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Papers of Note: Mar 10, 2009


Chemically modified primers for improved multiplex PCR.
Shum J, Paul N.
Anal Biochem. 2009 Feb 28. [Epub ahead of print]

Genome sequences of three Agrobacterium biovars help elucidate the evolution of multi-chromosome genomes in bacteria.
Slater SC, Goldman BS, Goodner B, Setubal JC, et al.
J Bacteriol. 2009 Feb 27. [Epub ahead of print]

ABySS: A parallel assembler for short read sequence data.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
Genome Res. 2009 Feb 27. [Epub ahead of print]

Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.
Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S.
PLoS ONE. 2009;4(2):e4619. Epub 2009 Feb 27.

Comparative analysis of H2A.Z nucleosome organization in human and yeast genome.
Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ.
Genome Res. 2009 Feb 26. [Epub ahead of print]

Statistical inferences for isoform expression in RNA-Seq.
Jiang H, Wong WH.
Bioinformatics. 2009 Feb 25. [Epub ahead of print]

Electrophysiological study of single gold nanoparticle/alpha-hemolysin complex formation: a nanotool to slow down ssDNA through the alpha-hemolysin nanopore.
Astier Y, Uzun O, Stellacci F.
Small. 2009 Feb 25. [Epub ahead of print] No abstract available.

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QSRA - a quality-value guided de novo short read assembler.
Bryant DW Jr, Wong WK, Mockler TC.
BMC Bioinformatics. 2009 Feb 24;10(1):69. [Epub ahead of print]

Alterations in genes of the EGFR signaling pathway and their relationship to EGFR tyrosine kinase inhibitor sensitivity in lung cancer cell lines.
Gandhi J, Zhang J, Xie Y, Soh J, Shigematsu H, Zhang W, Yamamoto H, et al.
PLoS ONE. 2009;4(2):e4576. Epub 2009 Feb 24.

Massive transcriptional start site analysis of human genes in hypoxia cells.
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto SI, et al.
Nucleic Acids Res. 2009 Feb 22. [Epub ahead of print]

Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere.
Méndez-Lago M, Wild J, Whitehead SL, Tracey A, de Pablos B, Rogers J, et al.
Nucleic Acids Res. 2009 Feb 23. [Epub ahead of print]

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, et al.
Genome Biol. 2009 Feb 23;10(2):R23. [Epub ahead of print]

Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.
Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R.
Proc Natl Acad Sci U S A. 2009 Feb 20. [Epub ahead of print]

Whole genome amplification of the rust Puccinia striiformis f. sp. tritici from single spores.
Wang Y, Zhu M, Zhang R, Yang H, Wang Y, Sun G, Jin S, Hsiang T.
J Microbiol Methods. 2009 Feb 20. [Epub ahead of print]

Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi.
Liu WQ, Feng Y, Wang Y, Zou QH, Chen F, Guo JT, Peng YH, Jin Y, et al.
PLoS ONE. 2009;4(2):e4510. Epub 2009 Feb 20.

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Analyzing gene expression from marine microbial communities using environmental transcriptomics.
Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA.
J Vis Exp. 2009 Feb 18;(24). pii: 1086. doi: 10.3791/1086.

Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete.
Zeschnigk M, Martin M, Betzl G, Kalbe A, Sirsch C, et al.
Hum Mol Genet. 2009 Feb 17. [Epub ahead of print]

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.
Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A.
Nucleic Acids Res. 2009 Feb 17. [Epub ahead of print]

Genotypic detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis strains by DNA sequencing: a randomized trial.
Abdelaal A, El-Ghaffar HA, Zaghloul MH, El Mashad N, Badran E, Fathy A.
Ann Clin Microbiol Antimicrob. 2009 Feb 16;8:5.

Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy.
Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, et al.
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3219-24. Epub 2009 Feb 13.

PASS: a Program to Align Short Sequences.
Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G.
Bioinformatics. 2009 Feb 13. [Epub ahead of print]

Nanoelectromechanics of methylated DNA in a synthetic nanopore.
Mirsaidov U, Timp W, Zou X, Dimitrov V, Schulten K, Feinberg AP, Timp G.
Biophys J. 2009 Feb;96(4):L32-4.

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Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.
Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, et al.
Retrovirology. 2009 Feb 12;6(1):15. [Epub ahead of print]

Sequencing and analyses of all known human rhinovirus genomes reveals structure and evolution.
Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, et al.
Science. 2009 Feb 12. [Epub ahead of print]

ChIP-seq accurately predicts tissue-specific activity of enhancers.
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, et al.
Nature. 2009 Feb 12;457(7231):854-8.

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, et al.
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9. Epub 2009 Feb 10.

Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils.
Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, et al.
Appl Environ Microbiol. 2009 Feb 5. [Epub ahead of print]

Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette-Guérin (BCG) Tokyo 172: A comparative study of BCG vaccine substrains.
Seki M, Honda I, Fujita I, Yano I, Yamamoto S, Koyama A.
Vaccine. 2009 Mar 10;27(11):1710-6. Epub 2009 Feb 4.

Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea.
Pinhassi J, Pujalte MJ, Pascual J, González JM, Lekunberri I, et al.
Int J Syst Evol Microbiol. 2009 Feb;59(Pt 2):373-7.

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Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, et al.
Nat Biotechnol. 2009 Feb;27(2):182-9. Epub 2009 Feb 1.

Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing.
Callaway TR, Dowd SE, Wolcott RD, Sun Y, McReynolds JL, Edrington TS, et al.
Poult Sci. 2009 Feb;88(2):298-302.

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing.
James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN.
Genome Res. 2009 Feb 17. [Epub ahead of print]

In situ
transcriptomic analysis of the globally important keystone N(2)-fixing taxon Crocosphaera watsonii.
Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, Bench SR, et al.
ISME J. 2009 Feb 19. [Epub ahead of print]

Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre.
Poretsky RS, Hewson I, Sun S, Allen AE, Zehr JP, Moran MA.
Environ Microbiol. 2009 Feb 3. [Epub ahead of print]

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

Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity.
Palenik B, Ren Q, Tai V, Paulsen IT.
Environ Microbiol. 2009 Feb;11(2):349-59.

Down-regulation of Gfi-1 expression by TGF-beta is important for differentiation of Th17 and CD103+ inducible regulatory T cells.
Zhu J, Davidson TS, Wei G, Jankovic D, Cui K, Schones DE, Guo L, et al.
J Exp Med. 2009 Feb 16;206(2):329-41. Epub 2009 Feb 2.

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS.
Science. 2009 Feb 12. [Epub ahead of print]

The Scan

Close Panel Vote on Califf Nomination

The New York Times reports there was a close committee vote to advance the nomination of Robert Califf to lead the US Food and Drug Administration to the full Senate.

Task Force Reports on Scientific Integrity

Nature News writes that that a new task force report recommends that the US establish a cross-agency scientific integrity council.

Across the Hall

Genetic testing, closed-circuit cameras, and more show how a traveler, without any contact, infected others at a New Zealand quarantine facility, CNN reports.

Science Paper Examines Influence of Chromatin Modifications on Obsessive-Compulsive Disorder

In Science this week: genes regulating chromatin modification may contribute to OCD risk.