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Recent Sequencing-Related Papers of Note: Oct 28, 2014


iDoComp: a compression scheme for assembled genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. [Epub ahead of print]

LFQC: A lossless compression algorithm for FASTQ files.
Pathak S, Rajasekaran S.
Bioinformatics. 2014 Oct 24. [Epub ahead of print]

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.
Moncunill V, Gonzalez S, Beà S, Andrieux LO, et al.
Nat Biotechnol. 2014 Oct 26. [Epub ahead of print]

Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire.
van Schaik B, Klarenbeek P, Doorenspleet M, van Kampen A, et al.
J Immunol. 2014 Oct 22. [Epub ahead of print]

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data.
León-Novelo LG, McIntyre LM, Fear JM, Graze RM.
BMC Genomics. 2014 Oct 23;15(1):920.

Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance.
Kumar P, Al-Shafai M, Al Muftah WA, Chalhoub N, et al.
BMC Res Notes. 2014 Oct 22;7(1):747.

Integration of mass spectrometry and RNA-seq data to confirm human ab initio predicted genes and lncRNAs.
Sun H, Chen C, Shi M, Wang D, et al.
Proteomics. 2014 Oct 22. [Epub ahead of print]

Effect of RNA integrity on uniquely mapped reads in RNA-seq.
Chen EA, Souaiaia T, Herstein JS, Evgrafov OV, et al.
BMC Res Notes. 2014 Oct 23;7(1):753.

Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing.
Ralf A, van Oven M, Zhong K, Kayser M.
Hum Mutat. 2014 Oct 22. [Epub ahead of print]

FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data.
Hoogstrate Y, Jenster G, Martens-Uzunova ES.
Bioinformatics. 2014 Oct 22. [Epub ahead of print]

Experiences building Globus Genomics: a next-generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services.
Madduri RK, Sulakhe D, Lacinski L, Liu B, et al.
Concurr Comput. 2014 Sep 10;26(13):2266-2279.

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.
Han BW, Wang W, Zamore PD, Weng Z.
Bioinformatics. 2014 Oct 17. [Epub ahead of print]

Genome sequence of a 45,000-year-old modern human from western Siberia.
Fu Q, Li H, Moorjani P, Jay F, et al.
Nature. 2014 Oct 22;514(7523):445-9.

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.
Mohan AM, Bibby KJ, Lipus D, Hammack RW, Gregory KB.
PLOS One. 2014 Oct 22;9(10):e107682.

Error estimates for the analysis of differential expression from RNA-seq count data.
Burden CJ, Qureshi SE, Wilson SR.
PeerJ. 2014 Sep 23;2:e576.

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
Willet CE, Haase B, Charleston MA, Wade CM.
Bioinformatics. 2014 Oct 21. [Epub ahead of print]

Camelid genomes reveal evolution and adaptation to desert environments.
Wu H, Guang X, Al-Fageeh MB, Cao J, et al.
Nat Commun. 2014 Oct 21;5:5188.

Internal vs. fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore.
Ding Y, Fleming AM, White HS, Burrows CJ.
J Phys Chem B. 2014 Oct 21. [Epub ahead of print]

Rational experiment design for sequencing-based RNA structure mapping.
Aviran S, Pachter L.
RNA. 2014 Oct 20. [Epub ahead of print]

SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.
Katz JP, Pipas JM.
BMC Bioinformatics. 2014 Oct 22;15(1):348.

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data.
Alberti A, Belser C, Engelen S, Bertrand L, et al.
BMC Genomics. 2014 Oct 20;15(1):912.

Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
Kamada M, Hase S, Sato K, Toyoda A, et al.
PLOS One. 2014 Oct 16;9(10):e109999.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.
Brozynska M, Furtado A, Henry RJ.
PLOS One. 2014 Oct 17;9(10):e110387.

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations.
Ardeshirdavani A, Souche E, Dehaspe L, Van Houdt J, et al.
Genome Med. 2014 Sep 17;6(9):71.

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
Adey A, Kitzman JO, Burton JN, Daza R, et al.
Genome Res. 2014 Oct 19. [Epub ahead of print]