205, p.766-70, (2008) Read More / View Supplemental Materials
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Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach.Taylor, DL, Booth MG, McFarland JW, Herriott IC, Lennon NJ, Nusbaum C., and Marr TG Molecular ecology resources, 2008/07/01, Volume 8, Issue 4, p.742-52, (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
2007
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.Mikkelsen, TS, Ku M., Jaffe DB, Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim TK, Koche RP, Lee W., Mendenhall E., O'Donovan A., Presser A., Russ C., Xie X., Meissner A., Wernig M., Jaenisch R., Nusbaum C., et al. Nature, 2007/08/02, Volume 448, Issue 7153, p.553-60, (2007) Read More / View Supplemental Materials
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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
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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
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
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.Vinson, JP, Jaffe DB, O'Neill K., Karlsson EK, Stange-Thomann N., Anderson S., Mesirov J. P., Satoh N., Satou Y., Nusbaum C., Birren B., Galagan JE, and Lander E. S. Genome research, 2005/08/01, Volume 15, Issue 8, p.1127-35, (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 1-43 of 43 Results