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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

Should've Been Spotted Sooner

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For Martian Fuel

Researchers have outlined a plan to produce rocket fuel on Mars that uses a combination of sunlight, carbon dioxide, frozen water, cyanobacteria, and engineered E. coli, according to Gizmodo.

To Boost Rapid Testing

The Washington Post writes that new US programs aim to boost the availability of rapid at-home SARS-CoV-2 tests.

PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

In PNAS this week: strawberry pan-genome, cell cycle-related roles for MDM2 and MDMX, and more.