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Papers of Note: Jun 9, 2009


Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo.
Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, et al.
PLoS ONE. 2009 May 25;4(5):e5683.

Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.
Champion MD, Zeng Q, Nix EB, Nano FE, Keim P, Kodira CD, Borowsky M, et al.
PLoS Pathog. 2009 May;5(5):e1000459. Epub 2009 May 29.

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing.
Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Benjamin Gordon D, et al.
Nat Protoc. 2009;4(6):960-74. Epub 2009 May 28.

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing.
Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM.
Science. 2009 May 29;324(5931):1210-3.

Topographical and temporal diversity of the human skin microbiome.
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC; NISC Comparative Sequencing Program, et al.
Science. 2009 May 29;324(5931):1190-2.

Whole genome assembly from 454 sequencing output via modified DNA graph concept.
Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, et al.
Comput Biol Chem. 2009 Jun;33(3):224-30. Epub 2009 May 3.

Phylogenetic understanding of clonal populations in an era of whole genome sequencing.
Pearson T, Okinaka RT, Foster JT, Keim P.
Infect Genet Evol. 2009 May 25. [Epub ahead of print]

The genome sequence of Geobacter metallireducens: features of metabolism, physiology, and regulation common and dissimilar to Geobacter sulfurreducens.
Aklujkar M, Krushkal J, Dibartolo G, Lapidus A, Land ML, Lovley DR.
BMC Microbiol. 2009 May 27;9(1):109. [Epub ahead of print]

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The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group.
Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim D, Kim BC, Kim SY, Kim WY, et al.
Genome Res. 2009 May 26. [Epub ahead of print]

Strain and virulence diversity in the mouse pathogen Chlamydia muridarum.
Ramsey KH, Sigar IM, Schripsema JH, Denman CJ, Bowlin AK, Meyers GA, Rank RG.
Infect Immun. 2009 May 26. [Epub ahead of print]

Lineage-specific biology revealed by a finished genome assembly of the mouse.
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, et al.
PLoS Biol. 2009 May 5;7(5):e1000112. Epub 2009 May 26.

The controlled fabrication of nanopores by focused electron-beam-induced etching.
Yemini M, Hadad B, Liebes Y, Goldner A, Ashkenasy N.
Nanotechnology. 2009 Jun 17;20(24):245302. Epub 2009 May 26.

Genome sequence of the recombinant protein production host Pichia pastoris.
De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, et al.
Nat Biotechnol. 2009 May 24. [Epub ahead of print]

Genome-wide and fine-resolution association analysis of malaria in West Africa.
Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, et al.
Nat Genet. 2009 May 24. [Epub ahead of print]

Complete genome sequence of Lactobacillus plantarum JDM1.
Zhang Z, Liu C, Zhu Y, Zhong Y, Zhu Y, Zheng H, Zhao GP, Wang SY, Guo X.
J Bacteriol. 2009 May 22. [Epub ahead of print]

Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time PCR profiling and small RNA sequencing.
Pant BD, Musialak-Lange M, Nuc P, May P, Walther D, Scheible WR.
Plant Physiol. 2009 May 22. [Epub ahead of print]

Complete genome sequence of the chemolithoautotrophic marine Magnetotactic coccus strain MC-1.
Schübbe S, Williams TJ, Xie G, Kiss HE, Brettin TS, Martinez D, Ross CA, et al.
Appl Environ Microbiol. 2009 May 22. [Epub ahead of print]

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WebGMAP: a web service for mapping and aligning cDNA sequences to genomes.
Liang C, Liu L, Ji G.
Nucleic Acids Res. 2009 May 22. [Epub ahead of print]

SHRiMP: accurate mapping of short color-space reads.
Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.
PLoS Comput Biol. 2009 May;5(5):e1000386. Epub 2009 May 22.

Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during C. elegans development.
Kato M, de Lencastre A, Pincus Z, Slack FJ.
Genome Biol. 2009 May 21;10(5):R54. [Epub ahead of print]

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies.
Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E.
FEMS Microbiol Lett. 2009 May 1. [Epub ahead of print]

Quantitative analysis of DNA methylation after whole bisulfitome amplification of a minute amount of DNA from body fluids.
Vaissière T, Cuenin C, Paliwal A, Vineis P, Hoek G, Krzyzanowski M, et al.
Epigenetics. 2009 May 24;4(4). [Epub ahead of print]

High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum.
Xie H, Wang M, Bonaldo MD, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB.
Nucleic Acids Res. 2009 May 20. [Epub ahead of print]

Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants.
Bontell IL, Hall N, Ashelford KE, Dubey J, Boyle JP, Lindh J, Smith JE.
Genome Biol. 2009 May 20;10(5):R53. [Epub ahead of print]

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis.
Hahn DA, Ragland GJ, Shoemaker DD, Denlinger DL.
BMC Genomics. 2009 May 19;10(1):234. [Epub ahead of print]

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A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley.
Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N.
Plant J. 2009 May 12. [Epub ahead of print]

Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R.
Bioinformatics. 2009 May 18. [Epub ahead of print]

Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing.
Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC, Sarles J, et al.
Eur J Clin Microbiol Infect Dis. 2009 May 16. [Epub ahead of print]

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.
Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.
Genome Res. 2009 May 15. [Epub ahead of print]

DNA Sudoku — harnessing high-throughput sequencing for multiplexed specimen analysis.
Erlich Y, Chang K, Gordon A, Ronen R, Navon O, Rooks M, Hannon GJ.
Genome Res. 2009 May 15. [Epub ahead of print]

Overlapping pools for high-throughput targeted resequencing.
Prabhu S, Pe'er I.
Genome Res. 2009 May 15. [Epub ahead of print]

Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis.
Wu KM, Li LH, Yan JJ, Tsao N, Liao TL, Tsai HC, Fung CP, Chen HJ, et al.
J Bacteriol. 2009 May 15. [Epub ahead of print]

Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.
Di Bonaventura MP, Desalle R, Pop M, Nagarajan N, Figurski D, Fine DH, et al.
J Bacteriol. 2009 May 15. [Epub ahead of print]

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Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.
Choi H, Nesvizhskii AI, Ghosh D, Qin Z.
Bioinformatics. 2009 May 14. [Epub ahead of print]

Data structures and compression algorithms for genomic sequence data.
Brandon MC, Wallace DC, Baldi P.
Bioinformatics. 2009 May 15. [Epub ahead of print]

Cost-effective sequence-based nonhuman primate MHC class I genotyping from RNA.
Karl JA, Wiseman RW, O'Connor DH.
Methods. 2009 May 12. [Epub ahead of print]

High-throughput bisulfite sequencing in mammalian genomes.
Smith ZD, Gu H, Bock C, Gnirke A, Meissner A.
Methods. 2009 May 12. [Epub ahead of print]

PanGEA: Identification of allele specific gene expression using the 454 technology.
Kofler R, Torres TT, Lelley T, Schlotterer C.
BMC Bioinformatics. 2009 May 14;10(1):143. [Epub ahead of print]

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
Schweiger MR, Kerick M, Timmermann B, Albrecht MW, Borodina T, et al.
PLoS ONE. 2009;4(5):e5548. Epub 2009 May 14.

An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines.
Li J, Gao F, Li N, Li S, Yin G, Tian G, Jia S, Wang K, Zhang X, Yang H, et al.
BMC Genomics. 2009 May 13;10(1):223. [Epub ahead of print]

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.
Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA.
BMC Genomics. 2009 May 12;10:221.

Sequencing and de novo analysis of a coral larval transcriptome using 454 GS FLX.
Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, et al.
BMC Genomics. 2009 May 12;10:219.

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miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.
Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM.
Nucleic Acids Res. 2009 May 11. [Epub ahead of print]

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.
Willerslev E, Gilbert M, Binladen J, Ho S, Campos P, Ratan A, Tomsho L, et al.
BMC Evol Biol. 2009 May 11;9(1):95. [Epub ahead of print]

How to map billions of short reads onto genomes.
Trapnell C, Salzberg SL.
Nat Biotechnol. 2009 May;27(5):455-7.

The genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes.
Setubal JC, Dos Santos P, Goldman BS, Ertesvåg H, Espin G, Rubio LM, et al.
J Bacteriol. 2009 May 8. [Epub ahead of print]

Barcoded pyrosequencing reveals shared bacterial community properties along two alkaline hot spring temperature gradients in Yellowstone National Park.
Miller SR, Strong AL, Jones KL, Ungerer MC.
Appl Environ Microbiol. 2009 May 8. [Epub ahead of print]

High-resolution mapping of sequence-directed nucleosome positioning on genomic DNA.
Fraser RM, Keszenman-Pereyra D, Simmen MW, Allan J.
J Mol Biol. 2009 May 7. [Epub ahead of print]

Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing.
Irvine DV, Goto DB, Vaughn MW, Nakaseko Y, McCombie WR, et al.
Genome Res. 2009 Jun;19(6):1077-83. Epub 2009 May 7.

High-throughput sequencing of the zebrafish antibody repertoire.
Weinstein JA, Jiang N, White RA 3rd, Fisher DS, Quake SR.
Science. 2009 May 8;324(5928):807-10.

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Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs.
Iida K, Fukami-Kobayashi K, Toyoda A, Sakaki Y, Kobayashi M, Seki M, Shinozaki K.
DNA Res. 2009 May 7. [Epub ahead of print]

Large-scale mRNA sequencing determines global regulation of RNA editing during brain development.
Wahlstedt H, Daniel C, Ensterö M, Ohman M.
Genome Res. 2009 Jun;19(6):978-86. Epub 2009 May 6.

SNP detection for massively parallel whole-genome resequencing.
Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J.
Genome Res. 2009 Jun;19(6):1124-32. Epub 2009 May 6.

High-throughput genotyping by whole-genome resequencing.
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, et al.
Genome Res. 2009 Jun;19(6):1068-76. Epub 2009 May 6.

16SrRNA bacterial tag-encoded amplicons pyrosequencing for rapid deciphering of the microbiome of fermented foods: the case of fermented pearl-millet slurries.
Humblot C, Guyot JP.
Appl Environ Microbiol. 2009 May 1. [Epub ahead of print]

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches.
Nasidze I, Quinque D, Li J, Li M, Tang K, Stoneking M.
Anal Biochem. 2009 May 3. [Epub ahead of print]

Transverse electronic transport in double-stranded DNA nucleotides.
Jauregui LA, Salazar-Salinas K, Seminario JM.
J Phys Chem B. 2009 May 7;113(18):6230-9.

Ionic field effect transistors with sub-10 nm multiple nanopores.
Nam SW, Rooks MJ, Kim KB, Rossnagel SM.
Nano Lett. 2009 May;9(5):2044-8.

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing.
Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ.
Plant Biotechnol J. 2009 May;7(4):347-54.

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Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance.
Feng J, Lupien A, Gingras H, Wasserscheid J, Dewar K, Légaré D, Ouellette M.
Genome Res. 2009 May 14. [Epub ahead of print]

Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus.
Al Rwahnih M, Daubert S, Golino D, Rowhani A.
Virology. 2009 May 10;387(2):395-401.

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients.
Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, et al.
J Infect Dis. 2009 May 1;199(9):1275-85.

Nano-sized bacterial magnetic particles displaying pyruvate phosphate dikinase for pyrosequencing.
Yoshino T, Nishimura T, Mori T, Suzuki S, Kambara H, Takeyama H, Matsunaga T.
Biotechnol Bioeng. 2009 May 1;103(1):130-7.

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.