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In Print: Last Week's Sequencing-Related Papers of Note: Oct 1, 2013


STAR: an integrated solution to management and visualization of sequencing data.
Wang T, Liu J, Shen L, Tonti-Filippini J, et al.
Bioinformatics. 2013 Sep 27. [Epub ahead of print]

Rapid TnLE-seq for gene fitness evaluation in underdeveloped bacterial systems.
Fels SR, Zane GM, Blake SM, Wall JD.
Appl Environ Microbiol. 2013 Sep 27. [Epub ahead of print]

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.
St Laurent G, Tackett MR, Nechkin S, Shtokalo D, et al.
Nat Struct Mol Biol. 2013 Sep 29. [Epub ahead of print]

eXtasy: variant prioritization by genomic data fusion.
Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, et al.
Nat Methods. 2013 Sep 29. [Epub ahead of print]

Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing.
Faiz F, Allcock RJ, Hooper AJ, van Bockxmeer FM.
Atherosclerosis. 2013 Oct;230(2):249-55.

Reliable identification of genomic variants from RNA-seq data.
Piskol R, Ramaswami G, Li JB.
Am J Hum Genet. 2013 Sep 25. pii: S0002-9297(13)00383-2.

Organism-specific rRNA capture system for application in next-generation sequencing.
Li SK, Zhou JW, Yim AK, Leung AK, et al.
PLOS One. 2013 Sep 20;8(9):e74286.

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.
Marschall T, Hajirasouliha I, Schönhuth A.
Bioinformatics. 2013 Sep 25. [Epub ahead of print]

Tagmentation-based whole-genome bisulfite sequencing.
Wang Q, Gu L, Adey A, Radlwimmer B, et al.
Nat Protoc. 2013 Oct;8(10):2022-32.

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data.
Piper J, Elze MC, Cauchy P, Cockerill PN, et al.
Nucleic Acids Res. 2013 Sep 25. [Epub ahead of print]

Long insert whole genome sequencing for copy number variant and translocation detection.
Liang WS, Aldrich J, Tembe W, Kurdoglu A, et al.
Nucleic Acids Res. 2013 Sep 25. [Epub ahead of print]

A SNP profiling panel for sample tracking in whole-exome sequencing studies.
Pengelly RJ, Gibson J, Andreoletti G, Collins A, et al.
Genome Med. 2013 Sep 27;5(9):89.

Combining next-generation sequencing and immune assays: a novel method for identification of antigen-specific T cells.
Klinger M, Kong K, Moorhead M, Weng L, et al.
PLOS One. 2013 Sep 19;8(9):e74231.

Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
Koshimizu E, Miyatake S, Okamoto N, Nakashima M, et al.
PLOS One. 2013 Sep 16;8(9):e74167.

Mutagenic and cytotoxic properties of oxidation products of 5-methylcytosine revealed by next-generation sequencing.
Xing XW, Liu YL, Vargas M, Wang Y, et al.
PLOS One. 2013 Sep 16;8(9):e72993.

BSeQC: quality control of bisulfite sequencing experiments.
Lin X, Sun D, Rodriguez B, Zhao Q, et al.
Bioinformatics. 2013 Sep 23. [Epub ahead of print]

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.
Mithani A, Belfield EJ, Brown C, Jiang C, et al.
BMC Genomics. 2013 Sep 24;14(1):653.

Evaluating statistical analysis models for RNA sequencing experiments.
Reeb PD, Steibel JP.
Front Genet. 2013 Sep 17;4:178.

Facile mutant identification via a single parental backcross method and application of whole genome sequencing based mapping pipelines.
Allen RS, Nakasugi K, Doran RL, Millar AA, Waterhouse PM.
Front Plant Sci. 2013 Sep 13;4:362.

Single-base DNA discrimination via transverse ionic transport.
Wilson J, Di Ventra M.
Nanotechnology. 2013 Sep 24;24(41):415101.

Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data.
Kruczyk M, Umer HM, Enroth S, Komorowski J.
BMC Bioinformatics. 2013 Sep 23;14(1):280.

Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.
Gao F, Lin E, Feng Y, Mack WJ, et al.
PLOS One. 2013 Sep 13;8(9):e75294.

Genomewide variation in an introgression line of rice-zizania revealed by whole-genome re-sequencing.
Wang ZH, Zhang D, Bai Y, Zhang YH, et al.
PLOS One. 2013 Sep 18;8(9):e74479.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.
Di Giallonardo F, Zagordi O, Duport Y, Leemann C, et al.
PLOS One. 2013 Sep 18;8(9):e74249.

Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing.
Xiong H, Barker SC, Burger TD, Raoult D, Shao R.
PLOS One. 2013 Sep 13;8(9):e73329.

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.
Wang X, Zhang B.
Bioinformatics. 2013 Sep 20. [Epub ahead of print]

Slow translocation of polynucleotides and their discrimination by α-hemolysin inside a single track-etched nanopore designed by atomic layer deposition.
Cabello-Aguilar S, Balme S, Chaaya AA, Bechelany M, et al.
Nanoscale. 2013 Sep 4. [Epub ahead of print]

Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, et al.
Nat Methods. 2013 Sep 22. [Epub ahead of print]

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches.
Brown Kav A, Benhar I, Mizrahi I.
J Microbiol Methods. 2013 Sep 17. [Epub ahead of print]

Alignment-free supervised classification of metagenomes by recursive SVM.
Cui H, Zhang X.
BMC Genomics. 2013 Sep 22;14(1):641.

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.