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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

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Small Study of Gene Editing to Treat Sickle Cell Disease

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Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

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Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.