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Papers of Note: May 5, 2009


The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.
Allen MA, Lauro FM, Williams TJ, Burg D, Siddiqui KS, et al.
ISME J. 2009 Apr 30. [Epub ahead of print]

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.
Hale MC, McCormick CR, Jackson JR, Dewoody JA.
BMC Genomics. 2009 Apr 29;10(1):203. [Epub ahead of print]

Parallel DNA pyrosequencing unveils new zebrafish microRNAs.
Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, et al.
BMC Genomics. 2009 Apr 27;10(1):195. [Epub ahead of print]

Metagenomic analysis of stressed coral holobionts.
Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, et al.
Environ Microbiol. 2009 Apr 22. [Epub ahead of print]

Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam.
Stewart FJ, Cavanaugh CM.
Environ Microbiol. 2009 Apr 21. [Epub ahead of print]

Electronic control of DNA polymerase binding and unbinding to single DNA molecules.
Wilson NA, Abu-Shumays R, Gyarfas B, Wang H, Lieberman KR, Akeson M, Dunbar WB
ACS Nano. 2009 Apr 28;3(4):995-1003.

Ionic field effect transistors with sub-10 nm multiple nanopores.
Nam SW, Rooks MJ, Kim KB, Rossnagel SM.
Nano Lett. 2009 Apr 27. [Epub ahead of print]

The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak.
Sato S, Feltus FA, Iyer P, Tien M.
Curr Genet. 2009 Apr 26. [Epub ahead of print]

Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression.
Kim J, Bartel DP.
Nat Biotechnol. 2009 Apr 26. [Epub ahead of print]

Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses.
Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R.
Virology. 2009 Apr 22. [Epub ahead of print]

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A whole-genome assembly of the domestic cow, Bos taurus.
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al.
Genome Biol. 2009 Apr 24;10(4):R42. [Epub ahead of print]

Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.
Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, Urban N, et al.
PLoS ONE. 2009;4(4):e5311. Epub 2009 Apr 23.

Assembling the marine metagenome, one cell at a time.
Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, et al.
PLoS ONE. 2009;4(4):e5299. Epub 2009 Apr 23.

The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Bovine Genome Sequencing and Analysis Consortium
Science. 2009 Apr 24;324(5926):522-8.

A practical algorithm for finding maximal exact matches in large sequence data sets using sparse suffix arrays.
Khan Z, Bloom JS, Kruglyak L, Singh M.
Bioinformatics. 2009 Apr 23. [Epub ahead of print]

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.
Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, et al.
Nucleic Acids Res. 2009 Apr 22. [Epub ahead of print]

Old can be new again: HAPPY whole genome sequencing, mapping and assembly.
Jiang Z, Rokhsar DS, Harland RM.
Int J Biol Sci. 2009;5(4):298-303. Epub 2009 Apr 15.

Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore.
Stoddart D, Heron AJ, Mikhailova E, Maglia G, Bayley H.
PNAS. 2009 Apr 20. [Epub ahead of print]

Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation.
Guryev V, Cuppen E.
FEBS Lett. 2009 Apr 18. [Epub ahead of print]

Preparation of genome-wide DNA fragment-libraries using bisulfite in polyacrylamide gel electrophoresis slices (Bis-PAGE), with formamide denaturation, and QC for massively parallel sequencing by oligonucleotide ligation and detection (SOLiD).
Ranade SS, Chung CB, Zon G, Boyd VL.
Anal Biochem. 2009 Apr 17. [Epub ahead of print]

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A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.
Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, Croft LJ, Taft RJ, Rizzi E, et al.
BMC Genomics. 2009 Apr 20;10(1):163. [Epub ahead of print]

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation.
Tarpey PS, Smith R, Pleasance E, Whibley A, et al.
Nat Genet. 2009 May;41(5):535-43. Epub 2009 Apr 19.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
FANTOM Consortium
Nat Genet. 2009 May;41(5):553-62. Epub 2009 Apr 19.

Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04.
Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, et al.
J Bacteriol. 2009 Apr 17. [Epub ahead of print]

Estimating accuracy of RNA-seq and microarrays with proteomics.
Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P.
BMC Genomics. 2009 Apr 16;10(1):161. [Epub ahead of print]

Transcript length bias in RNA-seq data confounds systems biology.
Oshlack A, Wakefield MJ.
Biol Direct. 2009 Apr 16;4(1):14. [Epub ahead of print]

Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera.
Pauchet Y, Wilkinson P, van Munster M, Augustin S, Pauron D, Ffrench-Constant RH.
Insect Biochem Mol Biol. 2009 Apr 11. [Epub ahead of print]

Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity.
Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, et al.
Environ Microbiol. 2009 Apr 1. [Epub ahead of print]

Methods for generating shotgun and mixed shotgun/paired-end libraries for the 454 DNA sequencer.
Wiley G, Macmil S, Qu C, Wang P, Xing Y, White D, Li J, White JD, Domingo A, Roe BA.
Curr Protoc Hum Genet. 2009 Apr; Chapter 18:Unit18.1.

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, et al.
Science. 2009 Apr 10;324(5924):268-72.

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Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis.
Chen HM, Wu SH.
Nucleic Acids Res. 2009 Apr 8. [Epub ahead of print]

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 Apr 6. [Epub ahead of print]

Sequence analysis of percent G+C fraction libraries of human faecal bacterial DNA reveals a high number of Actinobacteria.
Krogius-Kurikka L, Kassinen A, Paulin L, Corander J, Makivuokko H, Tuimala J, Palva A.
BMC Microbiol. 2009 Apr 8;9(1):68. [Epub ahead of print]

mRNA-Seq whole-transcriptome analysis of a single cell.
Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA.
Nat Methods. 2009 May;6(5):377-82. Epub 2009 Apr 6.

Genome sequence of the anaerobic, thermophilic and cellulolytic bacterium Anaerocellum thermophilum DSM 6725.
Kataeva IA, Yang SJ, Dam P, Poole FL 2nd, Yin Y, Zhou F, Chou WC, Xu Y, et al.
J Bacteriol. 2009 Apr 3. [Epub ahead of print]

High-throughput, high-accuracy array-based resequencing.
Zheng J, Moorhead M, Weng L, Siddiqui F, Carlton VE, Ireland JS, Lee L, et al.
PNAS. 2009 Apr 2. [Epub ahead of print]

The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.
Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, et al.
BMC Genomics. 2009 Apr 2;10(1):145. [Epub ahead of print]

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing.
Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA.
ISME J. 2009 Apr 2. [Epub ahead of print]

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands.
Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG.

EMBO J. 2009 Apr 2. [Epub ahead of print]

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.
Fullwood MJ, Wei CL, Liu ET, Ruan Y.
Genome Res. 2009 Apr;19(4):521-32.

Non-destructive sampling of ancient insect DNA.
Thomsen PF, Elias S, Gilbert MT, Haile J, Munch K, Kuzmina S, Froese DG, Sher A, Holdaway RN, Willerslev E.
PLoS ONE. 2009;4(4):e5048. Epub 2009 Apr 1.

Cost effective DNA sequencing and template preparation from bacterial colonies and plasmids.
Maruyama F, Nozawa T, Aikawa C, Sakurai A, Nakagawa I.
J Biosci Bioeng. 2009 Apr;107(4):471-3.

Planning the human variome project: the Spain report.
Kaput J, Cotton RG, Hardman L, Watson M, et al.
Hum Mutat. 2009 Apr;30(4):496-510.

Sequencing of single and double stranded RNA oligonucleotides by acid hydrolysis and MALDI mass spectrometry.
Bahr U, Aygün H, Karas M.
Anal Chem. 2009 Apr 15;81(8):3173-9.

ABySS: A parallel assembler for short read sequence data.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
Genome Res
. 2009 Apr 21. [Epub ahead of print]

The Scan

Comfort of Home

The Guardian reports that AstraZeneca is to run more clinical trials from people's homes with the aim of increasing participant diversity.

Keep Under Control

Genetic technologies are among the tools suggested to manage invasive species and feral animals in Australia, Newsweek says.

Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.