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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

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.