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In Print: Sequencing-Related Papers of Note of the Last Two Weeks: Nov 27, 2012


COPI transport complexes bind to specific RNAs in neuronal cells.
Todd AG, Lin H, Ebert AD, Liu Y, Androphy EJ.
Hum Mol Genet. 2012 Nov 21. [Epub ahead of print]

Population genomics based on low coverage sequencing: how low should we go?
Alex Buerkle C, Gompert Z.
Mol Ecol. 2012 Nov 22. [Epub ahead of print]

Intron-centric estimation of alternative splicing from RNA-seq data.
Pervouchine DD, Knowles DG, Guigó R.
Bioinformatics. 2012 Nov 21. [Epub ahead of print]

Diversity, distribution and sources of bacteria in residential kitchens.
Flores GE, Bates ST, Caporaso JG, Lauber CL, et al.
Environ Microbiol. 2012 Nov 5. [Epub ahead of print]

Limitations and possibilities of low cell number ChIP-seq.
Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, et al.
BMC Genomics. 2012 Nov 21;13(1):645.

Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.
Bellemain E, Davey ML, Kauserud H, Epp LS, et al.
Environ Microbiol. 2012 Oct 11. [Epub ahead of print]

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers.
Wang N, Thomson M, Bodles WJ, Crawford RM, et al.
Mol Ecol. 2012 Nov 21. [Epub ahead of print]

Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanic CCMP1779.
Vieler A, Wu G, Tsai CH, Bullard B, et al.
PLoS Genet. 2012 Nov;8(11):e1003064.

Controls of nucleosome positioning in the human genome.
Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, et al.
PLoS Genet. 2012 Nov;8(11):e1003036.

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.
Aagaard K, Petrosino J, Keitel W, Watson M, et al.
FASEB J. 2012 Nov 19. [Epub ahead of print]

Methods for high-throughput MethylCap-seq data analysis.
Rodriguez BA, Frankhouser D, Murphy M, Trimarchi M, et al.
BMC Genomics. 2012 Oct 26;13 Suppl 6:S14.

Effective normalization for copy number variation detection from whole genome sequencing.
Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N.
BMC Genomics. 2012 Oct 26;13 Suppl 6:S16.

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology.
Wu J, Liu B, Cheng F, Ramchiary N, et al.
Front Plant Sci. 2012;3:243. Epub 2012 Nov 8.

Scaffolding low quality genomes using orthologous protein sequences.
Li YI, Copley RR.
Bioinformatics. 2012 Nov 18. [Epub ahead of print]

VirusSeq: Software to identify viruses and their integration sites using nex-tgeneration sequencing of human cancer tissue.
Chen Y, Yao H, Thompson EJ, M Tannir N, et al.
Bioinformatics. 2012 Nov 17. [Epub ahead of print]

PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Campagna D, Telatin A, Forcato C, Vitulo N, Valle G.
Bioinformatics. 2012 Nov 17. [Epub ahead of print]

Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution.
Healy K, Ray V, Willis LJ, Peterman N, et al.
Electrophoresis. 2012 Sep 14. [Epub ahead of print]

Progress towards the application of molecular force spectroscopy to DNA sequencing.
Cheng P, Oliver PM, Barrett MJ, Vezenov D.
Electrophoresis. 2012 Sep 28. [Epub ahead of print]

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
Abyzov A, Mariani J, Palejev D, Zhang Y, et al.
Nature. 2012 Nov 18. [Epub ahead of print]

Streaming fragment assignment for real-time analysis of sequencing experiments.
Roberts A, Pachter L.
Nat Methods. 2012 Nov 18. [Epub ahead of print]

Multiple regulatory variants modulate expression of 5-hydroxytryptamine 2A receptors in human cortex.
Smith RM, Papp AC, Webb A, Ruble CL, et al.
Biol Psychiatry. 2012 Nov 13. [Epub ahead of print]

Copy number variation detection from 1000 Genomes Project exon capture sequencing data.
Wu J, Grzeda KR, Stewart C, Grubert F, et al.
BMC Bioinformatics. 2012 Nov 17;13(1):305.

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, et al.
Nucleic Acids Res. 2012 Nov 15. [Epub ahead of print]

RNA-seq and microarray complement each other in transcriptome profiling.
Kogenaru S, Qing Y, Guo Y, Wang N.
BMC Genomics. 2012 Nov 15;13(1):629.

Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines.
Frampton M, Houlston R.
PLoS One. 2012;7(11):e49110.

LDx: Estimation of linkage disequilibrium from high-throughput pooled resequencing data.
Feder AF, Petrov DA, Bergland AO.
PLoS One. 2012;7(11):e48588.

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model.
De Beuf K, De Schrijver J, Thas O, Van Criekinge W, et al.
BMC Bioinformatics. 2012 Nov 15;13(1):303.

Nascent-seq reveals novel features of mouse circadian transcriptional regulation.
Menet JS, Rodriguez J, Abruzzi KC, Rosbash M.
elife. 2012;1:e00011. Epub 2012 Nov 13.

Virtual metagenome reconstruction from 16S rRNA gene sequences.
Okuda S, Tsuchiya Y, Kiriyama C, Itoh M, Morisaki H.
Nat Commun. 2012 Nov 13;3:1203.

Genome sequences of wild and domestic bactrian camels.
The Bactrian Camels Genome Sequencing and Analysis Consortium, Jirimutu, Wang Z, Ding G, et al.
Nat Commun. 2012 Nov 13;3:1202.

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritime and Spartina alterniflora (Poaceae).
Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, et al.
Heredity. 2012 Nov 14. [Epub ahead of print]

The genome of pear (Pyrus bretschneideri Rehd.).
Wu J, Wang Z, Shi Z, Zhang S, et al.
Genome Res. 2012 Nov 13. [Epub ahead of print]

Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.
Shearer AE, Hildebrand MS, Ravi H, Joshi S, et al.
BMC Genomics. 2012 Nov 14;13(1):618.

Oculus: faster sequence alignment by streaming read compression.
Chinnaiyan AM, Iyer MK, Veeneman BA.
BMC Bioinformatics. 2012 Nov 13;13(1):297.

Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation.
Quail MA, Gu Y, Swerdlow H, Mayho M.
Electrophoresis. 2012 Sep 7. [Epub ahead of print]

K(+) , Na(+) , and Mg(2+) on DNA translocation in silicon nitride nanopores.
Uplinger J, Thomas B, Rollings R, Fologea D, et al.
Electrophoresis. 2012 Sep 4. [Epub ahead of print]

Modulating DNA translocation by a controlled deformation of a PDMS nanochannel device.
Fanzio P, Manneschi C, Angeli E, Mussi V, et al.
Sci Rep. 2012;2:791. Epub 2012 Nov 9.

MetaSee: An interactive and extendable visualization toolbox for metagenomic sample analysis and comparison.
Song B, Su X, Xu J, Ning K.
PLoS One. 2012;7(11):e48998.

Novel SNP discovery in African buffalo, Syncerus caffer, using high-throughput sequencing.
le Roex N, Noyes H, Brass A, Bradley DG, et al.
PLoS One. 2012;7(11):e48792.

Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples.
Galan M, Pagès M, Cosson JF.
PLoS One. 2012;7(11):e48374.

Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen.
Fouts DE, Szpakowski S, Purushe J, Torralba M, et al.
PLoS One. 2012;7(11):e48289.

Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions.
Schwarzbauer K, Bodenhofer U, Hochreiter S.
PLoS One. 2012;7(11):e47924.

A jungle in there: bacteria in belly buttons are highly diverse, but predictable.
Hulcr J, Latimer AM, Henley JB, Rountree NR, et al.
PLoS One. 2012;7(11):e47712.

A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.
Mijušković M, Brown SM, Tang Z, Lindsay CR, et al.
PLoS One. 2012;7(10):e48314.

Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound.
Port JA, Wallace JC, Griffith WC, Faustman EM.
PLoS One. 2012;7(10):e48000.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.