454 Life Sciences

Extreme positive selection on a new highly-expressed larval glycoprotein (LGP) gene in Galaxias fishes (Osmeriformes: Galaxiidae).  Wallis LJ, Wallis GP. (8/9/2010) Mol Biol Evol ePub:
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Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing.  Paruzynski A, Arens A, Gabriel R, Bartholomae CC, Scholz S, Wang W, Wolf S, Glimm H, Schmidt M, von Kalle C. (8/1/2010) Nature Protocols 5(8): 1379-95.
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Reliable resequencing of the human dystrophin locus by universal long PCR and massive pyrosequencing.  Bonnal RJ, Severgnini M, Castaldi A, Bordoni R, Iacono M, Trimarco A, Torella A, Piluso G, Aurino S, Condorelli G, De Bellis G, Nigro V. (7/26/2010) Analytical Biochemistry ePub:
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Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.  Varley KE, Mitra RD. (7/13/2010) Genome Research ePub:
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Next-Generation Sequencing: The Solution for High-Resolution, Unambiguous HLA Typing.  Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, Gai X, Goodridge D, Sayer D, Monos D. (7/2/2010) Human Immunology ePub:
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Comparison of gene order of GIGANTEA loci in yellow-poplar, monocots, and eudicots.  Liang H, Barakat A, Schlarbaum SE, Mandoli DF, Carlson JE. (7/1/2010) Genome 53(7): 533-44.
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Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer.  Chmielecki J, Peifer M, Jia P, Socci ND, Hutchinson K, Viale A, Zhao Z, Thomas RK, Pao W. (6/29/2010) Nucleic Acids Research ePub:
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Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons.  Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE. (6/25/2010) Cell 141(7): 1253-1261.
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Associations between Major Histocompatibility Complex genes and PUUV infection in Myodes glareolus are detected in wild populations but not from experimental infection data.  Guivier E, Galan M, Malé PJ, Kallio ER, Voutilainen L, Henttonen H, Olsson G, Lundkvist A, Tersago K, Augot D, Cosson JF, Charbonnel N. (6/23/2010) Journal of General Virology ePub:
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Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.  Wang GP, Berry CC, Malani N, Leboulch P, Fischer A, Hacein-Bey-Abina S, Cavazzana-Calvo M, Bushman FD. (6/3/2010) Blood 115(22): 4356-66.
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Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements.  Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM. (5/21/2010) Journal of Immunology 184(12): 6986-92.
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SNP discovery performance of two second-generation sequencing platforms in the NOD2 gene region.  Melum E, May S, Schilhabel MB, Thomsen I, Karlsen TH, Rosenstiel P, Schreiber S, Franke A. (5/18/2010) Human Mutation 31(7): 875-85.
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Deep sequencing reveals highly complex dynamics of human cytomegalovirus genotypes in transplant patients over time.  Görzer I, Guelly C, Trajanoski S, Puchhammer-Stöckl E. (5/12/2010) Journal of Virology 84(14): 7195-203.
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A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies.  Galan M, Guivier E, Caraux G, Charbonnel N, Cosson JF. (5/11/2010) BMC Genomics 11(1): 296.
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Whole human exome capture for high-throughput sequencing.  Dae-Won Kim, Seong-Hyeuk Nam, Ryong Nam Kim, Sang-Haeng Choi, and Hong-Seog Park (5/1/2010) Genome 53(7): 568-574.
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Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing.  Taudien S, Groth M, Huse K, Petzold A, Szafranski K, Hampe J, Rosenstiel P, Schreiber S, Platzer M. (4/19/2010) BMC Genomics 11(1): 252.
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Mutation spectrum revealed by breakpoint sequencing of human germline CNVs.  Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, Turner DJ, Hurles ME. (4/4/2010) Nature Genetics 42(5): 385-91.
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Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79.  Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, Ahmed ZM, Riazuddin S, Khan SN, Riazuddin S, Friedman TB. (3/12/2010) American Journal of Human Genetics 86(3): 378-88.
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Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon.  Lukacs MF, Harstad H, Bakke HG, Beetz-Sargent M, McKinnel L, Lubieniecki KP, Koop BF, Grimholt U. (3/5/2010) BMC Genomics 11(1): 154.
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Repeat subtraction-mediated sequence capture from a complex genome.  Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Brad Barbazuk W, Jeddeloh JA, Schnable PS. (3/4/2010) Plant Journal 62(5): 898-909.
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Rapid construction and characterization of synthetic antibody libraries without DNA amplification.  Ge X, Mazor Y, Hunicke-Smith SP, Ellington AD, Georgiou G. (3/2/2010) Biotechnol Bioeng 106(3): 347-57.
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Next-generation sequencing of a 40 Mb linkage interval reveals TSPAN12 mutations in patients with familial exudative vitreoretinopathy.  Nikopoulos K, Gilissen C, Hoischen A, van Nouhuys CE, Boonstra FN, Blokland EA, Arts P, Wieskamp N, Strom TM, Ayuso C, Tilanus MA, Bouwhuis S, Mukhopadhyay A, Scheffer H, Hoefsloot LH, Veltman JA, Cremers FP, Collin RW. (2/12/2010) American Journal of Human Genetics 86(2): 240-7.
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Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.).  Shinozuka H, Cogan NO, Smith KF, Spangenberg GC, Forster JW. (2/1/2010) Plant Mol Biol. 72(3): 343-55.
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Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.  Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC. (1/13/2010) Nature 463(7280): 536-9.
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High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.  Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, Gharizadeh B, Myers RM, Hudson JR Jr, Davis RW, Han J. (1/4/2010) PNAS 107(4): 1518-23.
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DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model.  Chou LS, Liu CS, Boese B, Zhang X, Mao R. (1/1/2010) Clinical Chemistry 56(1): 62-72.
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A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.  Parikh H et al. (1/1/2010) Human Genetics 127(1): 91-9.
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Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.  Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ. (12/23/2009) Science Translational Medicine 1(12): 12ra23.
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Exome sequencing of a multigenerational human pedigree.  Hedges D, Burges D, Powell E, Almonte C, Huang J, Young S, Boese B, Schmidt M, Pericak-Vance MA, Martin E, Zhang X, Harkins TT, Züchner S. (12/14/2009) PLoS One 4(12): e8232.
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Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library.  Castano-Sanchez C, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE 3rd. (11/25/2009) BMC Genomics 10(1): 559.
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High-throughput sequencing of microdissected chromosomal regions.  Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, Liehr T, Neitzel H, Konrat K, Bommer C, Dietrich C, Rajab A, Reinhardt R, Mundlos S, Lindner TH, Hoffmann K. (11/4/2009) European Journal of Human Genetics 18(4): 457-62.
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High-resolution, high-throughput HLA genotyping by next-generation sequencing.  Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA. (11/1/2009) Tissue Antigens 74(5): 393-403.
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Microdroplet-based PCR enrichment for large-scale targeted sequencing.  Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA. (11/1/2009) Nature Biotechnology 27(11): 1025-31.
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Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire.  Glanville J, Zhai W, Berka J, Telman D, Huerta G, Mehta GR, Ni I, Mei L, Sundar PD, Day GM, Cox D, Rajpal A, Pons J. (10/29/2009) PNAS 106(48): 21216-21.
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Major histocompatibility complex genotyping with massively parallel pyrosequencing.  Wiseman RW, Karl JA, Bimber BN, O'Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E Jr, Wright C, Harkins T, O'Connor DH. (10/11/2009) Nature Medicine 15(11): 1322-6.
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Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing.  O'Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O'Connor DH. (9/24/2009) Immunogenetics 61(10): 689-701.
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Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways.  Külheim C, Yeoh SH, Maintz J, Foley WJ, Moran GF. (9/24/2009) BMC Genomics 10: 452.
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Rapid High-throughput HLA Typing by Massively-parallel Pyrosequencing for High-Resolution Allele Identification.  Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J. (8/22/2009) Human Immunology 70(11): 960-4.
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Gene content and virtual gene order of barley chromosome 1H.  Mayer KF, Taudien S, Martis M, Simkova H, Suchankova P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N. (8/19/2009) Plant Physiology 151(2): 496-505.
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A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.  Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. (7/27/2009) PLoS One 4(7): e6372.
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Mutation discovery in the mouse using genetically guided array capture and resequencing.  D'Ascenzo M, Meacham C, Kitzman J, Middle C, Knight J, Winer R, Kukricar M, Richmond T, Albert TJ, Czechanski A, Donahue LR, Affourtit J, Jeddeloh JA, Reinholdt L. (7/21/2009) Mammalian Genome 20(7): 424-36.
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Novel TET2 Mutations Associated With UPD4q24 in Myelodysplastic Syndrome.  Mohamedali AM, Smith AE, Gaken J, Lea NC, Mian SA, Westwood NB, Strupp C, Gattermann N, Germing U, Mufti GJ. (6/15/2009) Journal of Clinical Oncology. 27(24): 4002-6.
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High-Throughput Sequencing of the Zebrafish Antibody Repertoire.  Joshua A. Weinstein, Ning Jiang, Richard A. White, III, Daniel S. Fisher, Stephen R. Quake (5/8/2009) Science 324(5928): 807-810.
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Large-scale mRNA sequencing determines global regulation of RNA editing during brain development.  Wahlstedt H, Daniel C, Ensterö M, Ohman M. (5/6/2009) Genome Research 19(6): 978-86.
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Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces.  Deagle BE, Kirkwood R, Jarman SN. (5/1/2009) Molecular Ecology 18(9): 2022-38.
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Pyrosequencing of the chaperonin-60 (cpn60) universal target as a tool for determining the composition of microbial communities.  Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, Tyler S, Ball TB, Severini A, Plummer FA. (5/1/2009) Applied Environmental Microbiology 75(9): 2889-98.
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Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing.  Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ. (5/1/2009) Plant Biotechnol Journal 7(4): 347-54
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Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam.  Stewart FJ, Cavanaugh CM. (4/21/2009) Environmental Microbiology 11(8): 2136-47.
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High-throughput detection of induced mutations and natural variation using KeyPoint technology.  Rigola D, van Oeveren J, Janssen A, Bonné A, Schneiders H, van der Poel HJ, van Orsouw NJ, Hogers RC, de Both MT, van Eijk MJ. (3/13/2009) PLoS ONE 4(3): e4761
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Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes.  Nejentsev S, Walker N, Riches D, Egholm M, Todd JA. (3/5/2009) Science 324(5925): 387-9.
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Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.  Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, Jonghe PD, Rijk PD, Del-Favero J. (3/1/2009) Human Mutations 30(3): 472-6
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SNP frequency estimation using massively parallel sequencing of pooled DNA.  Ingman M, Gyllensten U. (3/1/2009) European Journal of Human Genetics 17(3): 383-6
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Integration target site selection by a resurrected human endogenous retrovirus.  Brady T, Lee YN, Ronen K, Malani N, Berry CC, Bieniasz PD, Bushman FD. (3/1/2009) Genes & Development 23(5): 633-42.
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A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma.  Keng VW, Villanueva A, Chiang DY, Dupuy AJ, Ryan BJ, Matise I, Silverstein KA, Sarver A, Starr TK, Akagi K, Tessarollo L, Collier LS, Powers S, Lowe SW, Jenkins NA, Copeland NG, Llovet JM, Largaespada DA. (3/1/2009) Nature Biotechnology 27(3): 264-74.
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Microsatellite discovery by deep sequencing of enriched genomic libraries.  Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B. (2/1/2009) Biotechniques 46(30: 217-23
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Use of massively parallel ultra-deep pyrosequencing to characterize genetic diversity of HBV in drug-resistant and naive patients and to detect minor variants in RT and HBsAg.  M. Solmone, D. Vincenti, M. C. Prosperi, A. Bruselles, G. Ippolito, M.R. Capobianchi (2/1/2009) Journal of Virology 83(4): 1718-26
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Long-term survival of a urodele amphibian despite depleted major histocompatibility complex variation.  Babik W, Pabijan M, Arntzen JW, Cogalniceanu D, Durka W, Radwan J. (1/29/2009) Molecular Ecology ePub:
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Targeted screening of cis-regulatory variation in human haplotypes.  Verlaan DJ, Ge B, Grundberg E, Hoberman R, Lam KC, Koka V, Dias J, Gurd S, Martin NW, Mallmin H, Nilsson O, Harmsen E, Dewar K, Kwan T, Pastinen T. (1/1/2009) Genome Research 19(1): 118-27
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Sequencing the Full-Length of the Phosphatase and Tensin Homolog (PTEN) Gene in Hepatocellular Carcinoma (HCC) Using the 454 GS20 and Illumina GA DNA Sequencing Platforms.  Rodriguez JA, Guiteau JJ, Nazareth L, Reid JG, Goss JA, Gibbs RA, Gingras MC (12/10/2008) World Journal of Surgery 33(4): 647-52.
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Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.  Bordoni R, Bonnal R, Rizzi E, Carrera P, Benedetti S, Cremonesi L, Stenirri S, Colombo A, Montrasio C, Bonalumi S, Albertini A, Rossi Bernardi L, Ferrari M, de Bellis G. (10/8/2008) BMC Genomics 9: 433
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Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.  Yeager M, Xiao N, Hayes RB, Bouffard P, Desany B, Burdett L, Orr N, Matthews C, Qi L, Crenshaw A, Markovic Z, Fredrikson KM, Jacobs KB, Amundadottir L, Jarvie TP, Hunter DJ, Hoover R, Thomas G, Harkins TT, Chanock SJ. (9/1/2008) Human Genetics 124: 161-70
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Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing  Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, Lin C, Makowski K, Shen L, Murray RR, Szeto D, Tusneem N, Smith DR, Cusick ME, Hill DE, Roth FP, Vidal M (7/1/2008) Nature Methods 5: 597-600
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Generation of a 3D indexed Petunia insertion database for reverse genetics  Vandenbussche M, Janssen A, Zethof J, van Orsouw N, Peters J, van Eijk MJ, Rijpkema AS, Schneiders H, Santhanam P, de Been M, van Tunen A, Gerats T (5/8/2008) Plant Journal :
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DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer  Wang GP, Garrigue A, Ciuffi A, Ronen K, Leipzig J, Berry C, Lagresle-Peyrou C, Benjelloun F, Hacein-Bey-Abina S, Fischer A, Cavazzana-Calvo M, Bushman FD (4/14/2008) Nucleic Acids Research 36:
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Role of PSIP1/LEDGF/p75 in Lentiviral Infectivity and Integration Targeting  Heather M. Marshall, Keshet Ronen, Charles Berry, Manuel Llano, Heidi Sutherland, Dyana Saenz, Wendy Bickmore, Eric Poeschla, Frederic D. Bushman (12/1/2007) PLoS ONE 12:
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Direct selection of human genomic loci by microarray hybridization  Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA (11/1/2007) Nature Methods 4: 903-905
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Complexity Reduction of Polymorphic Sequences (CRoPSTM): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes  Nathalie J. van Orsouw*, Rene´ C. J. Hogers, Antoine Janssen, Feyruz Yalcin, Sandor Snoeijers, Esther Verstege, Harrie Schneiders, Hein van der Poel, Jan van Oeveren, Harold Verstegen, Michiel J. T. van Eijk (11/1/2007) PLoS ONE 11:
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The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing  Jonas Binladen, M. Thomas P. Gilbert, Jonathan P. Bollback, Frank Panitz, Christian Bendixen, Rasmus Nielsen, Eske Willerslev (2/1/2007) PLoS ONE 2:
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Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads  Pettersson E, Zajac P, Ståhl PL, Jacobsson JA, Fredriksson R, Marcus C, Schiöth HB, Lundeberg J, Ahmadian A (2/1/2007) Human Mutation 29: 323-329
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