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Papers of Note: Nov 16, 2010


A de novo paradigm for mental retardation.
Vissers LE, de Ligt J, Gilissen C, Janssen I, et al.
Nat Genet. 2010 Nov 14. [Epub ahead of print]

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.
Lam HM, Xu X, Liu X, Chen W, et al.
Nat Genet. 2010 Nov 14. [Epub ahead of print]

Identifying single bases in a DNA oligomer with electron tunnelling.
Huang S, He J, Chang S, Zhang P, et al.
Nat Nanotechnol. 2010 Nov 14. [Epub ahead of print]

Statistical confidence measures for genome maps: application to the validation of genome assemblies.
Servin B, de Givry S, Faraut T.
Bioinformatics. 2010 Nov 13. [Epub ahead of print]

The Uniqueome: A mappability resource for short-tag sequencing.
Koehler R, Issac H, Cloonan N, Grimmond SM.
Bioinformatics. 2010 Nov 12. [Epub ahead of print]

The honey bee epigenomes: differential methylation of brain DNA in queens and workers.
Lyko F, Foret S, Kucharski R, Wolf S, et al.
PLoS Biol. 2010 Nov 2;8(11):e1000506.

RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation.
Wang G, Wang Y, Shen C, Huang YW, et al.
PLoS One. 2010 Nov 2;5(11):e13798.

Cooperative translocation dynamics of biopolymer chains through nanopores in a membrane: Slow dynamics limit.
Wang HJ, Gu F, Hong XZ, Ba XW.
Eur Phys J E Soft Matter. 2010 Oct 31. [Epub ahead of print]

Sequence capture and next-generation resequencing of multiple tagged nucleic acid samples for mutation screening of urea cycle disorders.
Amstutz U, Andrey-Zürcher G, Suciu D, Jaggi R, et al.
Clin Chem. 2010 Nov 10. [Epub ahead of print]

Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy.
Otto EA, Ramaswami G, Janssen S, Chaki M, et al.
J Med Genet. 2010 Nov 10. [Epub ahead of print]

PriSM: A primer selection and matching tool for amplification and sequencing of viral genomes.
Yu Q, Ryan EM, Allen TM, Birren BW, et al.
Bioinformatics. 2010 Nov 9. [Epub ahead of print]

A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres.
Ellwood SR, Liu Z, Syme RA, Lai Z, et al.
Genome Biol. 2010 Nov 10;11(11):R109.

DNMT3A mutations in acute myeloid leukemia.
Ley TJ, Ding L, Walter MJ, McLellan MD, et al.
N Engl J Med. 2010 Nov 10. [Epub ahead of print]

Targeted resequencing of candidate genes using selector probes.
Johansson H, Isaksson M, Falk Sörqvist E, Roos F, et al.
Nucleic Acids Res. 2010 Nov 8. [Epub ahead of print]

Accurate quantification of transcriptome from RNA-seq data by effective length normalization.
Lee S, Seo CH, Lim B, Yang JO, et al.
Nucleic Acids Res. 2010 Nov 8. [Epub ahead of print]

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.
Szalkowski AM, Schmid CD.
Abstract Brief Bioinform. 2010 Nov 8. [Epub ahead of print]

Spatially differing bacterial communities in water columns of the northern Baltic Sea.
Koskinen K, Hultman J, Paulin L, Auvinen P, Kankaanpää H.
FEMS Microbiol Ecol. 2010 Oct 18. [Epub ahead of print]

Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data.
Rouchka E, Montoya-Durango DE, Stribinskis V, Ramos K, Kalbfleisch T.
BMC Bioinformatics. 2010 Oct 28;11 Suppl 9:S12.

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.