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In Print: Last Week's Sequencing-Related Papers of Note: Jun 12, 2012


A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE.
Keegan KP, Trimble WL, Wilkening J, Wilke A, et al.
PLoS Comput Biol. 2012 Jun;8(6):e1002541.

High-throughput sequencing detects subpopulations of bacteria not previously associated with artisanal cheeses.
Quigley L, O'Sullivan O, Beresford TP, Ross RP, et al.
Appl Environ Microbiol. 2012 Jun 8. [Epub ahead of print]

RobiNA: a user-friendly, integrated software solution for RNA-seq-based transcriptomics.
Lohse M, Bolger A, Nagel A, Fernie AR, et al.
Nucleic Acids Res. 2012 Jun 8. [Epub ahead of print]

Improved detection of microbial risk of releasing genetically modified bacteria in soil by using massive sequencing and antibiotic resistance selection.
Han I, Lee TK, Han J, Doan TV, et al.
J Hazard Mater. 2012 May 15. [Epub ahead of print]

Reference-free SNP calling: Improved accuracy by preventing incorrect calls from repetitive genomic regions.
Dou J, Zhao X, Fu X, Jiao W, et al.
Biol Direct. 2012 Jun 8;7(1):17.

DNA base-calling from a nanopore using a viterbi algorithm.
Timp W, Comer J, Aksimentiev A.
Biophys J. 2012 May 16;102(10):L37-9.

BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data.
Larsen PE, Collart FR.
BMC Res Notes. 2012 Jun 7;5(1):275.

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.
Swain MT, Tsai IJ, Assefa SA, Newbold C, et al.
Nat Protoc. 2012 Jun 7;7(7):1260-84.

Transcriptome profiling of citrus fruit response to huanglongbing disease.
Martinelli F, Uratsu SL, Albrecht U, Reagan RL, et al.
PLoS One. 2012;7(5):e38039.

Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species.
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE.
PLoS One. 2012;7(5):e37135.

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.
Lan X, Witt H, Katsumura K, Ye Z, et al.
Nucleic Acids Res. 2012 Jun 6. [Epub ahead of print]

Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H.
Genet Epidemiol. 2012 Jun 6. [Epub ahead of print]

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
Kahramanoglou C, Prieto AI, Khedkar S, Haase B, et al.
Nat Commun. 2012 Jun 6;3:886.

Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovács E, Maróti G, Bagi Z, et al.
Biotechnol Biofuels. 2012 Jun 6;5(1):41.

HomozygosityMapper2012 — bridging the gap between homozygosity mapping and deep sequencing.
Seelow D, Schuelke M.
Nucleic Acids Res. 2012 Jun 4. [Epub ahead of print]

Genomic Dark Matter: The reliability of short read mapping illustrated by the Genome Mappability Score.
Lee H, Schatz MC.
Bioinformatics. 2012 Jun 4. [Epub ahead of print]

DiNuP: A systematic approach to identify regions of differential nucleosome positioning.
Fu K, Tang Q, Feng J, Liu XS, Zhang Y.
Bioinformatics. 2012 Jun 4. [Epub ahead of print]

Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing.
Guo Y, Yang Y, Zhou J, Czajkowsky DM, et al.
Biotechniques. 2012 Apr;0(0):1-3.

Short-read, high-throughput sequencing technology for STR genotyping.
Bornman DM, Hester ME, Schuetter JM, Kasoji MD, et al.
Biotechniques. 2012 Apr;0(0):1-6.

Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing.
Querfurth R, Fischer A, Schweiger MR, Lehrach H, Mertes F.
Biotechniques. 2012 Jun;52(6):375-80.

Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.
Boyer S, Brown SD, Collins RA, Cruickshank RH, et al.
PLoS One. 2012;7(5):e38215.

High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.
Sergeant MJ, Constantinidou C, Cogan T, Penn CW, Pallen MJ.
PLoS One. 2012;7(5):e38094.

Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.
Illeghems K, De Vuyst L, Papalexandratou Z, Weckx S.
PLoS One. 2012;7(5):e38040.

Office space bacterial abundance and diversity in three metropolitan areas.
Hewitt KM, Gerba CP, Maxwell SL, Kelley ST.
PLoS One. 2012;7(5):e37849.

Artificial polyploidy improves bacterial single cell genome recovery.
Dichosa AE, Fitzsimons MS, Lo CC, Weston LL, et al.
PLoS One. 2012;7(5):e37387.

RNA-seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis:Hox supergenes.
Brunskill EW, Steven Potter S.
Dev Biol. 2012 Jun 1. [Epub ahead of print]

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.