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Papers of Note for Jan 2009


Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing.
Trick M, Long Y, Meng J, Bancroft I.
Plant Biotechnol J. 2009 Jan 16. [Epub ahead of print]

The deep evolution of metazoan microRNAs.
Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ.
Evol Dev. 2009 Jan-Feb;11(1):50-68.

Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution.
Dai Z, Chen Z, Ye H, Zhou L, Cao L, Wang Y, Peng S, Chen L.
Evol Dev. 2009 Jan-Feb;11(1):41-9.

Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
Strittmatter AW, Liesegang H, Rabus R, Decker I, et al.
Environ Microbiol. 2009 Jan 14. [Epub ahead of print]

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.
Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, et al.
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1886-91. Epub 2009 Jan 30.

Massively parallel sequencing of the poly-adenylated transcriptome of C. elegans.
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.
Genome Res. 2009 Jan 30. [Epub ahead of print]

Profile of the circulating DNA in apparently healthy individuals.
Beck J, Urnovitz HB, Riggert J, Clerici M, Schütz E.
Clin Chem. 2009 Jan 30. [Epub ahead of print]

Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis.
Ward PN, Holden MT, Leigh JA, Lennard N, Bignell A, et al.
BMC Genomics. 2009 Jan 28;10(1):54. [Epub ahead of print]

Profiling RE1/REST-mediated histone modifications in the human genome.
Zheng D, Zhao K, Mehler MF.
Genome Biol. 2009 Jan 27;10(1):R9. [Epub ahead of print]

Genomic location analysis by ChIP-Seq.
Barski A, Zhao K.
J Cell Biochem. 2009 Jan 27. [Epub ahead of print]

The complete genome sequence of Erythrobacter litoralis HTCC2594.
Oh HM, Giovannoni SJ, Ferriera S, Johnson J, Cho JC.
J Bacteriol. 2009 Jan 23. [Epub ahead of print]

Microscopic mechanics of hairpin DNA translocation through synthetic nanopores.
Comer J, Dimitrov V, Zhao Q, Timp G, Aksimentiev A.
Biophys J. 2009 Jan;96(2):593-608.

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
Touchon M, Hoede C, Tenaillon O, Barbe V, et al.
PLoS Genet. 2009 Jan;5(1):e1000344. Epub 2009 Jan 23.

Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes.
Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, et al.
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):2071-6. Epub 2009 Jan 22.

Human gut microbiota in obesity and after gastric bypass.
Zhang H, Dibaise JK, Zuccolo A, Kudrna D, Braidotti M, et al.
Proc Natl Acad Sci U S A. 2009 Jan 21. [Epub ahead of print]

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.
Lefrancois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.
BMC Genomics. 2009 Jan 21;10(1):37. [Epub ahead of print]

Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach.
Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, et al.
PLoS ONE. 2009;4(1):e4219. Epub 2009 Jan 19.

Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, et al.
PLoS ONE. 2009;4(1):e4207. Epub 2009 Jan 16.

Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust.
Wei Y, Chen S, Yang P, Ma Z, Kang L.
Genome Biol. 2009 Jan 16;10(1):R6. [Epub ahead of print]

Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome.
Wu CW, Schramm TM, Zhou S, Schwartz DC, Talaat AM.
BMC Genomics. 2009 Jan 15;10:25.

Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.
Mavromatis K, Ivanova N, Anderson I, Lykidis A, Hooper SD, et al.
PLoS ONE. 2009;4(1):e4192. Epub 2009 Jan 15.

Control of shape and material composition of solid-state nanopores.
Wu MY, Smeets RM, Zandbergen M, Ziese U, Krapf D, Batson PE, Dekker NH, Dekker C, Zandbergen HW.
Nano Lett. 2009 Jan;9(1):479-84.

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Miller W, Drautz DI, Janecka JE, Lesk AM, Ratan A, Tomsho LP, et al.
Genome Res. 2009 Feb;19(2):213-20. Epub 2009 Jan 12.

Controlling the translocation of single-stranded DNA through alpha-hemolysin ion channels using viscosity.
Kawano R, Schibel AE, Cauley C, White HS.
Langmuir. 2009 Jan 20;25(2):1233-7.

Developing a tissue resource to characterize the genome of pancreatic cancer.
Voidonikolas G, Gingras MC, Hodges S, McGuire AL, Chen C, Gibbs RA, Brunicardi FC, Fisher WE.
World J Surg. 2009 Jan 10. [Epub ahead of print]

Transcriptome sequencing to detect gene fusions in cancer.
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM.
Nature. 2009 Jan 11. [Epub ahead of print]

Profiling model T cell metagenomes with short reads.
Warren RL, Nelson BH, Holt RA.
Bioinformatics. 2009 Jan 9. [Epub ahead of print]

Alignment of biological sequences with quality scores.
Na JC, Roh K, Apostolico A, Park K.
Int J Bioinform Res Appl. 2009;5(1):97-113.

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses.
Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N.
ISME J. 2009 Jan 8. [Epub ahead of print]

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.
Nat Biotechnol. 2009 Jan;27(1):66-75. Epub 2009 Jan 4.

High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.
Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, et al.
PLoS ONE. 2009;4(1):e4108. Epub 2009 Jan 1.

A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.
Almeida NF, Yan S, Lindeberg M, Studholme DJ, et al.
Mol Plant Microbe Interact. 2009 Jan;22(1):52-62.

Continuous-flow polymerase chain reaction of single-copy DNA in microfluidic microdroplets.
Schaerli Y, Wootton RC, Robinson T, Stein V, Dunsby C, Neil MA, French PM, Demello AJ, Abell C, Hollfelder F.
Anal Chem. 2009 Jan 1;81(1):302-6.