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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.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.