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Last Week's Sequencing-Related Papers of Note: Oct 25, 2011


Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks.
Carpi G, Cagnacci F, Wittekindt NE, Zhao F, et al.
PLoS One. 2011;6(10):e25604.

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.
Vaysse A, Ratnakumar A, Derrien T, Axelsson E, et al.
PLoS Genet. 2011 Oct;7(10):e1002316.

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.
Finotello F, Lavezzo E, Fontana P, Peruzzo D, et al.
Brief Bioinform. 2011 Oct 21. [Epub ahead of print]

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.
Kircher M, Sawyer S, Meyer M.
Nucleic Acids Res. 2011 Oct 21. [Epub ahead of print]

Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP.
Nat Biotechnol. 2011 Oct 23. [Epub ahead of print]
(see our coverage of this paper in this week's issue here)

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing.
Sims D, Mendes-Pereira AM, Frankum J, Burgess D, et al.
Genome Biol. 2011 Oct 21;12(10):R104.

Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.
Karan M, Evans DS, Reilly D, Schulte K, et al.
Mol Ecol Resour. 2011 Oct 24. [Epub ahead of print]

Expression profiling without genome sequence information in a non-model species, pandalid shrimp (Pandalus latirostris), by next-generation sequencing.
Kawahara-Miki R, Wada K, Azuma N, Chiba S.
PLoS One. 2011;6(10):e26043.

Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge.
Zhang T, Zhang XX, Ye L.
PLoS One. 2011;6(10):e26041.

A bias-reducing strategy in profiling small RNAs using Solexa.
Sun G, Wu X, Wang J, Li H, et al.
RNA. 2011 Oct 20. [Epub ahead of print]

Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq).
Mamanova L, Turner DJ.
Nat Protoc. 2011 Oct 20;6(11):1736-47.

The draft genome and transcriptome of Cannabis sativa.
van Bakel H, Stout JM, Cote AG, Tallon CM, et al.
Genome Biol. 2011 Oct 20;12(10):R102.

The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing.
Lowe CD, Mello LV, Samatar N, Martin LE, et al.
BMC Genomics. 2011 Oct 20;12(1):519.

The evolution of gene expression levels in mammalian organs.
Brawand D, Soumillon M, Necsulea A, Julien P, et al.
Nature. 2011 Oct 19;478(7369):343-8.

Improving the population genetics toolbox for the study of the African malaria vector Anopheles nili: microsatellite mapping to chromosomes.
Peery A, Sharakhova MV, Antonio-Nkondjio C, Ndo C, et al.
Parasit Vectors. 2011 Oct 19;4(1):202.

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells.
Chen G, Zhou Q.
BMC Genomics. 2011 Oct 20;12(1):515.

Optimized detection of transcription factor-binding sites in ChIP-seq experiments.
Elo LL, Kallio A, Laajala TD, David Hawkins R, et al.
Nucleic Acids Res. 2011 Oct 18. [Epub ahead of print]

The sequence read archive: explosive growth of sequencing data.
Kodama Y, Shumway M, Leinonen R; et al.
Nucleic Acids Res. 2011 Oct 18. [Epub ahead of print]

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.
Dugas DV, Monaco MK, Olsen A, Klein RR, et al.
BMC Genomics. 2011 Oct 18;12(1):514.

Mapping personal functional data to personal genomes.
Rivas-Astroza M, Xie D, Cao X, Zhong S.
Bioinformatics. 2011 Oct 17. [Epub ahead of print]

Evidence of cellulose metabolism by the giant panda gut microbiome.
Zhu L, Wu Q, Dai J, Zhang S, Wei F.
Proc Natl Acad Sci U S A. 2011 Oct 17. [Epub ahead of print]

Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing.
Walsh T, Casadei S, Lee MK, Pennil CC, et al.
Proc Natl Acad Sci U S A. 2011 Oct 17. [Epub ahead of print]

Assessing the impact of non-differential genotyping errors on rare variant tests of association.
Powers S, Gopalakrishnan S, Tintle N.
Hum Hered. 2011 Oct 15;72(3):152-159.

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, et al.
Genome Biol. 2011 Oct 17;12(10):R100.

Transcriptome map of mouse isochores.
Arhondakis S, Frousios K, Iliopoulos CS, Pissis SP, et al.
BMC Genomics. 2011 Oct 17;12(1):511.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.