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Last Week's Sequencing-Related Papers of Note: Apr 1, 2014


Creating a single sensing zone within an alpha-hemolysin pore via site directed mutagenesis.
Ervin EN, Barrall GA, Pal P, Bean MK, et al.
Bionanoscience. 2014 Mar 1;4(1):78-84.

Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observations.
Rashid NU, Sun W, Ibrahim JG.
J Am Stat Assoc. 2014 Jan 1;109(505):78-94.

Estimating genome-wide significance for whole-genome sequencing studies.
Xu C, Tachmazidou I, Walter K, Ciampi A, et al.
Genet Epidemiol. 2014 Feb 14. [Epub ahead of print]

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, et al.
Genome Res. 2014 Mar 27. [Epub ahead of print]

HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.
Berger E, Yorukoglu D, Peng J, Berger B.
PLOS Comput Biol. 2014 Mar 27;10(3):e1003502.

TSSAR: TSS annotation regime for dRNA-seq data.
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, et al.
BMC Bioinformatics. 2014 Mar 27;15(1):89.

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level.
Shin DH, Lee HJ, Cho S, Kim HJ, et al.
BMC Genomics. 2014 Mar 27;15(1):240.

A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT).
Nature. 2014 Mar 27;507(7493):462-70.

Mod-seq: high-throughput sequencing for chemical probing of RNA structure.
Talkish J, May G, Lin Y, Woolford JL Jr, McManus CJ.
RNA. 2014 Mar 24. [Epub ahead of print]

Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture.
Gagnieur L, Cheval J, Gratigny M, Hébert C, et al.
Biologicals. 2014 Mar 21. [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.