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Papers of Note: Oct 12, 2010

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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.

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