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In Print: Last Week's Sequencing-Related Papers of Note: Sep 11, 2012


Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection.
Thiel WH, Bair T, Peek AS, Liu X, et al.
PLoS One. 2012;7(9):e43836.

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Wu YW, Rho M, Doak TG, Ye Y.
Bioinformatics. 2012 Sep 15;28(18):i363-i369.

MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample.
Wang Y, Leung HC, Yiu SM, Chin FY.
Bioinformatics. 2012 Sep 15;28(18):i356-i362.

Accurate estimation of short read mapping quality for next-generation genome sequencing.
Ruffalo M, Koyutürk M, Ray S, Laframboise T.
Bioinformatics. 2012 Sep 15;28(18):i349-i355.

DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Rausch T, Zichner T, Schlattl A, Stütz AM, et al.
Bioinformatics. 2012 Sep 15;28(18):i333-i339.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.
Mahmud MP, Wiedenhoeft J, Schliep A.
Bioinformatics. 2012 Sep 15;28(18):i325-i332.

Long read alignment based on maximal exact match seeds.
Liu Y, Schmidt B.
Bioinformatics. 2012 Sep 15;28(18):i318-i324.

Telescoper: de novo assembly of highly repetitive regions.
Bresler M, Sheehan S, Chan AH, Song YS.
Bioinformatics. 2012 Sep 15;28(18):i311-i317.

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.
Malboeuf CM, Yang X, Charlebois P, Qu J, et al.
Nucleic Acids Res. 2012 Sep 8. [Epub ahead of print]

Modelling and simulating generic RNA-seq experiments with the flux simulator.
Griebel T, Zacher B, Ribeca P, Raineri E, et al.
Nucleic Acids Res. 2012 Sep 7. [Epub ahead of print]

The algorithm of equal acceptance region for detecting copy number alterations: applications to next-generation sequencing data.
Lin YX.
Int J Bioinform Res Appl. 2012;8(3):245-62.

Robust 4C-seq data analysis to screen for regulatory DNA interactions.
van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, et al.
Nat Methods. 2012 Sep 9. [Epub ahead of print]

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.
Kelly TK, Liu Y, Lay FD, Liang G, et al.
Genome Res. 2012 Sep 7. [Epub ahead of print]

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica.
Krishnan NM, Pattnaik S, Jain P, Gaur P, et al.
BMC Genomics. 2012 Sep 9;13(1):464.

NG6: Integrated next generation sequencing storage and processing environment.
Mariette J, Escudie F, Allias N, Salin G, et al.
BMC Genomics. 2012 Sep 9;13(1):462.

A novel computational strategy to identify A-to-I RNA editing sites by RNA-seq data: de novo detection in human spinal cord tissue.
Picardi E, Gallo A, Galeano F, Tomaselli S, Pesole G.
PLoS One. 2012;7(9):e44184.

A novel approach for transcription factor analysis using SELEX with high-throughput sequencing (TFAST).
Reiss DJ, Howard FM, Mobley HL.
PLoS One. 2012;7(8):e42761.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, et al.
Genome Res. 2012 Sep;22(9):1813-31.

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J, Zhuang J, Iyer S, Lin X, et al.
Genome Res. 2012 Sep;22(9):1798-812.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Howald C, Tanzer A, Chrast J, Kokocinski F, et al.
Genome Res. 2012 Sep;22(9):1698-710.

HighSSR: High throughput SSR characterization and locus development from next gen sequencing data.
Alexander C, Ryan R, Hasan N, Bailey D, et al.
Bioinformatics. 2012 Sep 6. [Epub ahead of print]

Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules.
Boulanger J, Muresan L, Tiemann-Boege I.
PLoS One. 2012;7(4):e36064.

Implications of pyrosequencing error correction for biological data interpretation.
Bakker MG, Tu ZJ, Bradeen JM, Kinkel LL.
PLoS One. 2012;7(8):e44357.

Adaptive ridge regression for rare variant detection.
Zhan H, Xu S.
PLoS One. 2012;7(8):e44173.

Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring.
Kisand V, Valente A, Lahm A, Tanet G, Lettieri T .
PLoS One. 2012;7(8):e43630.

Comparative genome analysis of three eukaryotic parasites with differing abilities to transform leukocytes reveals key mediators of theileria-induced leukocyte transformation.
Hayashida K, Hara Y, Abe T, Yamasaki C, et al.
MBio. 2012 Sep 4;3(5).

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data.
Ni Y, Weber Hall A, Battenhouse A, Iyer VR.
BMC Genet. 2012 Sep 5;13:46.

Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing.
Dela Torre R, Larkin J, Singer A, Meller A.
Nanotechnology. 2012 Sep 5;23(38):385308.

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data.
Cabanski CR, Cavin K, Bizon C, Wilkerson MD, et al.
BMC Bioinformatics. 2012 Sep 4;13(1):221.

The Wasp System: An open source environment for managing and analyzing genomic data.
McLellan AS, Dubin RA, Jing Q, Broin PO, et al.
Genomics. 2012 Aug 27. [Epub ahead of print]

PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies.
Tabibian-Keissar H, Schibby G, Michaeli M, Rakovsky-Shapira A, et al.
Exp Mol Pathol. 2012 Aug 27. [Epub ahead of print]

Epistasis dominates the genetic architecture of Drosophila quantitative traits.
Huang W, Richards S, Carbone MA, Zhu D, et al.
Proc Natl Acad Sci U S A. 2012 Sep 4. [Epub ahead of print]