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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]

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.