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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.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.