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Papers of Note: Jul 27, 2010


Last Week's Sequencing-Related Papers of Note

A call for standardized classification of metagenome projects.
Ivanova N, Tringe SG, Liolios K, Liu WT, et al.
Environ Microbiol. 2010 Jul;12(7):1803-5.

Application of machine learning methods to histone methylation chIP-seq data reveals H4R3me2 globally represses gene expression.
Xu X, Hoang S, Mayo MW, Bekiranov S.
BMC Bioinformatics. 2010 Jul 23;11(1):396.

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.
Wetterbom A, Ameur A, Feuk L, Gyllensten U, Cavelier L.
Genome Biol. 2010 Jul 23;11(7):R78.

HBV mutations in untreated HIV-HBV co-infection using genomic length sequencing.
Audsley J, Littlejohn M, Yuen L, Sasadeusz J, et al.
Virology. 2010 Jul 22. [Epub ahead of print]

Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation (MeDIP) products.
Sengenès J, Daunay A, Charles MA, Tost J.
Anal Biochem. 2010 Jul 22. [Epub ahead of print]

Detection of DNA hybridizations using solid-state nanopores.
Balagurusamy VS, Weinger P, Sean Ling X.
Nanotechnology. 2010 Jul 26;21(33):335102.

Local solid-state modification of nanopore surface charges.
Kox R, Deheryan S, Chen C, Arjmandi N, Lagae L, Borghs G.
Nanotechnology. 2010 Jul 26;21(33):335703. [Epub ahead of print]

Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia.
Johansen CT, Wang J, Lanktree MB, Cao H, et al.
Nat Genet. 2010 Jul 25. [Epub ahead of print]

Whole-genome sequencing reveals distinct mutational patterns in closely related laboratory and naturally propagated Francisella tularensis strains.
Sjödin A, Svensson K, Lindgren M, Forsman M, Larsson P.
PLoS One. 2010 Jul 19;5(7):e11556.

Deriving enzymatic and taxonomic signatures of metagenomes from short read data.
Weingart U, Persi E, Gophna U, Horn D.
BMC Bioinformatics. 2010 Jul 22;11(1):390.

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A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class-I genotyping.
Lank SM, Wiseman RW, Dudley DM, O'Connor DH.
Hum Immunol. 2010 Jul 19. [Epub ahead of print]

DNA translocation through an array of kinked nanopores.
Chen Z, Jiang Y, Dunphy DR, Adams DP, et al.
Nat Mater. 2010 Aug;9(8):667-75.

De novo truncating mutation in kinesin 17 associated with schizophrenia.
Tarabeux J, Champagne N, Brustein E, Hamdan FF, et al.
Biol Psychiatry. 2010 Jun 18. [Epub ahead of print]

Deletions of the RUNX2 gene are present in about 10% of individuals with cleidocranial dysplasia.
Ott CE, Leschik G, Trotier F, Brueton L, et al.
Hum Mutat. 2010 Aug;31(8):E1587-93.

Deciphering ionic current signatures of DNA transport through a nanopore.
Aksimentiev A.
Nanoscale. 2010 Apr 8;2(4):468-83.

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data.
McKenna AH, Hanna M, Banks E, Sivachenko A, et al.
Genome Res. 2010 Jul 19. [Epub ahead of print]

Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1.
Kohlmann A, Grossmann V, Klein HU, Schindela S, et al.
J Clin Oncol. 2010 Jul 19. [Epub ahead of print]

Pig genome sequence — analysis and publication strategy.
Archibald AL, Bolund L, Churcher C, Fredholm M, et al.
BMC Genomics. 2010 Jul 19;11(1):438.

The Scan

Rare Genetic Disease Partnership

A public-private partnership plans to speed the development of gene therapies for rare genetic diseases, Stat News writes.

Approval Sought for Alzheimer's Drug

The Wall Street Journal reports Eli Lilly has initiated a rolling submission to the US Food and Drug Administration to seek approval for its drug to treat Alzheimer's disease.

DNA Barcoding Paper Retracted

Science reports that a 2014 DNA barcoding paper was retracted after a co-author brought up data validity concerns.

Nature Papers Present Genomic Analysis of Bronze Age Mummies, Approach to Study Host-Pathogen Interactions

In Nature this week: analysis finds Tarim mummies had local genetic origin, and more.