Skip to main content

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.

The Scan

UK Funds to Stay Ahead of Variants

The UK has announced a further £29.3 million to stay on top of SARS-CoV-2 variants, the Guardian reports.

Push for Access

In a letter, researchers in India seek easier access to COVID-19 data, Science reports.

Not as Cold

Late-stage trial results are expected soon for an RNA-based vaccine that could help meet global demand as it does not require very cold storage, the New York Times writes.

Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

In Genome Research this week: influence of microbes on transfer RNA patterns, evolutionary relationships of honeybees, and more.