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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

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.