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In Print: Last Week's Sequencing-Related Papers of Note: Nov 12, 2013


Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.
Jiang Y, Ninwichian P, Liu S, Zhang J, et al.
PLOS One. 2013 Oct 24;8(10):e78872.

Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-seq datasets.
Zhang W, Edwards A, Flemington EK, Zhang K.
PLOS One. 2013 Oct 30;8(10):e78868.

Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data.
Bryzgalov LO, Antontseva EV, Matveeva MY, Shilov AG, et al.
PLOS One. 2013 Oct 29;8(10):e78833.

Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.
Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, et al.
PLOS One. 2013 Oct 29;8(10):e78575.

RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.
Yuan C, Sun Y.
PLOS One. 2013 Oct 25;8(10):e77596.

Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-seq.
Borozan I, Watt SN, Ferretti V.
PLOS One. 2013 Oct 30;8(10):e76935.

Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments.
Jostins L, Levine AP, Barrett JC.
PLOS One. 2013 Oct 18;8(10):e76328.

A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.
Feehery GR, Yigit E, Oyola SO, Langhorst BW, et al.
PLOS One. 2013 Oct 28;8(10):e76096.

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.
Seth-Smith HM, Harris SR, Scott P, Parmar S, et al.
Nat Protoc. 2013 Dec;8(12):2404-12.

Modeling alternative splicing variants from RNA-seq data with isoform graphs.
Beretta S, Bonizzoni P, Vedova GD, Pirola Y, Rizzi R.
J Comput Biol. 2013 Nov 7. [Epub ahead of print]

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.
Aldridge S, Watt S, Quail MA, Rayner T, et al.
Genome Biol. 2013 Nov 7;14(11):R124.

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina-based approaches.
Drechsler A, Geller D, Freund K, Schmeller DS, et al.
Ecol Evol. 2013 Oct;3(11):3947-57.

Biases in small RNA deep sequencing data.
Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS.
Nucleic Acids Res. 2013 Nov 5. [Epub ahead of print]

Inference of tumor phylogenies with improved somatic mutation discovery.
Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, et al.
J Comput Biol. 2013 Nov;20(11):933-44.

SEME: a fast mapper of Illumina sequencing reads with statistical evaluation.
Chen S, Wang A, Li LM.
J Comput Biol. 2013 Nov;20(11):847-60.

Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.
Mason MR, Nagaraja HN, Camerlengo T, Joshi V, Kumar PS.
PLOS One. 2013 Oct 23;8(10):e77287.

Mu-seq: Sequence-based mapping and identification of transposon induced mutations.
McCarty DR, Latshaw S, Wu S, Suzuki M, et al.
PLOS One. 2013 Oct 23;8(10):e77172.

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.
Black MB, Parks BB, Pluta L, Chu TM, et al.
Toxicol Sci. 2013 Nov 5. [Epub ahead of print]

Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum.
Pang AW, Macdonald JR, Yuen RK, Hayes VM, Scherer SW.
G3 (Bethesda). 2013 Nov 5. [Epub ahead of print]

Design and analysis of Bar-seq experiments.
Robinson DG, Chen W, Storey JD, Gresham D.
G3 (Bethesda). 2013 Nov 5. [Epub ahead of print]

WaveCNV: allele specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.
Holt C, Losic B, Pai D, Zhao Z, et al.
Bioinformatics. 2013 Nov 4. [Epub ahead of print]

Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.
Spaethling JM, Piel D, Dueck H, Buckley PT, et al.
FASEB J. 2013 Nov 5. [Epub ahead of print]

Model-based clustering for RNA-seq data.
Si Y, Liu P, Li P, Brutnell TP.
Bioinformatics. 2013 Nov 4. [Epub ahead of print]

Likelihood-based inference of population history from low coverage de novo genome assemblies.
Hearn J, Stone GN, Bunnefeld L, Nicholls JA, et al.
Mol Ecol. 2013 Nov 4. [Epub ahead of print]

Optimal assembly for high throughput shotgun sequencing.
Bresler G, Bresler M, Tse D.
BMC Bioinformatics. 2013 Jul 9;14 Suppl 5:S18.

Bacterial colonization factors control specificity and stability of the gut microbiota.
Lee SM, Donaldson GP, Mikulski Z, Boyajian S, et al.
Nature. 2013 Sep 19;501(7467):426-9.