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Papers of Note: Nov 2, 2010


RISC RNA sequencing for context-specific identification of in vivo microRNA targets.
Matkovich SJ, Van Booven DJ, Eschenbacher WH, Dorn GW 2nd.
Circ Res. 2010 Oct 28. [Epub ahead of print]

Discovery of recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas by massively-parallel genomic sequencing.
Feldman AL, Dogan A, Smith DI, Law ME, et al.
Blood. 2010 Oct 28. [Epub ahead of print]

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation.
Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, et al.
Nucleic Acids Res. 2010 Oct 28. [Epub ahead of print]

Deleterious mutation in GPSM2 identified as cause for nonsyndromic deafness.
Schulze J.
Clin Genet. 2010 Sep 27. [Epub ahead of print]

Distant metastasis occurs late during the genetic evolution of pancreatic cancer.
Yachida S, Jones S, Bozic I, Antal T, et al.
Nature. 2010 Oct 28;467(7319):1114-7.

The patterns and dynamics of genomic instability in metastatic pancreatic cancer.
Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, et al.
Nature. 2010 Oct 28;467(7319):1109-13.

A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium
Nature. 2010 Oct 28;467(7319):1061-73.

Second-generation environmental sequencing unmasks marine metazoan biodiversity.
Fonseca VG, Carvalho GR, Sung W, Johnson HF, et al.
Nat Commun. 2010 Oct;1(7):98.

RNA-seq analysis of two closely related leukemia clones that differ in their self-renewal capacity.
Wilhelm BT, Briau M, Austin P, Faubert A, et al.
Blood. 2010 Oct 27. [Epub ahead of print]

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.
Le SQ, Durbin R.
Genome Res. 2010 Oct 27. [Epub ahead of print]

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads.
Lunter G, Goodson M.
Genome Res. 2010 Oct 27. [Epub ahead of print]

Dindel: Accurate indel calls from short-read data.
Albers CA, Lunter G, Macarthur DG, McVean G, et al.
Genome Res. 2010 Oct 27. [Epub ahead of print]

Scaffolding a Caenorhabditis nematode genome with RNA-seq.
Mortazavi A, Schwarz EM, Williams B, Schaeffer L, et al.
Genome Res. 2010 Oct 27. [Epub ahead of print]

Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans.
Ewing AD, Kazazian HH.
Genome Res. 2010 Oct 27. [Epub ahead of print]

Differential expression analysis for sequence count data.
Anders S, Huber W.
Genome Biol. 2010 Oct 27;11(10):R106.

A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions.
Liu DJ, Leal SM.
PLoS Genet. 2010 Oct 14;6(10):e1001156.

EDAR: An efficient error detection and removal algorithm for next generation sequencing data.
Zhao X, Palmer LE, Bolanos R, Mircean C, et al.
J Comput Biol. 2010 Oct 25. [Epub ahead of print]

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.