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In Print: Last Week's Sequencing-Related Papers of Note: May 28, 2013


Streaming Support for Data Intensive Cloud-Based Sequence Analysis.
Issa SA, Kienzler R, El-Kalioby M, Tonellato PJ, et al.
Biomed Res Int. 2013;2013:791051.

Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data.
Hu B, Ji Y, Xu Y, Ting AH.
Stat Biosci. 2013 May;5(1):179-197.

Deep Sequencing of Mixed Total DNA Without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes.
Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, et al.
Genome Biol Evol. 2013 May 23. [Epub ahead of print]

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.
Watson M, Schnettler E, Kohl A.
Bioinformatics. 2013 May 24. [Epub ahead of print]

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.
Han MV, Thomas GW, Lugo-Martinez J, Hahn MW.
Mol Biol Evol. 2013 May 24. [Epub ahead of print]

MicroRNA target site identification by integrating sequence and binding information.
Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, et al.
Nat Methods. 2013 May 26. [Epub ahead of print]

A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells.
Fritz EL, Rosenberg BR, Lay K, Mihailović A, et al.
Nat Immunol. 2013 May 26. [Epub ahead of print]

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.
Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, et al.
Nat Genet. 2013 May 26. [Epub ahead of print]

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, et al.
Nat Biotechnol. 2013 May 26. [Epub ahead of print]

The Genetic Basis of White Tigers.
Xu X, Dong GX, Hu XS, Miao L, et al.
Curr Biol. 2013 May 22. [Epub ahead of print]

Investigating Evolutionary Perspective of Carcinogenesis with Single-cell Transcriptome Analysis.
Zhang X, Zhang C, Li Z, Zhong J, et al.
Chin J Cancer. 2013 May 27. [Epub ahead of print]

An Integrated Workflow for DNA Methylation Analysis.
Li P, Demirci F, Mahalingam G, Demirci C, et al.
J Genet Genomics. 2013 May 20;40(5):249-260.

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.
Kim NK, Jayatillake RV, Spouge JL.
BMC Genomics. 2013 May 25;14(1):349.

Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods.
Gao F, Wei Z, Lu W, Wang K.
BMC Genomics. 2013 May 24;14(1):345.

RNA-seq analysis of single bovine blastocysts.
Chitwood JL, Rincon G, Kaiser GG, Medrano JF, Ross PJ.
BMC Genomics. 2013 May 25;14(1):350.

PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data.
Escaramís G, Tornador C, Bassaganyas L, Rabionet R, et al.
PLoS One. 2013 May 21;8(5):e63377.

High-Throughput Compression of FASTQ Data with SeqDB.
Howison M.
IEEE/ACM Trans Comput Biol Bioinform. 2013 January-February;10(1):213-218.

Genomic Region Operation Kit for Flexible Processing of Deep Sequencing Data.
Ovaska K, Lyly L, Sahu B, Jänne OA, Hautaniemi S.
IEEE/ACM Trans Comput Biol Bioinform. 2013 January-February;10(1):200-206.

Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data.
Doose G, Alexis M, Kirsch R, Findeiß S, et al.
RNA Biol. 2013 May 13;10(7).

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.
Cushing A, Flaherty P, Hopmans E, Bell JM, Ji HP.
BMC Res Notes. 2013 May 23;6(1):206.

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data.
Zeng F, Jiang R, Chen T.
Nucleic Acids Res. 2013 May 21. [Epub ahead of print]

CoRAL: predicting non-coding RNAs from small RNA-sequencing data.
Leung YY, Ryvkin P, Ungar LH, Gregory BD, Wang LS.
Nucleic Acids Res. 2013 May 21. [Epub ahead of print]

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription.
Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL.
Genes Dev. 2013 May 15;27(10):1146-1158.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Birol I, Raymond A, Jackman SD, Pleasance S, et al.
Bioinformatics. 2013 May 22. [Epub ahead of print]

MASS: meta-analysis of score statistics for sequencing studies.
Tang ZZ, Lin DY.
Bioinformatics. 2013 May 21. [Epub ahead of print]

DRISEE overestimates errors in metagenomic sequencing data.
Eren AM, Morrison HG, Huse SM, Sogin ML.
Brief Bioinform. 2013 May 22. [Epub ahead of print]

Topographic diversity of fungal and bacterial communities in human skin.
Findley K, Oh J, Yang J, Conlan S, et al.
Nature. 2013 May 22. [Epub ahead of print]

Negligible impact of rare autoimmune-locus coding-region variants on missing heritability.
Hunt KA, Mistry V, Bockett NA, Ahmad T, et al.
Nature. 2013 May 22. [Epub ahead of print]

The Norway spruce genome sequence and conifer genome evolution.
Nystedt B, Street NR, Wetterbom A, Zuccolo A, et al.
Nature. 2013 May 22. [Epub ahead of print]

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing.
Mohr S, Ghanem E, Smith W, Sheeter D, et al.
RNA. 2013 May 22. [Epub ahead of print]

Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues.
Meng W, McElroy JP, Volinia S, Palatini J, et al.
PLoS One. 2013 May 16;8(5):e64393.

RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels.
Gunawan A, Sahadevan S, Neuhoff C, Große-Brinkhaus C, et al.
PLoS One. 2013 May 16;8(5):e63259.

Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing.
Guilmatre A, Highnam G, Borel C, Mittelman D, Sharp AJ.
Hum Mutat. 2013 May 20. [Epub ahead of print]

HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment.
Vianello D, Sevini F, Castellani G, Laura L, et al.
Hum Mutat. 2013 May 20. [Epub ahead of print]

Whole-Genome Sequencing and Analysis of the Autoimmunity and Inflammation Phenotypically Dichotomous DA and F344 Rats.
Guo X, Brenner M, Zhang X, Laragione T, et al.
Genetics. 2013 May 20. [Epub ahead of print]

RESTseq - Efficient Benchtop Population Genomics with RESTriction Fragment SEQuencing.
Stolle E, Moritz RF.
PLoS One. 2013 May 17;8(5):e63960.

Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing.
De Donato M, Peters SO, Mitchell SE, Hussain T, Imumorin IG.
PLoS One. 2013 May 17;8(5):e62137.

Nanopore detection of DNA molecules in magnesium chloride solutions.
Zhang Y, Liu L, Sha J, Ni Z, et al.
Nanoscale Res Lett. 2013 May 20;8(1):245.