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Papers of Note: Mar 15, 2011


Note to readers: Beginning this week, all papers related to clinical sequencing will be included in Clinical Sequencing News, In Sequence's newly launched sister newsletter. In Sequence will continue to run papers related to research applications and new sequencing methods.

Critical assessment of assembly strategies for non-model species mRNA-seq data and application of next-generation sequencing to the comparison of C3 and C4 species.
Bräutigam A, Mullick T, Schliesky S, Weber AP.
J Exp Bot. 2011 Mar 11. [Epub ahead of print]

Simulation of ionic current through the nanopore in a double-layered semiconductor membrane.
Nikolaev A, Gracheva ME.
Nanotechnology. 2011 Apr 22;22(16):165202.

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: identification, annotation and profiling of microRNAs as targets for cellular engineering.
Hackl M, Jakobi T, Blom J, Doppmeier D, et al.
Biotechnol. 2011 Mar 7. [Epub ahead of print]

A comparison of single molecule and amplification based sequencing of cancer transcriptomes.
Sam LT, Lipson D, Raz T, Cao X, et al.
PLoS One. 2011 Mar 1;6(3):e17305.

Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis.
Bogaert D, Keijser B, Huse S, Rossen J, et al.
PLoS One. 2011 Feb 28;6(2):e17035.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.
Troshin PV, Postis VL, Ashworth D, Baldwin SA, et al.
BMC Res Notes. 2011 Mar 7;4(1):48.

Dynamic linear model for the identification of miRNAs in next-generation sequencing data.
Evan Johnson W, Welker NC, Bass BL
Biometrics. 2011 Mar 8. doi: 10.1111/j.1541-0420.2010.01570.x. [Epub ahead of print]

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.
Paşaniuc B, Zaitlen N, Halperin E.
J Comput Biol. 2011 Mar;18(3):459-68.

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Genovo: de novo assembly for metagenomes.
Laserson J, Jojic V, Koller D.
J Comput Biol. 2011 Mar;18(3):429-43.

Compressing genomic sequence fragments using SlimGene.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G.
J Comput Biol. 2011 Mar;18(3):401-13.

The Poisson margin test for normalization-free significance analysis of NGS data.
Kowalczyk A, Bedo J, Conway T, Beresford-Smith B.
J Comput Biol. 2011 Mar;18(3):391-400.

NaiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing.
Kao WC, Song YS.
J Comput Biol. 2011 Mar;18(3):365-77.

Inference of isoforms from short sequence reads.
Feng J, Li W, Jiang T.
J Comput Biol. 2011 Mar;18(3):305-21.

Helicobacter pylori genome evolution during human infection.
Kennemann L, Didelot X, Aebischer T, Kuhn S, et al.
Proc Natl Acad Sci U S A. 2011 Mar 7. [Epub ahead of print]

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.
Rasko DA, Worsham PL, Abshire TG, Stanley ST, et al.
Proc Natl Acad Sci U S A. 2011 Mar 7. [Epub ahead of print]

Responses of the pea aphid transcriptome to infection by facultative symbionts.
Burke GR, Moran NA.
Insect Mol Biol. 2011 Mar 7. doi: 10.1111/j.1365-2583.2011.01070.x. [Epub ahead of print]

The Scan

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.

Tibetan Study Finds Adaptive Variant Influencing Skin Pigmentation

With a combination of phenotyping and genetic data, researchers document at PNAS a Tibetan-enriched enhancer variant influencing melanin synthesis and ultraviolet light response.

Domestication Linked to Nervous System Genes in Inbred Mouse Strains

Researchers highlighted more than 300 positively selected genes in domesticated mice, including genes linked to nervous system function or behavior in Genome Biology.

ALS Genetic Testing May Be Informative Across Age Ranges, Study Finds

Researchers in the journal Brain identified clinically actionable variants in a significant subset of older ALS patients, prompting them to point to the potential benefits of broader test use.