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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

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.