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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.