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In Print: Last Week's Sequencing-Related Papers of Note: Mar 27, 2012


High throughput sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies.
Blythe MJ, Malla S, Everall R, Shih YH, et al.
PLoS One. 2012;7(3):e33784.

Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis.
Philipp EE, Kraemer L, Melzner F, Poustka AJ, et al.
PLoS One. 2012;7(3):e33091.

Simultaneous genome sequencing of symbionts and their hosts.
Kumar S, Blaxter ML.
Symbiosis. 2011 Nov;55(3):119-126.

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase.
Manrao EA, Derrington IM, Laszlo AH, Langford KW, et al.
Nat Biotechnol. 2012 Mar 25. [Epub ahead of print]
(See our coverage of this paper here.)

Using Tablet for visual exploration of second-generation sequencing data.
Milne I, Stephen G, Bayer M, Cock PJ, et al.
Brief Bioinform. 2012 Mar 24. [Epub ahead of print]

Nanosensors lost in space. A random walk study of single molecule detection with single-nanopore sensors.
Höfler L, Gyurcsányi RE.
Anal Chim Acta. 2012 Apr 13;722:119-26.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.
Peterlongo P, Chikhi R.
BMC Bioinformatics. 2012 Mar 23;13(1):48.

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.
Archer J, Baillie G, Watson SJ, Kellam P, et al.
BMC Bioinformatics. 2012 Mar 23;13(1):47.

Transcriptome profiling of testis during sexual maturation stages in Eriocheir sinensis using Illumina sequencing.
He L, Wang Q, Jin X, Wang Y, et al.
PLoS One. 2012;7(3):e33735.

The fine-scale architecture of structural variants in 17 mouse genomes.
Yalcin B, Wong K, Bhomra A, Goodson M, et al.
Genome Biol. 2012 Mar 22;13(3):R18.

High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis.
Ma XF, Jensen E, Alexandrov N, Troukhan M, et al.
PLoS One. 2012;7(3):e33821.

Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing.
Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, et al.
PLoS One. 2012;7(3):e33071.

Genetic divergence between freshwater and marine morphs of alewife (Alosa pseudoharengus): a 'next-generation' sequencing analysis.
Czesny S, Epifanio J, Michalak P.
PLoS One. 2012;7(3):e31803.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.
Macalalad AR, Zody MC, Charlebois P, Lennon NJ, et al.
PLoS Comput Biol. 2012 Mar;8(3):e1002417.

Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes.
Becker EA, Burns CM, León EJ, Rajabojan S, et al.
Genome Biol Evol. 2012 Mar 20. [Epub ahead of print]

Mechanism of strand displacement synthesis by DNA replicative polymerases.
Manosas M, Spiering MM, Ding F, Bensimon D, et al.
Nucleic Acids Res. 2012 Mar 20. [Epub ahead of print]

Grinder: a versatile amplicon and shotgun sequence simulator.
Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW.
Nucleic Acids Res. 2012 Mar 19. [Epub ahead of print]

Single cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).
Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC.
Genome Res. 2012 Mar 20. [Epub ahead of print]

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers.
Kaur S, Pembleton L, Cogan N, Savin K, et al.
BMC Genomics. 2012 Mar 20;13(1):104.

Genome features of "dark-fly", a Drosophila line reared long-term in a dark environment.
Izutsu M, Zhou J, Sugiyama Y, Nishimura O, et al.
PLoS One. 2012;7(3):e33288.

Insights into the bovine rumen plasmidome.
Brown Kav A, Sasson G, Jami E, Doron-Faigenboim A, et al.
Proc Natl Acad Sci U S A. 2012 Mar 19. [Epub ahead of print]

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.
Krampis K, Booth T, Chapman B, Tiwari B, et al.
BMC Bioinformatics. 2012 Mar 19;13(1):42.

Chestnut resistance to the blight disease: insights from transcriptome analysis.
Barakat A, Staton M, Cheng CH, Park J, et al.
BMC Plant Biol. 2012 Mar 19;12(1):38.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.