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Papers of Note: Apr 21, 2009


RNA-Seq - Quantitative measurement of expression through massively parallel RNA-sequencing.
Wilhelm BT, Landry JR.
Methods. 2009 Mar 28. [Epub ahead of print]

Determination of enriched histone modifications in non-genic portions of the human genome.
Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ.
BMC Genomics. 2009 Mar 31;10:143.

Well-ordered thin-film nanopore arrays formed using a block-copolymer template.
Jung YS, Ross CA.
Small. 2009 Mar 30. [Epub ahead of print]

Improved PCR-BSP assay for multiplex methylation pattern analysis in minimal amount of DNA.
Wang J, Yu M, Li K, Xiao J, Zhou Y.
Mol Biotechnol. 2009 Mar 31. [Epub ahead of print]

Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences.
Fendt L, Zimmermann B, Daniaux M, Parson W.
BMC Genomics. 2009 Mar 30;10(1):139. [Epub ahead of print]

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.
Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, Gao Y, Zhang K.
Nat Biotechnol. 2009 Apr;27(4):353-60. Epub 2009 Mar 29.

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM.
Nat Biotechnol. 2009 Apr;27(4):361-8. Epub 2009 Mar 29.

Complete genome sequence of Burkholderia glumae BGR1.
Lim J, Lee TH, Nahm BH, Choi YD, Kim M, Hwang I.
J Bacteriol. 2009 Mar 27. [Epub ahead of print]

High throughput sequencing of microRNAs in chicken somites.
Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, Dalmay T.
FEBS Lett. 2009 Mar 27. [Epub ahead of print]

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Evaluation of next generation sequencing platforms for population targeted sequencing studies.
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA.
Genome Biol. 2009 Mar 27;10(3):R32. [Epub ahead of print]

DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution.
Zhang Y, Rohde C, Tierling S, Jurkowski TP, Bock C, Santacruz D, Ragozin S, Reinhardt R, Groth M, Walter J, Jeltsch A.
PLoS Genet. 2009 Mar;5(3):e1000438. Epub 2009 Mar 27.

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.
Galand PE, Casamayor EO, Kirchman DL, Potvin M, Lovejoy C.
ISME J. 2009 Mar 26. [Epub ahead of print]

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI.
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5859-64. Epub 2009 Mar 24.

Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences.
Liu X, Maxwell TJ, Boerwinkle E, Fu YX.
Mol Biol Evol. 2009 Mar 24. [Epub ahead of print]

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces.
Deagle BE, Kirkwood R, Jarman SN.
Mol Ecol. 2009 Mar 20. [Epub ahead of print]

Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology.
Harismendy O, Frazer K.
Biotechniques. 2009 Mar;46(3):229-31.

Microsatellite discovery by deep sequencing of enriched genomic libraries.
Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B.
Biotechniques. 2009 Mar;46(3):217-23.

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Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data.
Allentoft M, Schuster S, Holdaway R, Hale M, McLay E, Oskam C, Gilbert MT, Spencer P, Willerslev E, Bunce M.
Biotechniques. 2009 Mar;46(3):195-200.

Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing.
Abdelkrim J, Robertson B, Stanton JA, Gemmell N.
Biotechniques. 2009 Mar;46(3):185-92.

Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis.
Qi X, Bao FS, Xie Z.
PLoS ONE. 2009;4(3):e4971. Epub 2009 Mar 24.

Identification of EMS-induced mutations in Drosophila melanogaster by whole genome sequencing.
Blumenstiel JP, Noll AC, Griffiths JA, Perera AG, Walton KN, Gilliland WD, Hawley RS, Staehling-Hampton K.
Genetics. 2009 Mar 30. [Epub ahead of print]

The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans.
Klasson L, Westberg J, Sapountzis P, Näslund K, Lutnaes Y, Darby AC, Veneti Z, Chen L, Braig HR, Garrett R, Bourtzis K, Andersson SG.
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5725-30. Epub 2009 Mar 23.

Computational and analytical framework for small RNA profiling by high-throughput sequencing.
Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Givan SA, Carrington JC.
RNA. 2009 Mar 23. [Epub ahead of print]

Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease.
Chu T, Bunce K, Hogge WA, Peters DG.
Bioinformatics. 2009 Mar 23. [Epub ahead of print]

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.
Ziolkowski PA, Koczyk G, Galganski L, Sadowski J.
Nucleic Acids Res. 2009 Mar 21. [Epub ahead of print]

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The structure and complexity of a bacterial transcriptome.
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH.
J Bacteriol. 2009 Mar 20. [Epub ahead of print]

Flow cytometry for enrichment and titration in massively parallel DNA sequencing.
Sandberg J, Ståhl PL, Ahmadian A, Bjursell MK, Lundeberg J.
Nucleic Acids Res. 2009 Mar 20. [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 Mar 20. [Epub ahead of print]

Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens.
Duan CJ, Xian L, Zhao GC, Feng Y, Pang H, Bai XL, Tang JL, Ma QS, Feng JX.
J Appl Microbiol. 2009 Mar 13. [Epub ahead of print]

Digital PCR provides sensitive and absolute calibration for high throughput sequencing.
White RA 3rd, Blainey PC, Fan HC, Quake SR.
BMC Genomics. 2009 Mar 19;10:116.

The sequence analysis and management system -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A.
J Biotechnol. 2009 Mar 10;140(1-2):3-12.

Estimation of allele frequencies from high-coverage genome-sequencing projects.
Lynch M.
Genetics. 2009 Mar 16. [Epub ahead of print]

TopHat: discovering splice junctions with RNA-Seq.
Trapnell C, Pachter L, Salzberg SL.
Bioinformatics. 2009 Mar 16. [Epub ahead of print]

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NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.
Gargiulo G, Levy S, Bucci G, Romanenghi M, Fornasari L, Beeson KY, Goldberg SM, Cesaroni M, Ballarini M, Santoro F, Bezman N, Frigè G, Gregory PD, Holmes MC, Strausberg RL, Pelicci PG, Urnov FD, Minucci S.
Dev Cell. 2009 Mar;16(3):466-81.

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.
Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ.
Nat Methods. 2009 Apr;6(4):291-5. Epub 2009 Mar 15.

High-throughput detection of induced mutations and natural variation using KeyPoint technology.
Rigola D, van Oeveren J, Janssen A, Bonné A, Schneiders H, van der Poel HJ, van Orsouw NJ, Hogers RC, de Both MT, van Eijk MJ.
PLoS ONE. 2009;4(3):e4761. Epub 2009 Mar 13.

The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.
Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, Yuen KY.
PLoS Genet. 2009 Mar;5(3):e1000416. Epub 2009 Mar 13.

Novel method for high-throughput colony PCR screening in nanoliter-reactors.
Marcel W, Rene P, Andreas M, Matthias B, Herve V, Richard R, Joseph M, Sven P, Martin H.
Nucleic Acids Res. 2009 Mar 12. [Epub ahead of print]

Estimating the number of unseen variants in the human genome.
Ionita-Laza I, Lange C, M Laird N.
Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5008-13. Epub 2009 Mar 10.

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: Genome-wide localization studies reveal widespread regulation of transcription elongation.
Gilchrist DA, Fargo DC, Adelman K.
Methods. 2009 Mar 9. [Epub ahead of print]

Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore.
Hurt N, Wang H, Akeson M, Lieberman KR.
J Am Chem Soc. 2009 Mar 18;131(10):3772-8.

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CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.
Wang Z, Tollervey J, Briese M, Turner D, Ule J.
Methods. 2009 Mar 9. [Epub ahead of print]

Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1).
Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, Lapidus A, Hugenholtz P, Brune A.
Appl Environ Microbiol. 2009 Mar 6. [Epub ahead of print]

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.
Bioinformatics. 2009 Mar 5. [Epub ahead of print]

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.
Xie C, Tammi MT.
BMC Bioinformatics. 2009 Mar 6;10:80.

Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene.
Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP.
Science. 2009 Apr 10;324(5924):217. Epub 2009 Mar 5.

Insect-specific microRNA involved in the development of the silkworm Bombyx mori.
Zhang Y, Zhou X, Ge X, Jiang J, Li M, Jia S, Yang X, Kan Y, Miao X, Zhao G, Li F, Huang Y.
PLoS ONE. 2009;4(3):e4677. Epub 2009 Mar 5.

Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.
Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, Albertyn Z, Shaban B, Motro Y, Dunn DS, Schibeci D, Hunter A, Barrero R, Phillips ND, Hampson DJ.
PLoS ONE. 2009;4(3):e4641. Epub 2009 Mar 5.

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.
Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D.
Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4828-33. Epub 2009 Mar 4.

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Genome sequence of the lager brewing yeast, an interspecies hybrid.
Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S, Nakamura N, Shimonaga T, Hattori M, Ashikari T.
DNA Res. 2009 Mar 4. [Epub ahead of print]

Chemically modified primers for improved multiplex polymerase chain reaction.
Shum J, Paul N.
Anal Biochem. 2009 Mar 1. [Epub ahead of print]

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.
Ebhardt HA, Tsang HH, Dai DC, Liu Y, Bostan B, Fahlman RP.
Nucleic Acids Res. 2009 Mar 2. [Epub ahead of print]

Quantification of rare allelic variants from pooled genomic DNA.
Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD.
Nat Methods. 2009 Apr;6(4):263-5. Epub 2009 Mar 1.

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes.
Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ; Terry Beirn Community Programs for Clinical Research on AIDS.
J Infect Dis. 2009 Mar 1;199(5):693-701.

Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.
Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, De Jonghe P, De Rijk P, Del-Favero J.
Hum Mutat. 2009 Mar;30(3):472-6.

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