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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.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.