Sequencing-Related Papers of Note, June 2008
Authors Title Citation
Achaz G.

Testing for neutrality in samples with sequencing errors.

 Genetics. 2008 Jun 18. [Epub ahead of print]
Alves PM, Lévy N, Stevenson BJ, Bouzourene H, Theiler G, et al. Identification of tumor-associated antigens by large-scale analysis of genes expressed in human colorectal cancer. Cancer Immun. 2008 Jun 27;8:11.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS. 2008 Jun;12(2):137-41.
Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, et al. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Appl Environ Microbiol. 2008 Jun 6. [Epub ahead of print]
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, et al. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells. 2008 Jun 26. [Epub ahead of print]
Bouchez V, Caro V, Levillain E, Guigon G, Guiso N. Genomic content of Bordetella pertussis clinical isolates circulating in areas of intensive children vaccination. PLoS ONE. 2008 Jun 18;3(6):e2437.
Chen Z, Fu B, Schweller R, Yang B, Zhao Z, Zhu B. Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. J Comput Biol. 2008 Jun;15(5):535-46.
Chung GT, Yoo JS, Oh HB, Lee YS, Cha SH, Kim SJ, Yoo CK. The complete genome sequence of Neisseria gonorrhoeae NCCP11945. J Bacteriol. 2008 Jun 27. [Epub ahead of print]
DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, et al. Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol. 2008 Aug;190(15):5455-63. Epub 2008 Jun 13.
Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, Tu AH, Loraine AE. The genome of Mycoplasma arthritidis. Infect Immun. 2008 Jun 23. [Epub ahead of print]
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):8102-7. Epub 2008 Jun 5.
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, et al. Meeting Report: The Fifth Genomic Standards Consortium (GSC) Workshop. OMICS. 2008 Jun;12(2):109-13.
Garrity GM, Field D, Kyrpides N, Hirschman L, et al. Toward a standards-compliant genomic and metagenomic publication record. OMICS. 2008 Jun;12(2):101-8.
German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol. 2008 Jun 9. [Epub ahead of print]
Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, et al. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8327-32. Epub 2008 Jun 9.
Guo J, Xu N, Li Z, Zhang S, Wu J, Kim DH, et al. Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9145-50. Epub 2008 Jun 30.
Haslam NJ, Whiteford NE, Weber G, Prügel-Bennett A, Essex JW, Neylon C. Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes. PLoS ONE. 2008 Jun 18;3(6):e2500.
Hayatsu H, Shiraishi M, Negishi K. Bisulfite modification for analysis of DNA methylation. Curr Protoc Nucleic Acid Chem. 2008 Jun;Chapter 6:Unit 6.10
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008 Jul;18(7):1100-11. Epub 2008 Jun 18.
Huang W, Marth GT. EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 2008 Jun 11. [Epub ahead of print]
Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, et al. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics. 2008 Jun 4;9:271.
Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, et al. A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9272-7. Epub 2008 Jun 26.
Marioni J, Mason C, Mane S, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008 Jun 11. [Epub ahead of print]
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 2008 Jul;18(7):1073-83. Epub 2008 Jun 12.
McGrath KC, Thomas-Hall SR, Cheng CT, Leo L, Alexa A, Schmidt S, Schenk PM. Isolation and analysis of mRNA from environmental microbial communities. J Microbiol Methods. 2008 Jun 24. [Epub ahead of print]
Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, et al. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res. 2008 Jun 3. [Epub ahead of print]
Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics. 2008 Jun 30;9(1):312.
Paul D, Bridges S, Burgess SC, Dandass Y, Lawrence ML. Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T. J Bacteriol. 2008 Aug;190(15):5531-2. Epub 2008 Jun 6.
Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, et al. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol. 2008 Jun 17. [Epub ahead of print]
Salehi-Ashtiani K, Yang X, Derti A, Tian W, Hao T, et al. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nat Methods. 2008 Jul;5(7):597-600. Epub 2008 Jun 15.
Sischka A, Kleimann C, Hachmann W, Schäfer MM, Seuffert I, Tönsing K, Anselmetti D. Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores. Rev Sci Instrum. 2008 Jun;79(6):063702.
Sobreira TJ, Gruber A. Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data. Bioinformatics. 2008 Jun 9. [Epub ahead of print]
Szczepanowski R, Bekel T, Goesmann A, Krause L, Krömeke H, Kaiser O, Eichler W, Pühler A, Schlüter A. Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. J Biotechnol. 2008 Jun 10. [Epub ahead of print]
Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE. 2008 Jun 25;3(6):e2527
Valach M, Tomaska L, Nosek J. Preparation of yeast mitochondrial DNA for direct sequence analysis. Curr Genet. 2008 Jun 21. [Epub ahead of print]
Wang Y, Kleespies RG, Ramle MB, Jehle JA, et al. Sequencing of the large dsDNA genome of Oryctes rhinoceros nudivirus using multiple displacement amplification of nanogram amounts of virus DNA. J Virol Methods. 2008 Jun 30. [Epub ahead of print]
Zhu W, Ouyang S, Iovene M, O'Brien K, Vuong H, Jiang J, Buell CR. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics. 2008 Jun 13;9:286.