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Papers of Note: Jan 4, 2011


Origin and evolution of HIV-1 in breast milk determined by single genome amplification and sequencing.
Salazar-Gonzalez JF, Salazar MG, Learn GH, et al.
J Virol. 2010 Dec 29. [Epub ahead of print]

The genome of woodland strawberry (Fragaria vesca).
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, et al.
Nat Genet. 2010 Dec 26. [Epub ahead of print]

The genome of Theobroma cacao.
Argout X, Salse J, Aury JM, Guiltinan MJ, et al.
Nat Genet. 2010 Dec 26. [Epub ahead of print]

Functional null mutations of MSRB3 encoding methionine sulfoxide reductase are associated with human deafness DFNB74.
Ahmed ZM, Yousaf R, Lee BC, Khan SN, et al.
Am J Hum Genet. 2010 Dec 22. [Epub ahead of print]

Three ways of combining genotyping and resequencing in case-control association studies.
Longmate JA, Larson GP, Krontiris TG, Sommer SS.
PLoS One. 2010 Dec 20;5(12):e14318.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, et al.
Proc Natl Acad Sci U S A. 2010 Dec 27. [Epub ahead of print]

De novo. assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas.).
Wang Z, Fang B, Chen J, Zhang X, et al.
BMC Genomics. 2010 Dec 24;11(1):726. [Epub ahead of print]

A 265-base DNA sequencing read by capillary electrophoresis with no separation matrix.
Albrecht JC, Lin JS, Barron AE.
Anal Chem. 2010 Dec 23. [Epub ahead of print]

A population-specific HTR2B stop codon predisposes to severe impulsivity.
Bevilacqua L, Doly S, Kaprio J, Yuan Q, et al.
Nature. 2010 Dec 23;468(7327):1061-1066.

Genetic history of an archaic hominin group from Denisova Cave in Siberia.
Reich D, Green RE, Kircher M, Krause J, et al.
Nature. 2010 Dec 23;468(7327):1053-1060.

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The developmental transcriptome of Drosophila melanogaster.
Graveley BR, Brooks AN, Carlson JW, Duff MO, et al.
Nature. 2010 Dec 22. [Epub ahead of print]

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.
Lamm AT, Stadler MR, Zhang H, Gent JI, Fire AZ.
Genome Res. 2010 Dec 22. [Epub ahead of print]

seqMINER: an integrated ChIP-seq data interpretation platform.
Ye T, Krebs AR, Choukrallah MA, Keime C, et al.
Nucleic Acids Res. 2010 Dec 21. [Epub ahead of print]

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Fiston-Lavier AS, Carrigan M, Petrov DA, González J.
Nucleic Acids Res. 2010 Dec 21. [Epub ahead of print]

New bioinspired membrane made of a biological ion channel confined into the cylindrical nanopore of a solid-state polymer.
Balme S, Janot JM, Berardo L, Henn F, et al.
Nano Lett. 2010 Dec 21. [Epub ahead of print]

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease.
Worthey EA, Mayer AN, Syverson GD, Helbling D, et al.
Genet Med. 2010 Dec 17. [Epub ahead of print]

Genetic evidence for patrilocal mating behavior among Neandertal groups.
Lalueza-Fox C, Rosas A, Estalrrich A, Gigli E, et al.
Proc Natl Acad Sci U S A. 2010 Dec 20. [Epub ahead of print]

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression.
Lalonde E, Ha KC, Wang Z, Bemmo A, et al.
Genome Res. 2010 Dec 20. [Epub ahead of print]

New methods for next generation sequencing based microRNA expression profiling.
Buermans HP, Ariyurek Y, van Ommen GJ, den Dunnen JT, 't Hoen PA.
BMC Genomics. 2010 Dec 20;11(1):716.

NGSQC: cross-platform quality analysis pipeline for deep sequencing data.
Dai M, Thompson RC, Maher C, Contreras-Galindo R, et al.
BMC Genomics. 2010 Dec 2;11 Suppl 4:S7.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.