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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

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.