454 Life Sciences

Rapid Microsatellite Development for Water Striders by Next-Generation Sequencing.  Perry JC, Rowe L. (9/1/2010) Journal of Heredity ePub:
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The genome of the domesticated apple (Malus × domestica Borkh.)  Velasco R et al. (8/29/2010) Nature Genetics ePub:
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High-throughput SNP discovery and assay development in common bean.  Hyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB. (8/16/2010) BMC Genomics 11(1): 475.
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A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging.  Timmermann B, Jarolim S, Rußmayer H, Kerick M, Michel S, Krüger A, Bluemlein K, Laun P, Grillari J, Lehrach H, Breitenbach M, Ralser M. (8/13/2010) Aging (Albany NY) ePub:
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When Technology Meets Conservation: Increased Microsatellite Marker Production Using 454 Genome Sequencing on the Endangered Okaloosa Darter (Etheostoma okaloosae).  Saarinen EV, Austin JD. (7/11/2010) J Hered ePub:
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Cost-Effective, Species-Specific Microsatellite Development for the Endangered Dwarf Bulrush (Typha minima) Using Next-Generation Sequencing Technology.  Csencsics D, Brodbeck S, Holderegger R. (6/18/2010) Journal of Heredity ePub:
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Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus.  Guerrero FD, Moolhuijzen P, Peterson DG, Bidwell S, Caler E, Bellgard M, Nene VM, Djikeng A. (6/11/2010) BMC Genomics 11: 374.
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Second generation sequencing of the mesothelioma tumor genome.  Bueno R, De Rienzo A, Dong L, Gordon GJ, Hercus CF, Richards WG, Jensen RV, Anwar A, Maulik G, Chirieac LR, Ho KF, Taillon BE, Turcotte CL, Hercus RG, Gullans SR, Sugarbaker DJ. (5/13/2010) PLoS One 5(5): e10612.
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De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.  Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M. (4/8/2010) PLoS Genetics 6(4): e1000891.
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Initial genomics of the human nucleolus.  Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G. (3/26/2010) PLoS Genetics 6(3): e10000889.
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Complete Khoisan and Bantu genomes from southern Africa.  Schuster SC et al. (2/18/2010) Nature 463(7283): 943-7.
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Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.  Swaminathan K, Alabady M, Varala K, De Paoli E, Ho I, Rokhsar DS, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME, Arumuganathan AK. (2/3/2010) Genome Biology 11(2): R12.
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The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships.  Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S. (12/10/2009) DNA Research 17(1): 11-22.
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Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.)Wilczek).  Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. (11/24/2009) BMC Plant Biology 9(1): 137.
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De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley.  Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, Mayer KF, Platzer M, Stein N. (11/20/2009) BMC Genomics 10(1): 547.
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Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production.  Argueso et al. (10/7/2009) Genome Research 19(12): 2258-70.
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Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118.  Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S, Dequin S. (9/22/2009) PNAS 106(38): 16333-8.
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De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.  Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ. (9/1/2009) Genome Biology 10(9): R94.
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Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?  Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG. (8/21/2009) PLos Pathogens 5(8): 31000560.
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Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform.  van der Vaart M, Semenov DV, Kuligina EV, Richter VA, Pretorius PJ. (8/19/2009) Clinical Chemistry Acta 409(1-2): 21-7.
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What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae).  David A Rasmussen and Mohamed AF Noor (8/18/2009) BMC Genomics 10: 382.
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Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.  Ramos et al. (8/5/2009) PLoS One 4(8): e6524.
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The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage.  Libants S, Carr K, Wu H, Teeter JH, Chung-Davidson YW, Zhang Z, Wilkerson C, Li W. (7/31/2009) BMC Evolutionary Biology 9(1): 180.
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Large-Scale Discovery of Gene-Enriched SNPs.  Gore M, Wright M, Ersoz E, Bouffard P, Szekeres E, Jarvie T, Hurwitz B, Narechania A, Harkins T, Grills G, Ware D and Buckler E. (7/1/2009) The Plant Genome 2: 121-133.
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Genome sequence of the recombinant protein production host Pichia pastoris.  De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouzé P, Van de Peer Y, Callewaert N. (6/1/2009) Nature Biotechnology 27(6): 561-6.
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Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees.  Cornman RS, Chen YP, Schatz MC, Street C, Zhao Y, Desany B, Egholm M, Hutchison S, Pettis JS, Lipkin WI, Evans JD. (6/1/2009) PLoS Pathogens 5(6): e1000466.
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Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants.  Lindstrom Bontell I, Hall N, Ashelford KE, Dubey JP, Boyle JP, Lindh J, Smith JE. (5/20/2009) Genome Biology 10(5): R53.
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A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley.  Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. (5/12/2009) Plant Journal 59(5): 712-22.
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Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei.  Nagendran S, Hallen-Adams HE, Paper JM, Aslam N, Walton JD. (5/1/2009) Fungal Genetic Biology 46(5): 427-35
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De novo next generation sequencing of plant genomes.  Steve Rounsley, Pradeep Reddy Marri, Yeisoo Yu, Ruifeng He, Nick Sisneros, Jose Luis Goicoechea, So Jeong Lee, Angelina Angelova, Dave Kudrna, Meizhong Luo, Jason Affourtit, Brian Desany, James Knight, Faheem Niazi, Michael Egholm and Rod A. Wing (3/7/2009) Rice 2(1): 35-43
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Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing.  Abdelkrim J, Robertson B, Stanton JA, Gemmell N. (3/1/2009) Biotechniques 46(3): 185-92
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A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.  Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. (2/1/2009) Genome Research 19(2): 167-77
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Profile of the Circulating DNA in Apparently Healthy Individuals.  Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E. (1/30/2009) Clinical Chemistry 55(4): 730-8.
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Genic Regions of a Large Salamander Genome Contain Long Introns and Novel Genes.  Smith JJ, Putta S, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR. (1/13/2009) BMC Genomics 10: 19
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The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula.  Shin JH, Van K, Kim DH, Kim KD, Jang YE, Choi BS, Kim MY, Lee SH. (12/23/2008) BMC Plant Biology 8(1): 133
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SNP discovery in swine by reduced representation and high throughput pyrosequencing.  Wiedmann RT, Smith TP, Nonneman DJ. (12/4/2008) BMC Genetics 9: 81
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Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history.  Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB.  (12/1/2008) Genome Research 18(12): 1865-74
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Fibroblast derived induced pluripotent stem cells show no common retroviral vector insertions.  Varas F, Stadtfeld M, De Andres-Aguayo L, Maherali N, di Tullio A, Pantano L, Notredame C, Hochedlinger K, Graf T. (11/13/2008) Stem Cells :
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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.  Ley TJ et al. (11/6/2008) Nature 456(7218): 66-72.
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Comparative genome analysis of a Saccharomyces cerevisiae wine strain.  Borneman AR, Forgan AH, Pretorius IS, Chambers PJ. (11/1/2008) FEMS Yeast Research 8(7): 1185-95
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Comprehensive genomic characterization defines human glioblastoma genes and core pathways.  Cancer Genome Atlas Research Network (10/23/2008) Nature 455: 1061-8
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Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood.  Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. (10/21/2008) PNAS 105: 16266-71
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Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.  Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson DS. (8/28/2008) BMC Genomics 9: 404
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A genome-wide view of the spectrum of spontaneous mutations in yeast  Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, Thomas WK. (7/8/2008) PNAS 105: 9272-9277
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High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome  Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M. (6/30/2008) BMC Genomics 9:
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Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta)  Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS, Smith DG (5/29/2008) BMC Genomics 9: 256
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Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey  Kankshita Swaminathan, Kranthi Varala, and Matthew E. Hudson (5/1/2008) BMC Genomics 8:
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The complete genome of an individual by massively parallel DNA sequencing   David A. Wheeler, Maithreyan Srinivasan, Michael Egholm, Yufeng Shen, Lei Chen, Amy McGuire, Wen He, Yi-Ju Chen, Vinod Makhijani, G. Thomas Roth, Xavier Gomes, Karrie Tartaro, Faheem Niazi, Cynthia L. Turcotte, Gerard P. Irzyk, James R. Lupski, Craig Chinault, Xing-zhi Song, Yue Liu, Ye Yuan, Lynne Nazareth, Xiang Qin, Donna M. Muzny, Marcel Margulies, George M. Weinstock, Richard A. Gibbs, Jonathan M. Rothberg (4/17/2008) Nature 452: 872-876
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Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing  Bekal S, Craig JP, Hudson ME, Niblack TL, Domier LL, Lambert KN (3/7/2008) Mol Genet Genomics :
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Scanning the human genome at kilobase resolution  Jun Chen, Yeong C Kim, Yong-Chul Jung, Zhenyu Xuan, Geoff Dworkin, Yanming Zhang, Michael Q Zhang and San Ming Wang (2/21/2008) Genome Research 18: 751-62
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Genomic degradation of a young Y chromosome in Drosophila miranda  Bachtrog D, Hom E, Wong KM, Maside X, de Jong P (2/12/2008) Genome Biology 9:
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A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety  Riccardo Velasco, Andrey Zharkikh, Michela Troggio, Dustin A. Cartwright, Alessandro Cestaro, Dmitry Pruss, Massimo Pindo, Lisa M. FitzGerald, Silvia Vezzulli, Julia Reid, Giulia Malacarne, Diana Iliev, Giuseppina Coppola, Bryan Wardell, Diego Micheletti, Teresita Macalma, Marco Facci, Jeff T. Mitchell, Michele Perazzolli, Glenn Eldredge, Pamela Gatto, Rozan Oyzerski, Marco Moretto, Natalia Gutin, Marco Stefanini, Yang Chen, Cinzia Segala, Christine Davenport, Lorenzo Dematte, Amy Mraz, Juri Battilana, Keith Stormo, Fabrizio Costa, Quanzhou Tao, Azeddine Si-Ammour, Tim Harkins, Angie Lackey, Clotilde Perbost, Bruce Taillon, Alessandra Stella, Victor Solovyev, Jeffrey A. Fawcett, Lieven Sterck, Klaas Vandepoele, Stella M. Grando, Stefano Toppo, Claudio Moser, Jerry Lanchbury, Robert Bogden, Mark Skolnick, Vittorio Sgaramella, Satish K. Bhatnagar, Paolo Fontana, Alexander Gutin, Yves Van de Peer, Francesco Salamini, Roberto Viola (12/1/2007) PLoS ONE 12:
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Gene family encoding the major toxins of lethal Amanita mushrooms  Heather E. Hallen , Hong Luo, John S. Scott-Craig, and Jonathan D. Walton (11/27/2007) PNAS 104: 19097-19101
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Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula  Macas J, Neumann P, Navratilova A (11/21/2007) BMC Genomics 8:
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Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome  Jan O. Korbel, Alexander Eckehart Urban, Jason P. Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik Simons, Philip M. Kim, Dean Palejev, Nicholas J. Carriero, Lei Du, Bruce E. Taillon, Zhoutao Chen, Andrea Tanzer, A. C. Eugenia Saunders, Jianxiang Chi, Fengtang Yang, Nigel P. Carter, Matthew E. Hurles, Sherman M. Weissman, Timothy T. Harkins, Mark B. Gerstein, Michael Egholm, and Michael Snyder (10/19/2007) Science 318: 420-426
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MamuSNP: A Resource for Rhesus Macaque (Macaca mulatta) Genomics  Ripan S. Malhi, Brad Sickler, Dawei Lin, Jessica Satkoski, Raul Y. Tito, Debbie George, Sreetharan Kanthaswamy, David Glenn Smith (5/1/2007) PLOS One 5:
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454 sequencing put to the test using the complex genome of barley   Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J. Close, Beat Keller, and Nils Stein (10/26/2006) BMC Genomics 7:
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