Sequencing-Related Papers of Note, May 2008
Authors Title Citation
Amadou C, Pascal G, Mangenot S, Glew M, et al.

Genome sequence of the ß-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia.

 Genome Res. 2008 May 19. [Epub ahead of print]
Bruinsma JJ, Schneider D, Davis D, Kornfeld K. Identification of mutations in Caenorhabditis elegans that cause resistance to high levels of dietary zinc and analysis using a genome-wide map of single-nucleotide polymorphisms scored by pyrosequencing. Genetics. 2008 May 27. [Epub ahead of print]
Cloonan N, Forrest AR, Kolle G, Gardiner BB, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods. 2008 May 30. [Epub ahead of print]
Cole CG, McCann OT, Collins JE, Oliver K, et al. Finishing the finished human chromosome 22 sequence. Genome Biol. 2008 May 13;9(5):R78. [Epub ahead of print]
Crasta OR, Folkerts O, Fei Z, Mane SP, et al. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS ONE. 2008 May 14;3(5):e2193.
Dolan PC, Denver DR. TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics. 2008 May 28;9(1):250. [Epub ahead of print]
Espagne E, Lespinet O, Malagnac F, Da Silva C, et al. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol. 2008 May 6;9(5):R77. [Epub ahead of print]
Field D, Garrity G, Gray T, Morrison N, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May;26(5):541-7
Gilbert MT, Kivisild T, Grønnow B, Andersen PK, et al. Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science. 2008 May 29. [Epub ahead of print]
Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 2008 Jun;18(6):957-64. Epub 2008 May 9
Grice EA, Kong HH, Renaud G, Young AC et al. A diversity profile of the human skin microbiota. Genome Res. 2008 May 23. [Epub ahead of print]
Guermazi S, Daegelen P, Dauga C, Rivière D, Bouchez T, Godon JJ, et al. Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environ Microbiol. 2008 May 6. [Epub ahead of print]
Kidd JM, Cooper GM, Donahue WF, Hayden HS, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64.
Kottmann R, Gray T, Murphy S, Kagan L, et al. A standard MIGS/MIMS compliant XML schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS. 2008 May 14. [Epub ahead of print]
Kube M, Migdoll AM, Müller I, Kuhl H, et al. The genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia. Environ Microbiol. 2008 May 6. [Epub ahead of print]
Lee JH, Karamychev VN, Kozyavkin SA, Mills D, et al. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics. 2008 May 27;9(1):247. [Epub ahead of print]
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, et al. Evolution of mammals and their gut microbes. Science. 2008 May 22. [Epub ahead of print]
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 2;133(3):523-36
Martinez D, Berka RM, Henrissat B, Saloheimo M, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 2008 May;26(5):553-60. Epub 2008 May 4
Melchior L, Kivisild T, Lynnerup N, Dissing J. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years. PLoS ONE. 2008 May 28;3(5):e2214
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 May 30. [Epub ahead of print]
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 May 1. [Epub ahead of print]
Nakayama K, Yamashita A, Kurokawa K, Morimoto T, et al. The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res. 2008 May 28. [Epub ahead of print]
Paoletti M, Saupe SJ. The genome sequence of Podospora anserina, a classic model fungus. Genome Biol. 2008 May 15;9(5):223. [Epub ahead of print]
Paoletti M, Saupe SJ. Pihlak A, Baurén G, Hersoug E, Lönnerberg P, Metsis A, Linnarsson S. Rapid genome sequencing with short universal tiling probes. Nat Biotechnol. 2008 May 25. [Epub ahead of print]
Riley M, Staley JT, Danchin A, Wang TZ, et al. Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics. 2008 May 6;9:210.
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics. 2008 May 1;9(1):204. [Epub ahead of print]
Satkoski JA, Malhi RS, Kanthaswamy S, Tito RY, Malladi VS, Smith DG. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics. 2008 May 29;9(1):256. [Epub ahead of print]
Valouev A, Ichikawa J, Tonthat T, Stuart J, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 May 13. [Epub ahead of print]
Warren WC, Hillier LW, Marshall Graves JA, Birney E, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83
Weiner RM, Taylor LE 2nd, Henrissat B, Hauser L, et al. Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genet. 2008 May 30;4(5):e1000087.
Wendl MC, Wilson RK. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics. 2008 May 16;9(1):239. [Epub ahead of print]
Yang JS, Yang WJ. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics. 2008 May 30;9(1):257. [Epub ahead of print]
You FM, Huo N, Gu YQ, Luo MC, et al. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008 May 29;9(1):253. [Epub ahead of print]