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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]

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.