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In Print: Last Week's Sequencing-Related Papers of Note: Jul 9, 2013


Coupling unbiased mutagenesis to high-throughput DNA sequencing uncovers functional domains in the Ndc80 kinetochore protein of Saccharomyces cerevisiae.
Tien JF, Fong KK, Umbreit NT, Payen C, et al.
Genetics. 2013 Jul 5. [Epub ahead of print]

A practical method to detect SNVs and indels from whole genome and exome sequencing data.
Shigemizu D, Fujimoto A, Akiyama S, Abe T, et al.
Sci Rep. 2013;3:2161.

isomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets.
Sablok G, Milev I, Minkov G, Minkov I, et al.
FEBS Lett. 2013 Jul 4. [Epub ahead of print]

Deep sequencing as a method of typing bluetongue virus isolates.
Rao PP, Reddy YN, Ganesh K, Nair SG, et al.
J Virol Methods. 2013 Jul 3. [Epub ahead of print]

Predicting the functional consequences of non-synonymous DNA sequence variants - evaluation of bioinformatics tools and development of a consensus strategy.
Frousios K, Iliopoulos CS, Schlitt T, Simpson MA.
Genomics. 2013 Jul 3. [Epub ahead of print]

Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing.
Hollegaard MV, Grauholm J, Nielsen R, Grove J, et al.
Mol Genet Metab. 2013 Jun 13. [Epub ahead of print]

IDBA-MT: De novo assembler for metatranscriptomic data generated from next-generation sequencing technology.
Leung HC, Yiu SM, Parkinson J, Chin FY.
J Comput Biol. 2013 Jul;20(7):540-50.

Digital genotyping of sorghum − a diverse plant species with a large repeat-rich genome.
Morishige DT, Klein PE, Hilley JL, Sahraeian SM, et al.
BMC Genomics. 2013 Jul 5;14(1):448.

The long-term stability of the human gut microbiota.
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, et al.
Science. 2013 Jul 5;341(6141):1237439.

Slowing down DNA translocation through solid-state nanopores by pressure.
Zhang H, Zhao Q, Tang Z, Liu S, et al.
Small. 2013 Jul 5. [Epub ahead of print]

MiST: A new approach to variant detection in deep sequencing datasets.
Subramanian S, Di Pierro V, Shah H, Jayaprakash AD, et al.
Nucleic Acids Res. 2013 Jul 4. [Epub ahead of print]

Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage.
Jansen S, Aigner B, Pausch H, Wysocki M, et al.
BMC Genomics. 2013 Jul 4;14(1):446.

RNaseIII and T4 polynucleotide kinase sequence biases and solutions during RNA-seq library construction.
Lee C, Harris RA, Wall JK, Mayfield RD, Wilke CO .
Biol Direct. 2013 Jul 4;8(1):16.

Serum antibody repertoire profiling using in silico antigen screen.
Liu X, Hu Q, Liu S, Tallo LJ, et al.
PLoS One. 2013 Jun 27;8(6):e67181.

Preliminary assessment of microbiome changes following blood-feeding and survivorship in the Amblyomma americanum nymph-to-adult transition using semiconductor sequencing.
Menchaca AC, Visi DK, Strey OF, Teel PD, et al.
PLoS One. 2013 Jun 24;8(6):e67129.

Genomer - a Swiss army knife for genome scaffolding.
Barton MD, Barton HA.
PLoS One. 2013 Jun 24;8(6):e66922.

Evaluating the impact of sequencing depth on transcriptome profiling in human adipose.
Liu Y, Ferguson JF, Xue C, Silverman IM, et al.
PLoS One. 2013 Jun 24;8(6):e66883.

MicroRNA and piRNA profiles in normal human testis detected by next generation sequencing.
Yang Q, Hua J, Wang L, Xu B, et al.
PLoS One. 2013 Jun 24;8(6):e66809.

Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.
Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R.
PLoS Genet. 2013 Jun;9(6):e1003602.

LOcating Non-Unique matched Tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data.
Wang R, Hsu HK, Blattler A, Wang Y, et al.
PLoS One. 2013 Jun 25;8(6):e67788.

Leveraging multi-SNP reads from sequencing data for haplotype inference.
Yang WY, Hormozdiari F, Wang Z, He D, et al.
Bioinformatics. 2013 Jul 3. [Epub ahead of print]

MMuFLR: Missense Mutation and Frameshift Location Reporter.
Rathe SK, Johnson JE, Silverstein KA, Erdmann JJ, et al.
Bioinformatics. 2013 Jul 3. [Epub ahead of print]

Dissecting the characteristics and dynamics of human protein complexes at transcriptome cascade using RNA-seq data.
Chen G, Chen J, Shi C, Shi L, et al.
PLoS One. 2013 Jun 18;8(6):e66521.

Next generation sequencing of viral RNA genomes.
Marston DA, McElhinney LM, Ellis RJ, Horton DL, et al.
BMC Genomics. 2013 Jul 4;14(1):444.

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-seq data by variational Bayesian inference.
Nariai N, Hirose O, Kojima K, Nagasaki M.
Bioinformatics. 2013 Jul 2. [Epub ahead of print]

Data-based filtering for replicated high-throughput transcriptome sequencing experiments.
Rau A, Gallopin M, Celeux G, Jaffrézic F.
Bioinformatics. 2013 Jul 2. [Epub ahead of print]

Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.
Suetsugu Y, Futahashi R, Kanamori H, Kadono-Okuda K, et al.
G3 (Bethesda) . 2013 Jul 2. [Epub ahead of print]

DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.
Zhernakova DV, de Klerk E, Westra HJ, Mastrokolias A, et al.
PLoS Genet. 2013 Jun;9(6):e1003594.

Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs.
Hangauer MJ, Vaughn IW, McManus MT.
PLoS Genet. 2013 Jun;9(6):e1003569.

The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster.
Bushley KE, Raja R, Jaiswal P, Cumbie JS, et al.
PLoS Genet. 2013 Jun;9(6):e1003496.

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks.
White MA, Myers CA, Corbo JC, Cohen BA.
Proc Natl Acad Sci U S A. 2013 Jul 1. [Epub ahead of print]

Characterization and comparison of human nuclear and cytosolic editomes.
Chen L.
Proc Natl Acad Sci U S A. 2013 Jul 1. [Epub ahead of print]

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.
Haudry A, Platts AE, Vello E, Hoen DR, et al.
Nat Genet. 2013 Jun 30. [Epub ahead of print]

Kraken: A set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, Dongen SV, Abreu-Goodger C, Bartonicek N, Enright AJ.
Methods. 2013 Jun 28. [Epub ahead of print]

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
Li S, Liberman L, Mukherjee N, Benfey P, Ohler U.
Genome Res. 2013 Jul 1. [Epub ahead of print]

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
Gonzalez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.
Genome Biol. 2013 Jul 1;14(7):R70.

De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration.
Wu CH, Tsai MH, Ho CC, Chen CY, Lee HS.
BMC Genomics. 2013 Jul 1;14(1):434.

Fragmentation of genomic DNA using microwave irradiation.
Yang Y, Hang J.
J Biomol Tech. 2013 Jul;24(2):98-103.

Comparison of commercially available target enrichment methods for next-generation sequencing.
Bodi K, Perera AG, Adams PS, Bintzler D, et al.
J Biomol Tech. 2013 Jul;24(2):73-86.

Short read alignment with populations of genomes.
Huang L, Popic V, Batzoglou S.
Bioinformatics. 2013 Jul 1;29(13):i361-i370.

Using state machines to model the Ion Torrent sequencing process and to improve read error rates.
Golan D, Medvedev P.
Bioinformatics. 2013 Jul 1;29(13):i344-i351.

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels.
Peng Y, Leung HC, Yiu SM, Lv MJ, et al.
Bioinformatics. 2013 Jul 1;29(13):i326-i334.

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.
Zhang Z, Huang S, Wang J, Zhang X, et al.
Bioinformatics. 2013 Jul 1;29(13):i291-i299.

Aneuploidy underlies a multicellular phenotypic switch.
Tan Z, Hays M, Cromie GA, Jeffery EW, et al.
Proc Natl Acad Sci U S A. 2013 Jun 28. [Epub ahead of print]

De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements.
Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E.
Genome Res. 2013 Jun 28. [Epub ahead of print]

Rapid construction of Parallel Analysis of RNA End (PARE) libraries for Illumina sequencing.
Zhai J, Arikit S, Simon SA, Kingham BF, Meyers BC.
Methods. 2013 Jun 27. [Epub ahead of print]

Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.
Spencer DH, Sehn JK, Abel HJ, Watson MA, et al.
J Mol Diagn. 2013 Jun 25. [Epub ahead of print]