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Last Week's Sequencing-Related Papers of Note: May 20, 2014


Objective and comprehensive evaluation of bisulfite short read mapping tools.
Tran H, Porter J, Sun MA, Xie H2, Zhang L.
Adv Bioinformatics. 2014;2014:472045.

Solid-state nanopores and nanopore arrays optimized for optical detection.
Sawafta F, Clancy B, Carlsen AT, Huber M, Hall AR.
Nanoscale. 2014 May 19. [Epub ahead of print]

Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.
Laurence M, Hatzis C, Brash DE.
PLOS One. 2014 May 16;9(5):e97876.

Bayesian approach to single-cell differential expression analysis.
Kharchenko PV, Silberstein L, Scadden DT.
Nat Methods. 2014 May 18. [Epub ahead of print]

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Van Allen EM, Wagle N, Stojanov P, Perrin DL, et al.
Nat Med. 2014 May 18. [Epub ahead of print]

methylSig: a whole genome DNA methylation analysis pipeline.
Park Y, Figueroa ME, Rozek LS, Sartor MA.
Bioinformatics. 2014 May 16. [Epub ahead of print]

Genome sequence of the cultivated cotton Gossypium arboretum.
Li F, Fan G, Wang K, Sun F, et al.
Nat Genet. 2014 May 18. [Epub ahead of print]

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation.
Zhao L, Sun MA, Li Z, Bai X, et al.
Genome Res. 2014 May 16. [Epub ahead of print]

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.
Kunze G, Gaillardin C, Czernicka M, Durrens P, et al.
Biotechnol Biofuels. 2014 Apr 24;7:66.

Quality control of next-generation sequencing data without a reference.
Trivedi UH, Cézard T, Bridgett S, Montazam A, et al.
Front Genet. 2014 May 6;5:111.

A Bayesian semi-parametric approach for the differential analysis of sequence counts data.
Guindani M, Sepúlveda N, Paulino CD, Müller P.
J R Stat Soc Ser C Appl Stat. 2014 Apr;63(3):385-404.

RNASeqExpressionBrowser − a web interface to browse and visualize high-throughput expression data.
Nussbaumer T, Kugler KG, Bader KC, Sharma S, et al.
Bioinformatics. 2014 May 14. [Epub ahead of print]

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
Wang W, Wang P, Xu F, Luo R, et al.
Bioinformatics. 2014 May 14. [Epub ahead of print]

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.
Wong LP, Lai JK, Saw WY, Ong RT, et al.
PLOS Genet. 2014 May 15;10(5):e1004377.

Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire.
Lepore M, Kalinicenko A, Colone A, Paleja B, et al.
Nat Commun. 2014 May 15;5:3866.

Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data.
Yi M, Zhao Y, Jia L, He M, et al.
Nucleic Acids Res. 2014 May 15. [Epub ahead of print]

OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from Ion Torrent data.
Zhu P, He L, Li Y, Huang W, et al.
PLOS One. 2014 May 13;9(5):e97507.

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.
Pires DE, Ascher DB, Blundell TL.
Nucleic Acids Res. 2014 May 14. [Epub ahead of print]

Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.
Huang J, Zhao Y, Shiraigol W, Li B, et al.
Sci Rep. 2014 May 14;4:4958.

Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics.
Tin MM, Economo EP, Mikheyev AS.
PLOS One. 2014 May 14;9(5):e96793.

Identification of the genomic insertion site of Pmel-1 TCR α and β transgenes by next-generation sequencing.
Ji Y, Abrams N, Zhu W, Salinas E, et al.
PLOS One. 2014 May 14;9(5):e96650.

Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation.
Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, et al.
Sci Signal. 2014 May 13;7(325):rs3.

Stabilization of graphene nanopore.
Lee J, Yang Z, Zhou W, Pennycook SJ, et al.
Proc Natl Acad Sci U S A. 2014 May 12. [Epub ahead of print]

Selective detection and quantification of modified DNA with solid-state nanopores.
Carlsen AT, Zahid OK, Ruzicka JA, Taylor EW, Hall AR.
Nano Lett. 2014 May 13. [Epub ahead of print]

Applicability of next-generation sequencing to decalcified formalin-fixed and paraffin-embedded chronic myelomonocytic leukaemia samples.
Bernard V, Gebauer N, Dinh T, Stegemann J, et al.
Int J Clin Exp Pathol. 2014 Mar 15;7(4):1667-76.

Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.
Miranda KC, Bond DT, Levin JZ, Adiconis X, et al.
PLOS One. 2014 May 9;9(5):e96094.

cDNA hybrid capture improves transcriptome analysis on low-input and archived samples.
Cabanski CR, Magrini V, Griffith M, Griffith OL, et al.
J Mol Diagn. 2014 May 8. [Epub ahead of print]

Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.
Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, et al.
Cell Rep. 2014 May 7. [Epub ahead of print]

compcodeR - an R package for benchmarking differential expression methods for RNA-seq data.
Soneson C.
Bioinformatics. 2014 May 9. [Epub ahead of print]

Efficient RNA isoform identification and quantification from RNA-seq data with network flows.
Bernard E, Jacob L, Mairal J, Vert JP.
Bioinformatics. 2014 May 9. [Epub ahead of print]

Detection of gene rearrangements in targeted clinical next-generation sequencing.
Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, et al.
J Mol Diagn. 2014 May 6. [Epub ahead of print]