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In Print: Last Week's Sequencing-Related Papers of Note: Nov 12, 2013


Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.
Jiang Y, Ninwichian P, Liu S, Zhang J, et al.
PLOS One. 2013 Oct 24;8(10):e78872.

Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-seq datasets.
Zhang W, Edwards A, Flemington EK, Zhang K.
PLOS One. 2013 Oct 30;8(10):e78868.

Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data.
Bryzgalov LO, Antontseva EV, Matveeva MY, Shilov AG, et al.
PLOS One. 2013 Oct 29;8(10):e78833.

Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.
Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, et al.
PLOS One. 2013 Oct 29;8(10):e78575.

RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.
Yuan C, Sun Y.
PLOS One. 2013 Oct 25;8(10):e77596.

Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-seq.
Borozan I, Watt SN, Ferretti V.
PLOS One. 2013 Oct 30;8(10):e76935.

Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments.
Jostins L, Levine AP, Barrett JC.
PLOS One. 2013 Oct 18;8(10):e76328.

A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.
Feehery GR, Yigit E, Oyola SO, Langhorst BW, et al.
PLOS One. 2013 Oct 28;8(10):e76096.

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.
Seth-Smith HM, Harris SR, Scott P, Parmar S, et al.
Nat Protoc. 2013 Dec;8(12):2404-12.

Modeling alternative splicing variants from RNA-seq data with isoform graphs.
Beretta S, Bonizzoni P, Vedova GD, Pirola Y, Rizzi R.
J Comput Biol. 2013 Nov 7. [Epub ahead of print]

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.
Aldridge S, Watt S, Quail MA, Rayner T, et al.
Genome Biol. 2013 Nov 7;14(11):R124.

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina-based approaches.
Drechsler A, Geller D, Freund K, Schmeller DS, et al.
Ecol Evol. 2013 Oct;3(11):3947-57.

Biases in small RNA deep sequencing data.
Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS.
Nucleic Acids Res. 2013 Nov 5. [Epub ahead of print]

Inference of tumor phylogenies with improved somatic mutation discovery.
Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, et al.
J Comput Biol. 2013 Nov;20(11):933-44.

SEME: a fast mapper of Illumina sequencing reads with statistical evaluation.
Chen S, Wang A, Li LM.
J Comput Biol. 2013 Nov;20(11):847-60.

Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.
Mason MR, Nagaraja HN, Camerlengo T, Joshi V, Kumar PS.
PLOS One. 2013 Oct 23;8(10):e77287.

Mu-seq: Sequence-based mapping and identification of transposon induced mutations.
McCarty DR, Latshaw S, Wu S, Suzuki M, et al.
PLOS One. 2013 Oct 23;8(10):e77172.

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.
Black MB, Parks BB, Pluta L, Chu TM, et al.
Toxicol Sci. 2013 Nov 5. [Epub ahead of print]

Performance of high-throughput sequencing for the discovery of genetic variation across the complete size spectrum.
Pang AW, Macdonald JR, Yuen RK, Hayes VM, Scherer SW.
G3 (Bethesda). 2013 Nov 5. [Epub ahead of print]

Design and analysis of Bar-seq experiments.
Robinson DG, Chen W, Storey JD, Gresham D.
G3 (Bethesda). 2013 Nov 5. [Epub ahead of print]

WaveCNV: allele specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.
Holt C, Losic B, Pai D, Zhao Z, et al.
Bioinformatics. 2013 Nov 4. [Epub ahead of print]

Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.
Spaethling JM, Piel D, Dueck H, Buckley PT, et al.
FASEB J. 2013 Nov 5. [Epub ahead of print]

Model-based clustering for RNA-seq data.
Si Y, Liu P, Li P, Brutnell TP.
Bioinformatics. 2013 Nov 4. [Epub ahead of print]

Likelihood-based inference of population history from low coverage de novo genome assemblies.
Hearn J, Stone GN, Bunnefeld L, Nicholls JA, et al.
Mol Ecol. 2013 Nov 4. [Epub ahead of print]

Optimal assembly for high throughput shotgun sequencing.
Bresler G, Bresler M, Tse D.
BMC Bioinformatics. 2013 Jul 9;14 Suppl 5:S18.

Bacterial colonization factors control specificity and stability of the gut microbiota.
Lee SM, Donaldson GP, Mikulski Z, Boyajian S, et al.
Nature. 2013 Sep 19;501(7467):426-9.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.