Sequencing-Related Papers of Note, July 2008
Authors Title Citation
Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, et al.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

 Nat Biotechnol. 2008 Aug;26(8):909-15. Epub 2008 Jul 27.
Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE. 2008 Jul 30;3(7):e2836.
Batista PJ, Ruby JG, Claycomb JM, Chiang R, et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell. 2008 Jul 11;31(1):67-78. Epub 2008 Jun 19.
Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10583-8. Epub 2008 Jul 23.
Das PP, Bagijn MP, Goldstein LD, Woolford JR, et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell. 2008 Jul 11;31(1):79-90.
Dmitriev DA, Rakitov RA. Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Comput Biol. 2008 Jul 25;4(7):e1000113.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008 Jul 26. [Epub ahead of print]
Doostzadeh J, Shokralla S, Absalan F, Jalili R, et al. High throughput automated allele frequency estimation by pyrosequencing. PLoS ONE. 2008 Jul 16;3(7):e2693.
Dowd SE, Callaway TR, Wolcott RD, Sun Y, et al. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008 Jul 24;8(1):125. [Epub ahead of print]
Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods. 2008 Aug;5(8):679-82. Epub 2008 Jul 6.
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics. 2008 Aug 1;24(15):1729-30. Epub 2008 Jul 3.
Fouts DE, Tyler HL, DeBoy RT, Daugherty S, et al. Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet. 2008 Jul 25;4(7):e1000141.
Hajirasouliha I, Hormozdiari F, Sahinalp SC, Birol I. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics. 2008 Jul 1;24(13):i32-40.
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella typhi. Nat Genet. 2008 Aug;40(8):987-93. Epub 2008 Jul 27.
Hou S, Makarova KS, Saw JH, Senin P, et al. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct. 2008 Jul 1;3:26.
Jakše J, Meyer JD, Suzuki G, McCallum J, Cheung F, Town CD, Havey MJ. Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration. Mol Genet Genomics. 2008 Jul 10.
Krause J, Unger T, Nocon A, Malaspinas AS, Kolokotronis SO, et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol. 2008 Jul 28;8(1):220. [Epub ahead of print]
Lee TH, Kim YK, Nahm BH. GBParsy: A GenBank flatfile parser library with high speed. BMC Bioinformatics. 2008 Jul 25;9(1):321. [Epub ahead of print]
Maeda N, Nishiyori H, Nakamura M, Kawazu C, et al. Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Biotechniques. 2008 Jul;45(1):95-7.
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008 Jul 30. [Epub ahead of print]
Meissner A, Mikkelsen TS, Gu H, Wernig M, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70. Epub 2008 Jul 6.
Morin R, Bainbridge M, Fejes A, Hirst M, et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques. 2008 Jul;45(1):81-94.
Moxon S, Jing R, Szittya G, Schwach F, et al. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res. 2008 Jul 24. [Epub ahead of print]
Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H. Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics. 2008 Jul 31. [Epub ahead of print]
Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, et al. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol. 2008 Jul 8;6:30.
Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol. 2008 Jul 22;6(7):e177.
Sultan M, Schulz MH, Richard H, Magen A, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008 Jul 3. [Epub ahead of print]
Wederell ED, Bilenky M, Cullum R, Thiessen N, et al. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008 Aug;36(14):4549-64. Epub 2008 Jul 8.
Weisenberger DJ, Trinh BN, Campan M, Sharma S, et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res. 2008 Aug;36(14):4689-98. Epub 2008 Jul 15.
Xu H, Wei CL, Lin F, Sung WK An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics. 2008 Jul 29. [Epub ahead of print]
Zheng D. Asymmetric histone modifications between the original and derived loci of human segmental duplications. Genome Biol. 2008 Jul 3;9(7):R105. [Epub ahead of print]