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In Print: Last Week's Sequencing-Related Papers of Note: Feb 12, 2013


Survey of MapReduce frame operation in bioinformatics.
Zou Q, Li XB, Jiang WR, Lin ZY, et al.
Brief Bioinform. 2013 Feb 7. [Epub ahead of print]

RNA-eXpress annotates novel transcript features in RNA-seq data.
Forster S, Finkel A, Gould J, Hertzog P.
Bioinformatics. 2013 Feb 8. [Epub ahead of print]

Genotyping 1,000 yeast strains by next-generation sequencing.
Wilkening S, Tekkedil MM, Lin G, Fritsch ES, et al.
BMC Genomics. 2013 Feb 9;14(1):90.

Analysis of black fungal biofilms occurring at domestic water taps (I): compositional analysis using tag-encoded FLX amplicon pyrosequencing.
Heinrichs G, Hübner I, Schmidt CK, de Hoog GS, Haase G.
Mycopathologia. 2013 Feb 6. [Epub ahead of print]

Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers.
Okoniewski MJ, Meienberg J, Patrignani A, Szabelska A, et al.
Biotechniques. 2013 Feb;54(2):98-100.

Hap-seq: an optimal algorithm for haplotype phasing with imputation using sequencing data.
He D, Han B, Eskin E.
J Comput Biol. 2013 Feb;20(2):80-92.

Alignment-free sequence comparison based on next-generation sequencing reads.
Song K, Ren J, Zhai Z, Liu X, et al.
J Comput Biol. 2013 Feb;20(2):64-79.

Statistics of DNA capture by a solid-state nanopore.
Mihovilovic M, Hagerty N, Stein D.
Phys Rev Lett. 2013 Jan 11;110(2):028102.

On combining reference data to improve imputation accuracy.
Chen J, Zhang JG, Li J, Pei YF, Deng HW.
PLoS One. 2013;8(1):e55600.

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
McCormack JE, Harvey MG, Faircloth BC, Crawford NG, et al.
PLoS One. 2013;8(1):e54848.

Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms.
Fantin YS, Neverov AD, Favorov AV, Alvarez-Figueroa MV, et al.
PLoS One. 2013;8(1):e54835.

The carcinogenic liver fluke, Clonorchis sinensis: new assembly, reannotation and analysis of the genome and characterization of tissue transcriptomes.
Huang Y, Chen W, Wang X, Liu H, et al.
PLoS One. 2013;8(1):e54732.

Unlocking the bottleneck in forward genetics using whole-genome sequencing and identity by descent to isolate causative mutations.
Bull KR, Rimmer AJ, Siggs OM, Miosge LA, et al.
PLoS Genet. 2013 Jan;9(1):e1003219.

Single molecule molecular inversion probes for targeted, high accuracy detection of low frequency variation.
Hiatt JB, Pritchard CC, Salipante SJ, O'Roak BJ, Shendure J.
Genome Res. 2013 Feb 4. [Epub ahead of print]

Viral population analysis and minority-variant detection using short read next-generation sequencing.
Watson SJ, Welkers MR, Depledge DP, Coulter E, et al.
Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120205.

Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat.
Oono Y, Kobayashi F, Kawahara Y, Yazawa T, et al.
BMC Genomics. 2013 Feb 4;14(1):77.

The Scan

Boosters Chasing Variants

The New York Times reports that an FDA advisory panel is to weigh updated booster vaccines for COVID-19.

Not Yet

The World Health Organization says monkeypox is not yet a global emergency, the Washington Post reports.

More Proposed for Federal Research

Science reports that US House of Representatives panels are seeking to increase federal research funding.

PLOS Papers on Breast Cancer Metastasis, Left-Sided Cardiac Defects, SARS-CoV-2 Monitoring

In PLOS this week: link between breast cancer metastasis and CLIC4, sequencing analysis of left-sided cardiac defects, and more.