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Papers of Note: Nov 9, 2010


Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency.
Haack TB, Danhauser K, Haberberger B, et al.
Nat Genet. 2010 Nov 7. [Epub ahead of print]

Analysis and design of RNA sequencing experiments for identifying isoform regulation.
Katz Y, Wang ET, Airoldi EM, Burge CB.
Nat Methods. 2010 Nov 7. [Epub ahead of print]

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
Underwood JG, Uzilov AV, Katzman S, Onodera CS, et al.
Nat Methods. 2010 Nov 7. [Epub ahead of print]

Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome.
Bonnefond A, Durand E, Sand O, De Graeve F, et al.
PLoS One. 2010 Oct 26;5(10):e13630.

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products.
Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, et al.
PLoS One. 2010 Oct 26;5(10):e15406.

Genome-wide fitness and genetic interactions determined by Tn-seq, a high-throughput massively parallel sequencing method for microorganisms.
Opijnen T, Camilli A.
Curr Protoc Microbiol. 2010 Nov;Chapter 1:Unit1E.3.

Mutation analysis in Bardet-Biedl syndrome by DNA pooling and massively parallel resequencing in 105 individuals.
Janssen S, Ramaswami G, Davis EE, Hurd T, et al.
Hum Genet. 2010 Oct 30. [Epub ahead of print]

Frequent mutation of BAP1 in metastasizing uveal melanomas.
Harbour JW, Onken MD, Roberson ED, Duan S, et al.
Science. 2010 Nov 4. [Epub ahead of print]

TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology.
Hong D, Park SS, Ju YS, Kim S, et al.
Nucleic Acids Res. 2010 Nov 4. [Epub ahead of print]

Quantifying microbial communities with 454 pyrosequencing: Does read abundance count?
Amend AS, Seifert KA, Bruns TD.
Mol Ecol. 2010 Nov 3. doi: 10.1111/j.1365-294X.2010.04898.x. [Epub ahead of print]

Development of a low bias method for characterizing viral populations using next-generation sequencing technology.
Willerth SM, Pedro HA, Pachter L, Humeau LM, et al.
PLoS One. 2010 Oct 22;5(10):e13564.

Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines.
Neverov A, Chumakov K.
Proc Natl Acad Sci U S A. 2010 Nov 1. [Epub ahead of print]

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing.
Juliano JJ, Porter K, Mwapasa V, Sem R, et al.
Proc Natl Acad Sci U S A. 2010 Nov 1. [Epub ahead of print]

High-throughput discovery of rare insertions and deletions in large cohorts.
Vallania FL, Druley TE, Ramos E, Wang J, et al.
Genome Res. 2010 Nov 1. [Epub ahead of print]

miRBase: integrating microRNA annotation and deep-sequencing data.
Kozomara A, Griffiths-Jones S.
Nucleic Acids Res. 2010 Oct 30. [Epub ahead of print]

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.
Pflueger D, Terry S, Sboner A, Habegger L, et al.
Genome Res. 2010 Oct 29. [Epub ahead of print]

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.
Stitzel ML, Sethupathy P, Pearson DS, Chines PS, et al.
Cell Metab. 2010 Nov 3;12(5):443-55.

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
Zhang ZD, Gerstein MB.
BMC Bioinformatics. 2010 Oct 31;11(1):539. [Epub ahead of print]

Genotator: A disease-agnostic tool for genetic annotation of disease.
Wall DP, Pivovarov R, Tong M, Jung JY, et al.
BMC Med Genomics. 2010 Oct 29;3(1):50. [Epub ahead of print]

DNA capture into a nanopore: Interplay of diffusion and electrohydrodynamics.
Grosberg AY, Rabin Y.
J Chem Phys. 2010 Oct 28;133(16):165102.

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.
Mercer TR, Dinger ME, Bracken CP, Kolle G, et al.
Genome Res. 2010 Nov 2. [Epub ahead of print]
Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation.
Robinson MD, Stirzaker C, Statham AL, Coolen MW, et al.
Genome Res. 2010 Nov 2. [Epub ahead of print]

Gene expression profiling of human breast tissue samples using SAGE-seq.
Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, et al.
Genome Res. 2010 Nov 2. [Epub ahead of print]

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.