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Recent Sequencing-Related Papers of Note: Aug 19, 2014


BESST — Efficient scaffolding of large fragmented assemblies.
Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L.
BMC Bioinformatics. 2014 Aug 15;15(1):281.

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-seq data.
Yan H, Evans J, Kalmbach M, Moore R, et al.
BMC Bioinformatics. 2014 Aug 15;15(1):280.

In silico analysis identifies novel restriction enzyme combinations that expand reduced representation bisulfite sequencing CpG coverage.
Martinez-Arguelles DB, Lee S, Papadopoulos V.
BMC Res Notes. 2014 Aug 15;7(1):534.

HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations.
Usuyama N, Shiraishi Y, Sato Y, Kume H, et al.
Bioinformatics. 2014 Aug 14. [Epub ahead of print]

READemption — a tool for the computational analysis of deep-sequencing-based transcriptome data.
Förstner KU, Vogel J, Sharma CM.
Bioinformatics. 2014 Aug 13. [Epub ahead of print]

MindTheGap: integrated detection and assembly of short and long insertions.
Rizk G, Gouin A, Chikhi R, Lemaitre C.
Bioinformatics. 2014 Aug 14. [Epub ahead of print]

FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets.
Shcherbina A.
BMC Res Notes. 2014 Aug 15;7(1):533.

A scalable and accurate targeted gene assembly tool (SAT-assembler) for next-generation sequencing data.
Zhang Y, Sun Y, Cole JR.
PLOS Comput Biol. 2014 Aug 14;10(8):e1003737.

A comparative study of techniques for differential expression analysis on RNA-seq data.
Zhang ZH, Jhaveri DJ, Marshall VM, Bauer DC, et al.
PLOS One. 2014 Aug 13;9(8):e103207.

A high-density genetic map for soybean based on specific length amplified fragment sequencing.
Qi Z, Huang L, Zhu R, Xin D, et al.
PLOS One. 2014 Aug 12;9(8):e104871.

Theoretical study of the transpore velocity control of single-stranded DNA.
Qian W, Doi K, Uehara S, Morita K, Kawano S.
Int J Mol Sci. 2014 Aug 11;15(8):13817-32.

Exome sequencing of three cases of familial exceptional longevity.
Cash TP, Pita G, Domínguez O, Alonso MR, et al.
Aging Cell. 2014 Aug 12. [Epub ahead of print]

The South Asian genome.
Chambers JC, Abbott J, Zhang W, Turro E, et al.
PLOS One. 2014 Aug 12;9(8):e102645.

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics.
Fabre PH, Vilstrup JT, Raghavan M, Sarkissian CD, et al.
Biol Lett. 2014 Jul;10(7).

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Fort A, Hashimoto K, Yamada D, Salimullah M, et al.
Nat Genet. 2014 Jun;46(6):558-66.

Random whole metagenomic sequencing for forensic discrimination of soils.
Khodakova AS, Smith RJ, Burgoyne L, Abarno D, Linacre A.
PLOS One. 2014 Aug 11;9(8):e104996.

Solving the problem of comparing whole bacterial genomes across different sequencing platforms.
Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.
PLOS One. 2014 Aug 11;9(8):e104984.

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population.
Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, et al.
BMC Genomics. 2014 Aug 10;15(1):673.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.
Andersen JD, Pereira V, Pietroni C, Mikkelsen M, et al.
Biotechniques. 2014 Aug 1;57(2):91-4.

Modeling genome coverage in single cell sequencing.
Daley T, Smith AD.
Bioinformatics. 2014 Aug 8. [Epub ahead of print]

Fast construction of FM-index for long sequence reads.
Li H.
Bioinformatics. 2014 Aug 8. [Epub ahead of print]

Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.
Heydt C, Fassunke J, Künstlinger H, Ihle MA, et al.
PLOS One. 2014 Aug 8;9(8):e104566.

High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy.
Li Q, Li Y, Song J, Xu H, et al.
New Phytol. 2014 Aug 8. [Epub ahead of print]

Single molecule investigation of Ag(+) interactions with single cytosine-, methylcytosine- and hydroxymethylcytosine-cytosine mismatches in a nanopore.
Wang Y, Luan BQ, Yang Z, Zhang X, et al.
Sci Rep. 2014 Aug 8;4:5883.

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.
Sato Y, Kojima K, Nariai N, Yamaguchi-Kabata Y, et al.
BMC Genomics. 2014 Aug 8;15(1):664.

Identification of copy number variants from exome sequence data.
Samarakoon PS, Sorte HS, Kristiansen BE, Skodje T, et al.
BMC Genomics. 2014 Aug 7;15(1):661.