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

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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.

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With Help from Mr. Fluffington, PurrhD

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Nature Papers Present Approach to Find Natural Products, Method to ID Cancer Driver Mutations, More

In Nature this week: combination of cryogenic electron microscopy with genome mining helps uncover natural products, driver mutations in cancer, and more.