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In Print: Last Week's Sequencing-Related Papers of Note: Sep 10, 2013

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DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
Pandey RV, Schlötterer C.
PLOS One. 2013 Aug 23;8(8):e72614.


Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.
Zhang G, Hoersch S, Amsterdam A, Whittaker CA, et al.
PLOS Genet. 2013 Aug;9(8):e1003734.


The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.
Wenger AM, Clarke SL, Notwell JH, Chung T, et al.
PLOS Genet. 2013 Aug;9(8):e1003728.


PAVIS: a tool for Peak Annotation and Visualization.
Huang W, Loganantharaj R, Schroeder B, Fargo D, Li L.
Bioinformatics. 2013 Sep 4. [Epub ahead of print]


Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.
Booth MJ, Ost TW, Beraldi D, Bell NM, et al.
Nat Protoc. 2013 Oct;8(10):1841-51.


Archival bone marrow trephines are suitable for high-throughput mutation analysis using next generation sequencing technology.
Hasemeier B, Geffers R, Bartels S, Schlegelberger B, et al.
Haematologica. 2013 Sep;98(9):e115-6.


Fast mitochondrial DNA isolation from mammalian cells for next-generation sequencing.
Quispe-Tintaya W, White RR, Popov VN, Vijg J, Maslov AY .
Biotechniques. 2013 Sep;55(3):133-6.


A cost-effective method for high-throughput construction of illumina sequencing libraries.
Dunham JP, Friesen ML.
Cold Spring Harb Protoc. 2013 Sep 1;2013(9).


Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome.
Lu Y, Zhou Y, Tian W.
Nucleic Acids Res. 2013 Sep 3. [Epub ahead of print]


Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing.
Alquezar-Planas DE, Mourier T, Bruhn CA, Hansen AJ, et al.
Sci Rep. 2013 Sep 3;3:2468.


A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads.
Kojima K, Nariai N, Mimori T, Takahashi M, et al.
Bioinformatics. 2013 Sep 3. [Epub ahead of print]


Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies.
Sah S, Chen L, Houghton J, Kemppainen J, et al.
Genome Med. 2013 Aug 30;5(8):77.


Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples.
Mosher JJ, Bernberg EL, Shevchenko O, Kan J, Kaplan LA.
J Microbiol Methods. 2013 Aug 30. [Epub ahead of print]


Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, et al.
Plant J. 2013 Sep 2. [Epub ahead of print]

The Scan

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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

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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.