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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]

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.