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Recent Sequencing-Related Papers of Note: Nov 4, 2014


Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.
Baes CF, Dolezal MA, Koltes JE, Bapst B, et al.
BMC Genomics. 2014 Nov 1;15(1):948.

deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach.
Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.
Bioinformatics. 2014 Oct 30. [Epub ahead of print]

Fast and accurate site frequency spectrum estimation from low coverage sequence data.
Han E, Sinsheimer JS, Novembre J.
Bioinformatics. 2014 Oct 30. [Epub ahead of print]

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.
Skums P, Artyomenko A, Glebova O, Ramachandran S, et al.
Bioinformatics. 2014 Oct 29. [Epub ahead of print]

Targeted sequencing of large genomic regions with CATCH-seq.
Day K, Song J, Absher D.
PLOS One. 2014 Oct 30;9(10):e111756.

FamSeq: a variant calling program for family-based sequencing data using graphics processing units.
Peng G, Fan Y, Wang W.
PLOS Comput Biol. 2014 Oct 30;10(10):e1003880.

Characterization of structural variants with single molecule and hybrid sequencing approaches.
Ritz A, Bashir A, Sindi S, Hsu D, et al.
Bioinformatics. 2014 Oct 28. [Epub ahead of print]

KmerStream: streaming algorithms for k-mer abundance estimation.
Melsted P, Halldórsson BV.
Bioinformatics. 2014 Oct 28. [Epub ahead of print]

Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data.
Lusk RW.
PLOS One. 2014 Oct 29;9(10):e110808.

VariantDB: a flexible annotation and filtering portal for next generation sequencing data.
Vandeweyer G, Van Laer L, Loeys B, Van den Bulcke T, Kooy RF.
Genome Med. 2014 Oct 2;6(10):74.

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Tang X, Baheti S, Shameer K, Thompson KJ, et al.
Nucleic Acids Res. 2014 Oct 28. [Epub ahead of print]

The complex jujube genome provides insights into fruit tree biology.
Liu MJ, Zhao J, Cai QL, Liu GC, et al.
Nat Commun. 2014 Oct 28;5:5315.

Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing.
Bauer MA, Chavan SS, Peterson EA, Heuck CJ, Johann DJ.
BMC Bioinformatics. 2014 Oct 21;15(Suppl 11):S3.

Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population.
Zhang W, Meehan J, Su Z, Ng HW, et al.
BMC Bioinformatics. 2014 Oct 21;15(Suppl 11):S6.

gDNA enrichment by a transposase-based technology for NGS analysis of the whole sequence of BRCA1, BRCA2, and 9 genes involved in DNA damage repair.
Chevrier S, Boidot R.
J Vis Exp. 2014 Oct 6;(92).

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.
Peng Y, Maxwell AS, Barker ND, Laird JG, et al.
BMC Bioinformatics. 2014 Oct 21;15(Suppl 11):S10.

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch.
Ng TF, Chen LF, Zhou Y, Shapiro B, et al.
Proc Natl Acad Sci U S A. 2014 Oct 27. [Epub ahead of print]

Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.
Xu C, Zhang J, Wang YP, Deng HW, Li J.
Genome Biol Evol. 2014 Oct 27. [Epub ahead of print]

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.
Pang YL, Abo R, Levine SS, Dedon PC.
Nucleic Acids Res. 2014 Oct 27. [Epub ahead of print]

Mobster: accurate detection of mobile element insertions in next generation sequencing data.
Thung D, de Ligt J, Vissers L, Steehouwer M, et al.
Genome Biol. 2014 Oct 28;15(10):488.

Nanopores discriminate among five C5-cytosine variants in DNA.
Wescoe ZL, Schreiber J, Akeson M.
J Am Chem Soc. 2014 Oct 27. [Epub ahead of print]

DNA translocations through solid-state plasmonic nanopores.
Nicoli F, Verschueren D, Klein M, Dekker C, Jonsson MP.
Nano Lett. 2014 Oct 27. [Epub ahead of print]

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.
Zhang H, Tan E, Suzuki Y, Hirose Y, et al.
Sci Rep. 2014 Oct 27;4:6780.

Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding.
He L, Sok D, Azadnia P, Hsueh J, et al.
Sci Rep. 2014 Oct 27;4:6778.

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.