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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

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.