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In Print: Last Week's Sequencing-Related Papers of Note: Jun 26, 2012


DySC: Software for greedy clustering of 16S rRNA reads.
Zheng Z, Kramer S, Schmidt B.
Bioinformatics. 2012 Jun 23. [Epub ahead of print]

gSearch: a fast and flexible general search tool for whole-genome sequencing.
Song T, Hwang KB, Hsing M, Lee K, et al.
Bioinformatics. 2012 Jun 23. [Epub ahead of print]

High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing.
Bus A, Hecht J, Huettel B, Reinhardt R, Stich B.
BMC Genomics. 2012 Jun 24;13(1):281.

Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N.
BMC Bioinformatics. 2012 Jun 22;13(1):145.

Statistical tests for detecting rare variants using variance-stabilising transformations.
Wang K, Fingert JH.
Ann Hum Genet. 2012 Jun 25. [Epub ahead of print]

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.
Andrews TD, Whittle B, Field MA, Balakishnan B, et al.
Open Biol. 2012 May;2(5):120061.

ccTSA: A Coverage-Centric Threaded Sequence Assembler.
Ahn JH.
PLoS One. 2012;7(6):e39232.

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
The Heliconius Genome Consortium, Dasmahapatra KK, Walters JR, et al.
Nature. 2012 May 16. [Epub ahead of print]

The bonobo genome compared with the chimpanzee and human genomes.
Prüfer K, Munch K, Hellmann I, Akagi K, et al.
Nature. 2012 Jun 13. [Epub ahead of print]

Detecting differential usage of exons from RNA-seq data.
Anders S, Reyes A, Huber W.
Genome Res. 2012 Jun 21. [Epub ahead of print]

Quality of prokaryote genomes assembly: Indispensable issues of factors affecting prokaryote genome assembly quality.
Carneiro AR, Ramos RT, Barbosa HP, Schneider MP, et al.
Gene. 2012 Jun 18. [Epub ahead of print]

Whole genome sequencing analysis of Plasmodium vivax using whole genome capture.
Bright AT, Tewhey R, Abeles S, Chuquiyauri R, et al.
BMC Genomics. 2012 Jun 21;13(1):262.

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments.
Wen M, Shen Y, Shi SH, Tang T.
BMC Bioinformatics. 2012 Jun 21;13(1):140.

Evaluation of 16S rDNA-based community profiling for human microbiome research.
Jumpstart Consortium Human Microbiome Project Data Generation Working Group.
PLoS One. 2012;7(6):e39315.

VoSeq: A voucher and DNA sequence web application.
Peña C, Malm T.
PLoS One. 2012;7(6):e39071.

MspA nanopores from subunit dimers.
Pavlenok M, Derrington IM, Gundlach JH, Niederweis M.
PLoS One. 2012;7(6):e38726.

A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.
Aagaard K, Riehle K, Ma J, Segata N, et al.
PLoS One. 2012;7(6):e36466.

Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.
Martin J, Sykes S, Young S, Kota K, et al.
PLoS One. 2012;7(6):e36427.

Novel bacterial taxa in the human microbiome.
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, et al.
PLoS One. 2012;7(6):e35294.

Analyses of the microbial diversity across the human microbiome.
Li K, Bihan M, Yooseph S, Methé BA.
PLoS One. 2012;7(6):e32118.

A novel self-ordered sub-10 nm nanopore template for nanotechnology.
Moyen E, Santinacci L, Masson L, Wulfhekel W, Hanbücken M.
Adv Mater. 2012 Jun 21. [Epub ahead of print]

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
Mason OU, Hazen TC, Borglin S, Chain PS, et al.
ISME J. 2012 Jun 21. [Epub ahead of print]

Consensus rules in variant detection from next-generation sequencing data.
Jia P, Li F, Xia J, Chen H, et al.
PLoS One. 2012;7(6):e38470.

Gene discovery using mutagen-induced polymorphisms and deep sequencing: application to plant disease resistance.
Zhu Y, Mang HG, Sun Q, Qian J, et al.
Genetics. 2012 Jun 19. [Epub ahead of print]

Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method.
Duhaime MB, Deng L, Poulos BT, Sullivan MB.
Environ Microbiol. 2012 Jun 20. [Epub ahead of print]

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
Lamour K, Mudge J, Gobena D, Hurtado-Gonzales OP, et al.
Mol Plant Microbe Interact. 2012 Jun 20. [Epub ahead of print]

Nanometer-thin solid-state nanopores by cold ion beam sculpting.
Kuan AT, Golovchenko JA.
Appl Phys Lett. 2012 May 21;100(21):213104-2131044.

Plasma membrane associated transcription of cytoplasmic DNA.
Cheng J, Torkamani A, Peng Y, Jones TM, Lerner RA.
Proc Natl Acad Sci U S A. 2012 Jun 18. [Epub ahead of print]

Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules.
An N, Fleming AM, White HS, Burrows CJ.
Proc Natl Acad Sci U S A. 2012 Jun 18. [Epub ahead of print] (see our coverage of this paper here)

Bellerophontes: A RNA-seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.
Abate F, Acquaviva A, Paciello G, Ficarra E, et al.
Bioinformatics. 2012 Jun 17. [Epub ahead of print]

TWARIT: An extremely rapid and efficient approach for phylogenetic classification of metagenomic sequences.
Rachamalla MR, Monzoorul HM, Mande SS.
Gene. 2012 Jun 15. [Epub ahead of print]

How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?
Yu X, Guda K, Willis J, Veigl M, et al.
BioData Min. 2012 Jun 18;5(1):6.

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.
O'Loughlin A, Lynn DJ, McGee M, Doyle S, et al.
BMC Genomics. 2012 Jun 18;13(1):250.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.