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Recent Sequencing-Related Papers of Note: Jun 3, 2014


Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics.
Mikkelsen M, Frank-Hansen R, Hansen AJ, Morling N.
Forensic Sci Int Genet. 2014 Apr 6;12C:30-37.

ChIP-Enrich: gene set enrichment testing for ChIP-seq data.
Welch RP, Lee C, Imbriano PM, Patil S, et al.
Nucleic Acids Res. 2014 May 30. [Epub ahead of print]

Correcting imbalanced reads coverage in bacterial transcriptome sequencing with extreme deep coverage.
Zhang X, Gangaiah D, Munson RS Jr, Spinola SM, Liu Y.
Int J Comput Biol Drug Des. 2014;7(2/3):195-213.

Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue.
Hedegaard J, Thorsen K, Lund MK, Hein AM, et al.
PLoS One. 2014 May 30;9(5):e98187.

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Wang C, Evans JM, Bhagwate AV, Prodduturi N, et al.
Bioinformatics. 2014 May 29. [Epub ahead of print]

Reference-free prediction of rearrangement breakpoint reads.
Wijaya E, Shimizu K, Asai K, Hamada M.
Bioinformatics. 2014 May 29. [Epub ahead of print]

Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing.
Nuttle X, Itsara A, Shendure J, Eichler EE.
Nat Protoc. 2014 Jun;9(6):1496-513.

Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data.
Cleary JG, Braithwaite R, Gaastra K, Hilbush BS, et al.
J Comput Biol. 2014 Jun;21(6):405-19.

The 3,000 rice genomes project.
[No authors listed]
Gigascience. 2014 May 28;3:7.

CODOC: Efficient access, analysis and compression of depth of coverage signals.
Popitsch N.
Bioinformatics. 2014 May 28. [Epub ahead of print]

MIPgen: Optimized modeling and design of molecular inversion probes for targeted resequencing.
Boyle EA, O'Roak BJ, Martin BK, Kumar A, Shendure J.
Bioinformatics. 2014 May 26. [Epub ahead of print]

Aptaligner: automated software for aligning pseudo-random DNA X-aptamers from next-generation sequencing data.
Lu EY, Elizondo-Riojas MA, Chang JT, Volk DE.
Biochemistry. 2014 May 27. [Epub ahead of print]

Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.
Hori K, Maruyama F, Fujisawa T, Togashi T, et al.
Nat Commun. 2014 May 28;5:3978.

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Alemán A, Garcia-Garcia F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 May 26. [Epub ahead of print]

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.
Wright IA, Travers SA.
Nucleic Acids Res. 2014 May 26. [Epub ahead of print]

Usability study of clinical exome analysis software: Top lessons learned and recommendations.
Shyr C, Kushniruk A, Wasserman WW.
J Biomed Inform. 2014 May 23. [Epub ahead of print]

shRNA-seq data analysis with edgeR.
Dai Z, Sheridan JM, Gearing LJ, Moore DL, et al.
F1000Res. 2014 Apr 24;3:95.

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps.
Burton JN, Liachko I, Dunham MJ, Shendure J.
G3. (Bethesda). 2014 May 22. [Epub ahead of print]

Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin.
Cooper KK, Mandrell RE, Louie JW, Korlach J, et al.
Genome Announc. 2014 May 22;2(3).

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.
Liu S, Liu Y, Yang X, Tong C, et al.
Nat Commun. 2014 May 23;5:3930.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.
Luo G, Angelidaki I.
Water Res. 2014 May 9;60C:156-163.

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly.
Lun AT, Smyth GK.
Nucleic Acids Res. 2014 May 22. [Epub ahead of print]

RNA-seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome.
Zwemer LM, Hui L, Wick HC, Bianchi DW.
Prenat Diagn. 2014 May 23. [Epub ahead of print]