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Papers of Note: Apr 5, 2011


Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm.
Yang CH, Chang HW, Ho CH, Chou YC, Chuang LY.
PLoS One. 2011 Mar 18;6(3):e17729.

High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq.
Schödel J, Oikonomopoulos S, Ragoussis J, Pugh CW, et al.
Blood. 2011 Mar 29. [Epub ahead of print]

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.
Liu Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2011 Mar 29;12(1):85.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells.
Wu H, D'Alessio AC, Ito S, Xia K, et al.
Nature. 2011 Mar 30. [Epub ahead of print]

Exact and complete short read alignment to microbial genomes using GPU programming.
Blom J, Jakobi T, Doppmeier D, Jaenicke S, et al.
Bioinformatics. 2011 Mar 30. [Epub ahead of print]

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.
Chen L, Wu G, Ji H.
Bioinformatics. 2011 Mar 30. [Epub ahead of print]

Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome.
Everett MV, Grau ED, Seeb JE.
Mol Ecol Resour. 2011 Mar;11 Suppl 1:93-108. doi: 10.1111/j.1755-0998.2010.02969.x.

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.
Ameur A, Stewart JB, Freyer C, Hagström E, et al.
PLoS Genet. 2011 Mar;7(3):e1002028. Epub 2011 Mar 24.

Effects of nickel treatment on H3K4 trimethylation and gene expression.
Tchou-Wong KM, Kiok K, Tang Z, Kluz T, et al.
PLoS One. 2011 Mar 24;6(3):e17728.

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays.
Bottomly D, Walter NA, Hunter JE, Darakjian P, et al.
PLoS One. 2011 Mar 24;6(3):e17820.

A vertebrate case study of the quality of assemblies derived from next-generation sequences.
Ye L, Hillier LW, Minx P, Thane N, et al.
Genome Biol. 2011 Mar 31;12(3):R31.

Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals.
Fuchs TM, Brandt K, Starke M, Rattei T.
BMC Genomics. 2011 Mar 31;12(1):168.

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.
Ficz G, Branco MR, Seisenberger S, Santos F, et al.
Nature. 2011 Apr 3. [Epub ahead of print]

Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads.
Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.
Appl Environ Microbiol. 2011 Apr 1. [Epub ahead of print]

Complete genome sequence of the thermophilic Exiguobacterium sp. AT1b.
Vishnivetskaya TA, Lucas S, Copeland A, Lapidus A, et al.
J Bacteriol. 2011 Apr 1. [Epub ahead of print]

Genome sequence of strain TW25, a novel member of the genus Ornithinibacillus in the family Bacillaceae.
Whon TW, Roh SW, Shin NR, Kim MS, et al.
J Bacteriol. 2011 Apr 1. [Epub ahead of print]

Low coverage sequencing: Implications for the design of complex trait association studies.
Li Y, Sidore C, Kang HM, Boehnke M, Abecasis G.
Genome Res. 2011 Apr 1. [Epub ahead of print]

Rethinking microbial diversity analysis in the high throughput sequencing era.
Lemos LN, Fulthorpe RR, Triplett EW, Roesch LF.
J Microbiol Methods. 2011 Mar 29. [Epub ahead of print]

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

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.