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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]

The Scan

Comfort of Home

The Guardian reports that AstraZeneca is to run more clinical trials from people's homes with the aim of increasing participant diversity.

Keep Under Control

Genetic technologies are among the tools suggested to manage invasive species and feral animals in Australia, Newsweek says.

Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.