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In Print: Last Week's Sequencing-Related Papers of Note: Aug 13, 2013


GobyWeb: Simplified management and analysis of gene expression and DNA methylation sequencing data.
Dorff KC, Chambwe N, Zeno Z, Simi M, et al.
PLoS One. 2013 Jul 23;8(7):e69666.

Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface.
Payne AC, Andregg M, Kemmish K, Hamalainen M, et al.
PLoS One. 2013 Jul 31;8(7):e69058.

Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.
Hall BG, Cardenas H, Barlow M.
PLoS One. 2013 Jul 23;8(7):e68901.

BlackOPs: increasing confidence in variant detection through mappability filtering.
Cabanski CR, Wilkerson MD, Soloway M, Parker JS, et al.
Nucleic Acids Res. 2013 Aug 8. [Epub ahead of print]

A novel approach to estimating heterozygosity from low-coverage genome sequence.
Bryc K, Patterson NJ, Reich D.
Genetics. 2013 Aug 9. [Epub ahead of print]

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.
Pattanayak V, Lin S, Guilinger JP, Ma E, et al.
Nat Biotechnol. 2013 Aug 11. [Epub ahead of print]

Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells.
Yan L, Yang M, Guo H, Yang L, et al.
Nat Struct Mol Biol. 2013 Aug 11. [Epub ahead of print]

Differential splicing across immune system lineages.
Ergun A, Doran G, Costello JC, Paik HH, et al.
Proc Natl Acad Sci U S A. 2013 Aug 9. [Epub ahead of print]

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing.
Nguyen-Dumont T, Pope BJ, Hammet F, Mahmoodi M, et al.
Anal Biochem. 2013 Aug 8. [Epub ahead of print]

A high-plex PCR approach for massively parallel sequencing.
Nguyen-Dumont T, Pope BJ, Hammet F, Southey MC, Park DJ.
Biotechniques. 2013 Aug;55(2):69-74.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.
Laurie MT, Bertout JA, Taylor SD, Burton JN, et al.
Biotechniques. 2013 Aug;55(2):61-7.

Mechanism of how salt-gradient-induced charges affect the translocation of DNA molecules through a nanopore.
He Y, Tsutsui M, Scheicher RH, Fan C, et al.
Biophys J. 2013 Aug 6;105(3):776-82.

NGSPE: A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms.
Huang K, Yellapantula V, Baier L, Dinu V.
Comput Biol Med. 2013 Sep 1;43(9):1171-6.

FNphasing: a novel fast heuristic algorithm for haplotype phasing based on flow network model.
Yang J, Xu Y, Yao X, Chen G.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):372-82.

Chinese hamster genome sequenced from sorted chromosomes.
Brinkrolf K, Rupp O, Laux H, Kollin F, et al.
Nat Biotechnol. 2013 Aug 8;31(8):694-5.

ASPeak: an abundance sensitive peak detection algorithm for RIP-seq.
Kucukural A, Ozadam H, Singh G, Moore MJ, Cenik C.
Bioinformatics. 2013 Aug 8. [Epub ahead of print]

OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.
Yau C.
Bioinformatics. 2013 Aug 7. [Epub ahead of print]

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line.
Adey A, Burton JN, Kitzman JO, Hiatt JB, et al.
Nature. 2013 Aug 8;500(7461):207-11.

Direct assessment of transcription fidelity by high-resolution RNA sequencing.
Imashimizu M, Oshima T, Lubkowska L, Kashlev M.
Nucleic Acids Res. 2013 Aug 7. [Epub ahead of print]

Charting a dynamic DNA methylation landscape of the human genome.
Ziller MJ, Gu H, Müller F, Donaghey J, et al.
Nature. 2013 Aug 7. [Epub ahead of print]

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.
Williams D, Trimble WL, Shilts M, Meyer F, Ochman H.
BMC Genomics. 2013 Aug 8;14(1):537.

Application of Illumina next-generation sequencing to characterize the bacterial community of the upper Mississippi river.
Staley C, Unno T, Gould TJ, Jarvis B, et al.
J Appl Microbiol. 2013 Aug 8. [Epub ahead of print]

Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing.
Dockter RB, Elzinga DB, Geary B, Maughan PJ, et al.
BMC Genet. 2013 Aug 8;14(1):66.

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.
Skums P, Mancuso N, Artyomenko A, Tork B, et al.
BMC Bioinformatics. 2013 Jun 28;14 Suppl 9:S2.

Parallel comparison of Illumina RNA-seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.
Xu X, Zhang Y, Williams J, Antoniou E , et al.
BMC Bioinformatics. 2013 Jun 28;14 Suppl 9:S1.

Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.
Shangguan L, Han J, Kayesh E, Sun X, et al.
PLoS One. 2013 Jul 29;8(7):e69890.

Optimizing information in next-generation-sequencing (NGS) reads for improving de novo genome assembly.
Liu T, Tsai CH, Lee WB, Chiang JH.
PLoS One. 2013 Jul 29;8(7):e69503.

Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.
Staats M, Erkens RH, van de Vossenberg B, Wieringa JJ, et al.
PLoS One. 2013 Jul 29;8(7):e69189.

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants.
Mogno I, Kwasnieski JC, Cohen BA.
Genome Res. 2013 Aug 6. [Epub ahead of print]

Efficient identification of Y chromosome sequences in the human and Drosophila genomes.
Carvalho AB, Clark AG.
Genome Res. 2013 Aug 6. [Epub ahead of print]

Detecting Alu insertions from high-throughput sequencing data.
David M, Mustafa H, Brudno M.
Nucleic Acids Res. 2013 Aug 5. [Epub ahead of print]

Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome.
Stevenson KR, Coolon JD, Wittkopp PJ.
BMC Genomics. 2013 Aug 7;14(1):536.

Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications.
He Z, Li X, Ling S, Fu YX, et al.
BMC Genomics. 2013 Aug 7;14(1):535.

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species.
Carew ME, Pettigrove VJ, Metzeling L, Hoffmann AA.
Front Zool. 2013 Aug 7;10(1):45.

RNA-seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium.
Ruffing AM.
Biotechnol Biofuels. 2013 Aug 6;6(1):113. [Epub ahead of print]

Distilled single cell genome sequencing and de novo assembly for sparse microbial communities.
Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.
Bioinformatics. 2013 Aug 5. [Epub ahead of print]

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.
Spindel J, Wright M, Chen C, Cobb J, et al.
Theor Appl Genet. 2013 Aug 6. [Epub ahead of print]

Identification of differentially expressed microRNAs across the developing human brain.
Ziats MN, Rennert OM.
Mol Psychiatry. 2013 Aug 6. [Epub ahead of print]

Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.
Wan QH, Pan SK, Hu L, Zhu Y, et al.
Cell Res. 2013 Aug 6. [Epub ahead of print]

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.
Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, et al.
BMC Genomics. 2013 Aug 2;14(1):530.