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In Print: Last Week's Sequencing-Related Papers of Note: Oct 22, 2013


Draft genome of the kiwifruit Actinidia chinensis.
Huang S, Ding J, Deng D, Tang W, et al.
Nat Commun. 2013 Oct 18;4:2640.

A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG enriched genomic fraction from blood in over 700 subjects.
McClay JL, Aberg KA, Clark SL, Nerella S, et al.
Hum Mol Genet. 2013 Oct 16. [Epub ahead of print]

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.
Ruan J, Jiang L, Chong Z, Gong Q, et al.
BMC Genomics. 2013 Oct 17;14(1):711.

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
Wu CS, Yu CY, Chuang CY, Hsiao M, et al.
Genome Res. 2013 Oct 16. [Epub ahead of print]

An improved SELEX-seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.
Gu G, Wang T, Yang Y, Xu X, Wang J.
PLOS One. 2013 Oct 10;8(10):e76109.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.
Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, et al.
Bioinformatics. 2013 Oct 15. [Epub ahead of print]

Optimal resolution of ambiguous RNA-seq multimappings in the presence of novel isoforms.
Dao P, Numanagic I, Lin YY, Hach F, et al.
Bioinformatics. 2013 Oct 15. [Epub ahead of print]

StreamingTrim 1.0: a Java software for dynamic trimming of 16SrRNA sequence data from metagenetic studies.
Bacci G, Bazzicalupo M, Benedetti A, Mengoni A.
Mol Ecol Resour. 2013 Oct 15. [Epub ahead of print]

Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation.
Schneider GF, Xu Q, Hage S, Luik S, et al.
Nat Commun. 2013 Oct 15;4:2619.

NeSSM: a next-generation sequencing simulator for metagenomics.
Jia B, Xuan L, Cai K, Hu Z, et al.
PLOS One. 2013 Oct 4;8(10):e75448.

CEQer: a graphical tool for copy number and allelic imbalance detection from whole-exome sequencing data.
Piazza R, Magistroni V, Pirola A, Redaelli S, et al.
PLOS One. 2013 Oct 4;8(10):e74825.

Somatic point mutations occurring early in development: a monozygotic twin study.
Li R, Montpetit A, Rousseau M, Wu SY, et al.
J Med Genet. 2013 Oct 11. [Epub ahead of print]

GIIRA - RNA-seq driven gene finding incorporating ambiguous reads.
Zickmann F, Lindner MS, Renard BY.
Bioinformatics. 2013 Oct 11. [Epub ahead of print]

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
Wu J, Zhang W, Huang S, He Z, et al.
Bioinformatics. 2013 Oct 11. [Epub ahead of print]

Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM).
Parson W, Strobl C, Huber G, Zimmermann B, et al.
Forensic Sci Int Genet. 2013 Sep 27. [Epub ahead of print]

Accuracy of allele frequency estimation using pooled RNA-seq.
Konczal M, Koteja P, Stuglik MT, Radwan J, Babik W.
Mol Ecol Resour. 2013 Oct 14. [Epub ahead of print]

Modeling the next generation sequencing sample processing pipeline for the purposes of classification.
Ghaffari N, Youse MR, Johnson CD, Ivanov I, Dougherty ER.
BMC Bioinformatics. 2013 Oct 11;14(1):307.

Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences.
Keith Barker F, Oyler-McCance S, Tomback DF.
Mitochondrial DNA. 2013 Oct 14. [Epub ahead of print]

The sequencing bead array (SBA), a next-generation digital suspension array.
Akhras MS, Pettersson E, Diamond L, Unemo M, et al.
PLOS One. 2013 Oct 7;8(10):e76696.

RNA-seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution.
Osmundson J, Dewell S, Darst SA.
PLOS One. 2013 Oct 7;8(10):e76572.

Giardia lamblia transcriptome analysis using TSS-seq and RNA-seq.
Tolba ME, Kobayashi S, Imada M, Suzuki Y, Sugano S.
PLOS One. 2013 Oct 7;8(10):e76184.

Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines.
Knutsen E, Fiskaa T, Ursvik A, Jørgensen TE, et al.
PLOS One. 2013 Oct 8;8(10):e75813.

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Kosugi S, Natsume S, Yoshida K, Maclean D, et al.
PLOS One. 2013 Oct 8;8(10):e75402.

Single-cell based high-throughput sequencing of full-length immunoglobulin heavy and light chain genes.
Busse CE, Czogiel I, Braun P, Arndt PF, Wardemann H.
Eur J Immunol. 2013 Sep 24. [Epub ahead of print]