Sequencing-Related Papers of Note, August 2008
Authors Title Citation
Bansal V, Bafna V.

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.

Bioinformatics. 2008 Aug 15;24(16):i153-9.
Bansal V, Halpern AL, Axelrod N, Bafna V. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res. 2008 Aug;18(8):1336-46.
Beres SB, Sesso R, Pinto SW, Hoe NP, Porcella SF, Deleo FR, Musser JM. Genome sequence of a lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease. PLoS ONE. 2008 Aug 21;3(8):e3026.
Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13081-6. Epub 2008 Aug 22.
Cronn R, Liston A, Parks
M, Gernandt DS, Shen R, Mockler T.
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 2008 Aug 27. [Epub ahead of print]
Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC, Markowitz VM. Annotation of metagenome short reads using proxygenes. Bioinformatics. 2008 Aug 15;24(16):i7-13.
De Bona F, Ossowski S, Schneeberger K, Rätsch G. Optimal spliced alignments of short sequence reads. Bioinformatics. 2008 Aug 15;24(16):i174-80.
Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis. 2008 Aug;5(4):459-72.
Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P,
Joint I.
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE. 2008 Aug 22;3(8):e3042.
Green RE, Malaspinas AS, Krause J, Briggs AW, et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 2008 Aug 8;134(3):416-26.
Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK. Characterization of unique small RNA populations from rice grain. PLoS ONE. 2008 Aug 6;3(8):e2871.
Jiang H, Wong WH. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics. 2008 Aug 12. [Epub ahead of print]
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008 Sep;36(16):5221-31. Epub 2008 Aug 6.
Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008 Aug 17. [Epub ahead of print]
Kim BS, Kim BK, Lee JH, Kim M, Lim YW, Chun J. Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J Microbiol. 2008 Aug;46(4):357-63. Epub 2008 Aug 31.
Lawniczak MK, Holloway AK, Begun DJ, Jones CD. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol. 2008 Aug 12;9(8):R125. [Epub ahead of print]
Lebet T, Chiles R, Hsu AP, Mansfield ES, Warrington JA, Puck JM. Mutations causing severe combined immunodeficiency: detection with a custom resequencing microarray. Genet Med. 2008 Aug;10(8):575-85.
Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008 Aug 19. [Epub ahead of print]
Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM! Zillions Of Oligos Mapped. Bioinformatics. 2008 Aug 6. [Epub ahead of print]
Liu Z, Desantis TZ, Andersen GL, Knight R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008 Aug 22. [Epub ahead of print]
Lu JQ, Zhang X. Nucleotide capacitance calculation for DNA sequencing. Biophys J. 2008 Aug 15. [Epub ahead of print]
Luo Y, Xu X, Ding Z, Liu Z, Zhang B, Yan Z, Sun J, Hu S, Hu X. Complete genome of Phenylobacterium zucineum — a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562. BMC Genomics. 2008 Aug 13;9:386.
Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res. 2008 Sep 1;36(16):5180-5188. Epub 2008 Aug 5.
Mathur D, Danford TW, Boyer LA, Young RA, Gifford DK, Jaenisch R. Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol. 2008 Aug 13;9(8):R126. [Epub ahead of print]
Mattes TE, Alexander AK, Richardson PM, Munk AC, Han CS, Stothard P, Coleman NV. The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology. Appl Environ Microbiol. 2008 Aug 22. [Epub ahead of print]
McNally B, Wanunu M, Meller A. Electromechanical unzipping of individual DNA molecules using synthetic sub-2 nm pores. Nano Lett. 2008 Aug 30. [Epub ahead of print]
Miller WG, Wang G, Binnewies TT, Parker CT. The complete genome sequence and analysis of the human pathogen Campylobacter lari. Foodborne Pathog Dis. 2008 Aug;5(4):371-86.
Moxon S, Schwach F, Maclean D, Dalmay T, Studholme DJ, Moulton V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics. 2008 Aug 19. [Epub ahead of print]
Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC. Genetic variation in an individual human exome. PLoS Genet. 2008 Aug 15;4(8):e1000160.
Purnell RF, Mehta KK, Schmidt JJ. Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore. Nano Lett. 2008 Aug 13. [Epub ahead of print]
Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, et al. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE. 2008 Aug 13;3(8):e2945.
Quinn NL, Levenkova N, Chow W, Bouffard P, et al. Assessing the feasibility of GS FLX pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics. 2008 Aug 28;9:404.
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sperandio V, Ravel J. The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 2008 Aug 1. [Epub ahead of print]
Sarin S, Prabhu S, O'Meara MM, Pe'er I, Hobert O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods. 2008 Aug 1. [Epub ahead of print]
Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC,
Vogel J.
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 2008 Aug 22;4(8):e1000163.
Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, et al. The Trichoplax genome and the nature of placozoans. Nature. 2008 Aug 21;454(7207):955-60.
Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008 Aug 1;4(8):e1000139.
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods. 2008 Aug 17. [Epub ahead of print]
Vigneault F, Sismour AM, Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods. 2008 Aug 17. [Epub ahead of print]
Wanunu M, Sutin J, McNally B, Chow A, Meller A. DNA translocation governed by interactions with solid state nanopores. Biophys J. 2008 Aug 15. [Epub ahead of print]
Wiens GD, Rockey DD, Wu Z, Chang J, Levy R, et al. The genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor. J Bacteriol. 2008 Aug 22. [Epub ahead of print]
Williams JG, Steffens DL, Anderson JP, Urlacher TM, Lamb DT, Grone DL,
Egelhoff JC.
An artificial processivity clamp made with streptavidin facilitates oriented attachment of polymerase-DNA complexes to surfaces. Nucleic Acids Res. 2008 Aug 22. [Epub ahead of print]
Xu Y, Gao S, Bruno JF, Luft BJ, Dunn JJ. Rapid detection and identification of a pathogen's DNA using Phi29 DNA polymerase. Biochem Biophys Res Commun. 2008 Aug 26. [Epub ahead of print]
Yeager M, Xiao N, Hayes RB, Bouffard P, Desany B, et al. Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum Genet. 2008 Sep;124(2):161-70. Epub 2008 Aug 14.
Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Modeling ChIP sequencing in silico with applications. PLoS Comput Biol. 2008 Aug 22;4(8):e1000158.
Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res. 2008 Sep;18(9):1456-65. Epub 2008 Aug 7.