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Last Week's Sequencing-Related Papers of Note: Oct 11, 2011


Comparison of four ChIP-seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.
Malone BM, Tan F, Bridges SM, Peng Z.
PLoS One. 2011;6(9):e25260.

Knime4Bio: a set of custom nodes for the interpretation of next generation sequencing data with KNIME.
Lindenbaum P, Le Scouarnec S, Portero V, Redon R.
Bioinformatics. 2011 Oct 7. [Epub ahead of print]

Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming.
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, et al.
Cell Stem Cell. 2011 Oct 4;9(4):366-73.

Computational investigation of DNA detection using graphene nanopores.
Sathe C, Zou X, Leburton JP, Schulten K.
ACS Nano. 2011 Oct 7. [Epub ahead of print]

Electrophoretic time-of-flight measurements of single DNA molecules with two stacked nanopores.
Langecker M, Pedone D, Simmel FC, Rant U.
Nano Lett. 2011 Oct 10. [Epub ahead of print]

Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.
Lahiry P, Lee LJ, Frey BJ, Rupar CA, et al.
PLoS One. 2011;6(9):e25400.

A global clustering algorithm to identify long intergenic non-coding RNA — with applications in mouse macrophages.
Garmire LX, Garmire DG, Huang W, Yao J, et al.
PLoS One. 2011;6(9):e24051.

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-seq data.
Barozzi I, Termanini A, Minucci S, Natoli G.
Biol Direct. 2011 Oct 6;6(1):51.

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Pantano L, Estivill X, Marti E.
Bioinformatics. 2011 Oct 5. [Epub ahead of print]

RNA-seq analysis in MeV.
Howe EA, Sinha R, Schlauch D, Quackenbush J.
Bioinformatics. 2011 Oct 5. [Epub ahead of print]

Next generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content.
Hernandez P, Martis M, Dorado G, Pfeifer M, et al.
Plant J. 2011 Oct 4. [Epub ahead of print]

Extending KNIME for next-generation sequencing data analysis.
Jagla B, Wiswedel B, Coppée JY.
Bioinformatics. 2011 Oct 15;27(20):2907-9.

Comparative analysis of algorithms for next-generation sequencing read alignment.
Ruffalo M, Laframboise T, Koyutürk M.
Bioinformatics. 2011 Oct 15;27(20):2790-6.

Raw sewage harbors diverse viral populations.
Cantalupo PG, Calgua B, Zhao G, Hundesa A, et al.
MBio. 2011 Oct 4;2(5).

Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in human.
Birzele F, Fauti T, Stahl H, Lenter MC, et al.
Nucleic Acids Res. 2011 Oct 1;39(18):7946-60.

Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes).
Kukekova AV, Johnson JL, Teiling C, Li L, et al.
BMC Genomics. 2011 Oct 3;12(1):482.

Discriminative prediction of mammalian enhancers from DNA sequence.
Lee D, Karchin R, Beer MA.
Genome Res. 2011 Oct 3. [Epub ahead of print]

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.