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In Print: Last Week's Sequencing-Related Papers of Note: Dec 17, 2013


A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.
Song Q, Decato B, Hong EE, Zhou M, et al.
PLoS One. 2013 Dec 6;8(12):e81148.

SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
Ding J, Hu H, Li X.
Nucleic Acids Res. 2013 Dec 9. [Epub ahead of print]

QPLOT: a quality assessment tool for next generation sequencing data.
Li B, Zhan X, Wing MK, Anderson P, et al.
Biomed Res Int. 2013;2013:865181.

RNA-seq differential expression studies: more sequence, or more replication?
Liu Y, Zhou J, White KP.
Bioinformatics. 2013 Dec 6. [Epub ahead of print]

Transcription-generated torsional stress destabilizes nucleosomes.
Teves SS, Henikoff S.
Nat Struct Mol Biol. 2013 Dec 8. [Epub ahead of print]

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.
He HH, Meyer CA, Hu SS, Chen MW, et al.
Nat Methods. 2013 Dec 8. [Epub ahead of print]

Non-uniform phenotyping of D12S391 resolved by second generation sequencing.
Dalsgaard S, Rockenbauer E, Buchard A, Mogensen HS, et al.
Forensic Sci Int Genet. 2014 Jan;8(1):195-9.

Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing.
Rockenbauer E, Hansen S, Mikkelsen M, Børsting C, Morling N.
Forensic Sci Int Genet. 2014 Jan;8(1):68-72.

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data.
Li CI, Su PF, Shyr Y.
BMC Bioinformatics. 2013 Dec 6;14(1):357.

The Scan

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.