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Recent Sequencing-Related Papers of Note: Jul 15, 2014


Proovread: large-scale high accuracy PacBio correction through iterative short read consensus.
Hackl T, Hedrich R, Schultz J, Förster F.
Bioinformatics. 2014 Jul 10. [Epub ahead of print]

High resolution mapping of modified DNA nucleobases using excision repair enzymes.
Bryan DS, Ransom M, Adane B, York K, Hesselberth JR.
Genome Res. 2014 Jul 11. [Epub ahead of print]

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Boeva V, Popova T, Lienard M, Toffoli S, et al.
Bioinformatics. 2014 Jul 12. [Epub ahead of print]

Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing.
Giuliani C, Barbieri C, Li M, Bucci L, et al.
Aging. 2014 Jun;6(6):454-67.

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence.
Deakin CT, Deakin JJ, Ginn SL, Young P, et al.
Nucleic Acids Res. 2014 Jul 10. [Epub ahead of print]

The ctenophore genome and the evolutionary origins of neural systems.
Moroz LL, Kocot KM, Citarella MR, Dosung S, et al.
Nature. 2014 Jun 5;510(7503):109-14.

DNA base detection using a single-layer MoS2.
Barati Farimani A, Min K, Aluru NR.
ACS Nano. 2014 Jul 9. [Epub ahead of print]

A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing.
Quek K, Nones K, Patch AM, Fink JL, et al.
Biotechniques. 2014 Jul 1;57(1):31-8.

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.
Qi X, Li MW, Xie M, Liu X, et al.
Nat Commun. 2014 Jul 9;5:4340.

High-throughput single nucleotide variants discovery in E14 mouse embryonic stem cells provides a new reference genome assembly.
Incarnato D, Krepelova A, Neri F.
Genomics. 2014 Jul 5. [Epub ahead of print]

Four methods of preparing mRNA 5' end libraries using the Illumina sequencing platform.
Machida RJ, Lin YY.
PLOS One. 2014 Jul 8;9(7):e101812.

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.
Azam S, Rathore A, Shah TM, Telluri M, et al.
PLOS One. 2014 Jul 8;9(7):e101754.

Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles.
Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD.
Appl Environ Microbiol. 2014 Jul 7. [Epub ahead of print]

Comparing reference-based RNA-seq mapping methods for non-human primate data.
Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE.
BMC Genomics. 2014 Jul 7;15(1):570.

Evaluating bias-reducing protocols for RNA sequencing library preparation.
Jackson TJ, Spriggs RV, Burgoyne NJ, Jones C, Willis AE.
BMC Genomics. 2014 Jul 7;15(1):569.

Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.
Nguyen UT, Bittova L, Müller MM, Fierz B, et al.
Nat Methods. 2014 Jul 6. [Epub ahead of print]

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, et al.
Nat Biotechnol. 2014 Jul 6. [Epub ahead of print]

Highly sensitive amplicon-based transcript quantification by semiconductor sequencing.
Zhang JD, Schindler T, Küng E, Ebeling M, Certa U.
BMC Genomics. 2014 Jul 5;15(1):565.