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


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

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.