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In Print: Last Week's Sequencing-Related Papers of Note: Dec 10, 2013


Next generation sequencing uncovers unexpected bacterial pathogens in ticks in Western Europe.
Vayssier-Taussat M, Moutailler S, Michelet L, Devillers E, et al.
PLoS One. 2013 Nov 27;8(11):e81439.

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
Fagerberg L, Hallstrom BM, Oksvold P, Kampf C, et al.
Mol Cell Proteomics. 2013 Dec 5. [Epub ahead of print]

Optimization of virus detection in cells using massively parallel sequencing.
McClenahan SD, Uhlenhaut C, Krause PR.
Biologicals. 2013 Dec 2. [Epub ahead of print]

Nanopore integrated nanogaps for DNA detection.
Fanget A, Floriano T, Khlybov S, Granjon P, et al.
Nano Lett. 2013 Dec 6. [Epub ahead of print]

A platform independent RNA-seq protocol for the detection of transcriptome complexity.
Calabrese C, Mangiulli M, Manzari C, Paluscio AM, et al.
BMC Genomics. 2013 Dec 5;14(1):855.

Viral quasispecies inference from 454 pyrosequencing.
Poh WT, Xia E, Chin-Inmanu K, Wong LP, et al.
BMC Bioinformatics. 2013 Dec 5;14(1):355.

Joint estimation of isoform expression and isoform-specific read distribution using multi-sample RNA-seq data.
Suo C, Calza S, Salim A, Pawitan Y.
Bioinformatics. 2013 Dec 3. [Epub ahead of print]

HomSI: a homozygous stretch identifier from next-generation sequencing data.
Gormez Z, Bakir-Gungor B, Sagiroglu MS.
Bioinformatics. 2013 Dec 3. [Epub ahead of print]

TIGRA: a Targeted Iterative Graph Routing Assembler for breakpoint assembly.
Chen K, Chen L, Fan X, Wallis J, et al.
Genome Res. 2013 Dec 4. [Epub ahead of print]

Amplification and thrifty single molecule sequencing of recurrent somatic structural variations.
Patel AD, Schwab R, Liu YT, Bafna V.
Genome Res. 2013 Dec 4. [Epub ahead of print]

Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis.
Damerla RR, Chatterjee B, Li Y, Francis RJ, et al.
Mamm Genome. 2013 Dec 5. [Epub ahead of print]

GARM: Genome Assembly, Reconciliation and Merging pipeline.
Soto-Jimenez LM, Estrada K, Berriman M, Sanchez-Flores A.
Curr Top Med Chem. 2013 Dec 3. [Epub ahead of print]

Towards the integration, annotation and association of historical microarray experiments with RNA-seq.
Chavan SS, Bauer MA, Peterson EA, Heuck CJ, Johann DJ.
BMC Bioinformatics. 2013;14 Suppl 14:S4.

Comparative studies of differential gene calling using RNA-seq data.
Zheng X, Moriyama EN.
BMC Bioinformatics. 2013;14 Suppl 13:S7.

VarBin, a novel method for classifying true and false positive variants in NGS data.
Durtschi J, Margraf RL, Coonrod EM, Mallempati KC, Voelkerding KV.
BMC Bioinformatics. 2013;14 Suppl 13:S2.

Improved picoliter-sized micro-reactors for high-throughput biological analysis.
Han W, Yuan L, Wei Q, Li Y, et al.
Sci China Life Sci. 2013 Dec;56(12):1134-41.

A generic plant RNA isolation method suitable for RNA-seq and suppression subtractive hybridization.
Zhu YQ, Wu WJ, Xiao HW, Chen HB, et al.
Genet Mol Res. 2013 Nov 18;12(4):5537-46.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.
Luo GZ, Yang W, Ma YK, Wang XJ.
Bioinformatics. 2013 Dec 3. [Epub ahead of print]

Comparison of software packages for detecting differential expression in RNA-seq studies.
Seyednasrollah F, Laiho A, Elo LL.
Brief Bioinform. 2013 Dec 2. [Epub ahead of print]

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
Marinov GK, Williams BA, McCue K, Schroth GP, et al.
Genome Res. 2013 Dec 3. [Epub ahead of print]

Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes.
González E, Joly S.
BMC Res Notes. 2013 Dec 3;6(1):503.

Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.
Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, et al.
Front Immunol. 2013 Nov 15;4:358.

Genome-block expression-assisted association studies discover malaria resistance genes in Anopheles gambiae.
Li J, Wang X, Zhang G, Githure JI, et al.
Proc Natl Acad Sci U S A. 2013 Dec 2. [Epub ahead of print]

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.
Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, et al.
Proc Natl Acad Sci U S A. 2013 Dec 2. [Epub ahead of print]

Variant priorization and analysis incorporating problematic regions of the genome.
Patwardhan A, Clark M, Morgan A, Chervitz S, et al.
Pac Symp Biocomput. 2014;19:277-87.

Detecting statistical interaction between somatic mutational events and germline variation from next-generation sequence data.
Hu H, Huff CD.
Pac Symp Biocomput. 2014;19:51-62.

NextClip: an analysis and read preparation tool for Nextera long mate pair libraries.
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M.
Bioinformatics. 2013 Dec 2. [Epub ahead of print]

Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.
Rico C, Normandeau E, Dion-Côté AM, Rico MI, et al.
Sci Rep. 2013 Dec 3;3:3376.

DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification.
El Templeton J, Brotherton PM, Llamas B, Soubrier J, et al.
Investig Genet. 2013 Dec 2;4(1):26.