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Sequencing-Related Papers of Note of the Last Two Weeks


VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer.
Teer JK, Green ED, Mullikin JC, Biesecker LG.
Bioinformatics. 2011 Dec 30. [Epub ahead of print]

Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage.
Okoniewski MJ, Lesniewska A, Szabelska A, Zyprych-Walczak J, et al.
Nucleic Acids Res. 2011 Dec 30. [Epub ahead of print]

A new strategy for better genome assembly from very short reads.
Ji Y, Shi Y, Ding G, Li Y.
BMC Bioinformatics. 2011 Dec 30;12(1):493.

Optimal enzymes for amplifying sequencing libraries.
Quail MA, Otto TD, Gu Y, Harris SR, et al.
Nat Methods. 2011 Dec 28;9(1):10-1.

GeneProf: analysis of high-throughput sequencing experiments.
Halbritter F, Vaidya HJ, Tomlinson SR.
Nat Methods. 2011 Dec 28;9(1):7-8.

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, et al.
Genome Res. 2011 Dec 29. [Epub ahead of print]

Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome.
Brebi-Mieville P, Ili-Gangas C, Leal-Rojas P, Noordhuis MG, et al.
Epigenetics. 2012 Jan 1;7(1).

Read count approach for DNA copy number variants detection.
Magi A, Tattini L, Pippucci T, Torricelli F, Benelli M.
Bioinformatics. 2011 Dec 23. [Epub ahead of print]

ART: a next-generation sequencing read simulator.
Huang W, Li L, Myers JR, Marth GT.
Bioinformatics. 2011 Dec 23. [Epub ahead of print]

Artemis: An integrated platform for visualisation and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA.
Bioinformatics. 2011 Dec 22. [Epub ahead of print]

MeQA: A pipeline for MeDIP-seq data quality assessment and analysis.
Huang J, Renault V, Sengenès J, Touleimat N, et al.
Bioinformatics. 2011 Dec 22. [Epub ahead of print]

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.
Planet E, Stephan-Otto Attolini C, Reina O, Flores O, Rossell D.
Bioinformatics. 2011 Dec 22. [Epub ahead of print]

RNASEQR-a streamlined and accurate RNA-seq sequence analysis program.
Chen LY, Wei KC, Huang AC, Wang K, et al.
Nucleic Acids Res. 2011 Dec 22. [Epub ahead of print]

Hobbes: optimized gram-based methods for efficient read alignment.
Ahmadi A, Behm A, Honnalli N, Li C, et al.
Nucleic Acids Res. 2011 Dec 22. [Epub ahead of print]

DNA origami nanopores.
Bell N, Engst C, Ablay M, Divitini G, et al.
Nano Lett. 2011 Dec 23. [Epub ahead of print]

A pangenomic study of Bacillus thuringiensis..
Fang Y, Li Z, Liu J, Shu C, et al.
J Genet Genomics. 2011 Dec 20;38(12):567-76.

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.
Schloss PD, Gevers D, Westcott SL.
PLoS One. 2011;6(12):e27310.

A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.
Yin H, Sweeney S, Raha D, Snyder M, Lin H.
PLoS Genet. 2011 Dec;7(12):e1002380.

A pilot study for channel catfish whole genome sequencing and de novo assembly.
Jiang Y, Lu J, Peatman E, Kucuktas H, et al.
BMC Genomics. 2011 Dec 22;12(1):629.

Profiling conserved microRNA expression in recombinant CHO cell lines using Illumina sequencing.
Hammond S, Swanberg JC, Polson SW, Lee KH.
Biotechnol Bioeng. 2011 Dec 21. [Epub ahead of print]

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-Bruijn-graph.
Li Z, Chen Y, Mu D, Yuan J, et al.
Brief Funct Genomics. 2011 Dec 19. [Epub ahead of print]

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.
Greenblum S, Turnbaugh PJ, Borenstein E.
Proc Natl Acad Sci U S A. 2011 Dec 19. [Epub ahead of print]

The Scan

Sick Newborns Selected for WGS With Automated Pipeline

Researchers successfully prioritized infants with potential Mendelian conditions for whole-genome sequencing or rapid whole-genome sequencing, as they report in Genome Medicine.

Acne-Linked Loci Found Through GWAS Meta-Analysis

Researchers in the European Journal of Human Genetics find new and known acne vulgaris risk loci with a genome-wide association study and meta-analysis, highlighting hair follicle- and metabolic disease-related genes.

Retina Cell Loss Reversed by Prime Editing in Mouse Model of Retinitis Pigmentosa

A team from China turns to prime editing to correct a retinitis pigmentosa-causing mutation in the PDE6b gene in a mouse model of the progressive photoreceptor loss condition in the Journal of Experimental Medicine.

CRISPR Screens Reveal Heart Attack-Linked Gene

Researchers in PLOS Genetics have used CRISPR screens to home in on variants associated with coronary artery disease that affect vascular endothelial function.