Sequencing-Related Papers of Note, March 2008
Authors Title Citation
Bekal S, Craig JP, Hudson ME, Niblack TL, Domier LL, Lambert KN.

Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing.

 Mol Genet Genomics. 2008 Mar 7 [Epub ahead of print]
Brockman W, Alvarez P, Young S, Garber M, et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res. 2008 Mar 17 [Epub ahead of print]
Butler J, Maccallum I, Kleber M, Shlyakhter IA, et al. ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res. 2008 Mar 13 [Epub ahead of print]
Chen D, Ahlford A, Schnorrer F, Kalchhauser I, et al. High-resolution, high-throughput SNP mapping in Drosophila melanogaster. Nat Methods. 2008 Apr;5(4):323-9. Epub 2008 Mar 9.
Chen J, Kim YC, Jung YC, Xuan Z, et al. Scanning the human genome at kilobase resolution. Genome Res. 2008 Mar 27 [Epub ahead of print]
Chen W, Kalscheu V, Tzschach A, Menzel C, et al. Mapping translocation breakpoints by next-generation sequencing. Genome Res. 2008 Mar 7 [Epub ahead of print]
Dinsdale EA, Edwards RA, Hall D, Angly F, et al. Functional metagenomic profiling of nine biomes. Nature. 2008 Apr 3;452(7187):629-32. Epub 2008 Mar 12.
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, et al. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.
Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008 Mar 27 [Epub ahead of print]
Lu C, Jeong DH, Kulkarni K, Pillay M, et al. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4951-6. Epub 2008 Mar 19.
Lu J, Shen Y, Wu Q, Kumar S, et al. The birth and death of microRNA genes in Drosophila. Nat Genet. 2008 Mar;40(3):351-5. Epub 2008 Feb 17.
Martin F, Aerts A, Ahrén D, Brun A, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008 Mar 6;452(7183):88-92.
Meagher RJ, Won JI, Coyne JA, Lin J, Barron AE. Sequencing of DNA by free-solution capillary electrophoresis using a genetically engineered protein polymer drag-tag. Anal Chem. 2008 Mar 5 [Epub ahead of print]
Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008 Apr 4;133(1):116-27. Epub 2008 Mar 13.
Montgomery TA, Howell MD, Cuperus JT, Li D, et al. Specificity of Argonaute7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008 Apr 4;133(1):128-41. Epub 2008 Mar 13.
Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 2008 Apr;18(4):571-84. Epub 2008 Mar 6.
Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics. 2008 Mar 24 [Epub ahead of print]
Ohnishi Y, Ishikawa J, Hara H, Suzuki H, et al. The genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol. 2008 Mar 28 [Epub ahead of print]
Paul B, Cloninger C, Felton M, Khachatoorian R, Metzenberg S. A nonalkaline method for isolating sequencing-ready plasmids. Anal Biochem. 2008 Mar 7 [Epub ahead of print]
Pearson MM, Sebaihia M, Churcher C, Quail MA, et al. The complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol. 2008 Mar 28 [Epub ahead of print]
Raphael BJ, Volik S, Yu P, Wu C, et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008 Mar 25;9(3):R59 [Epub ahead of print]
Sanchez-Villeda H, Schroeder S, Flint-Garcia S, Guill KE, et al. DNAAlignEditor: DNA alignment editor tool. BMC Bioinformatics. 2008 Mar 19;9(1):154 [Epub ahead of print]
Schones DE, Cui K, Cuddapah S, Roh TY, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell. 2008 Mar 7;132(5):887-98.
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 2008 Mar 18;6(3):e65.
Starkenburg SR, Larimer FW, Stein LY, Klotz MG, et al. The complete genome sequence of Nitrobacter hamburgensis X14 and a comparative genomic analysis of species within the Genus Nitrobacter. Appl Environ Microbiol. 2008 Mar 7 [Epub ahead of print]
Tauch A, Trost E, Tilker A, Ludewig U, et al. The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. J Biotechnol. 2008 Mar 10 [Epub ahead of print]
Tribolium Genome Sequencing Consortium The genome of the model beetle and pest Tribolium castaneum. Nature. 2008 Mar 23 [Epub ahead of print]
Vallenet D, Nordmann P, Barbe V, Poirel L, et al. Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS ONE. 2008 Mar 19;3(3):e1805.
Vorhölter FJ, Schneiker S, Goesmann A, Krause L, et al. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. J Biotechnol. 2008 Mar 20;134(1-2):33-45. Epub 2008 Jan 20.