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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]