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Papers of Note: Oct 12, 2010


Designing efficient spaced seeds for SOLiD read mapping.
Noé L, Gîrdea M, Kucherov G.
Adv Bioinformatics. 2010;2010. pii: 708501. Epub 2010 Sep 16.

De novo assembly and analysis of RNA-seq data.
Robertson G, Schein J, Chiu R, Corbett R, et al.
Nat Methods. 2010 Oct 10. [Epub ahead of print]

Next-generation sequencing identifies the natural killer cell microRNA transcriptome.
Fehniger TA, Wylie T, Germino E, Leong JW, et al.
Genome Res. 2010 Oct 8. [Epub ahead of print]

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.
Homer N, Nelson SF.
Genome Biol. 2010 Oct 8;11(10):R99.

Analysis of high-throughput sequencing data.
Mane SP, Modise T, Sobral BW.
Methods Mol Biol. 2011;678:1-11.

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.
Wang Y, Antonopoulos DA, Zhu X, Harrell L, et al.
Biotechnol. 2010 Oct 8. [Epub ahead of print]

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Arensburger P, Megy K, Waterhouse RM, Abrudan J, et al.
Science. 2010 Oct 1;330(6000):86-8.

Tenofovir (TDF)-selected or Abacavir (ABC)-selected low-frequency HIV type 1 subpopulations during failure with persistent viremia as detected by ultradeep pyrosequencing.
D'Aquila RT, Geretti AM, Horton JH, Rouse E, et al.
AIDS Res Hum Retroviruses. 2010 Oct 7. [Epub ahead of print]

Identification of epigenetic DNA modifications with a protein nanopore.
Wallace EV, Stoddart D, Heron AJ, Mikhailova E, et al.
Chem Commun (Camb). 2010 Oct 6. [Epub ahead of print]

Ultra high throughput sequencing in human DNA variation detection: A comparative study on the NDUFA3-PRPF31 region.
Benaglio P, Rivolta C.
PLoS One. 2010 Sep 29;5(9). pii: e13071.

Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing.
Choi JH, Li Y, Guo J, Pei L, et al.
PLoS One. 2010 Sep 29;5(9). pii: e13020.

TURNIP: Tracking Unresolved Nucleotide Polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.
Davey RP, James SA, Dicks J, Roberts IN.
Bioinformatics. 2010 Oct 5. [Epub ahead of print]

A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples.
Ellison G, Donald E, McWalter G, Knight L, et al.
J Exp Clin Cancer Res. 2010 Oct 6;29(1):132.

Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole genome sequencing.
Birkeland SR, Jin N, Ozdemir AC, Lyons RH, et al.
Genetics. 2010 Oct 5. [Epub ahead of print]

Definition of disease-risk stratification groups in childhood medulloblastoma using combined clinical, pathologic, and molecular variables.
Ellison DW, Kocak M, Dalton J, Megahed H, et al.
J Clin Oncol. 2010 Oct 4. [Epub ahead of print]

Exome sequencing in Brown-Vialetto-Van Laere syndrome.
Johnson JO, Gibbs JR, Van Maldergem L, Houlden H, Singleton AB.
Am J Hum Genet. 2010 Oct 8;87(4):567-9.

Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform.
Plant Methods. 2010 Sep 28;6(1):22.

Study of inter- and intra-individual variations in the salivary microbiota.
Lazarevic V, Whiteson K, Hernandez D, Francois P, Schrenzel J.
BMC Genomics. 2010 Sep 28;11(1):523.

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.