Sequencing-Related
Papers of Note, August 2008
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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. |