July 2012 archive

Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. g., n. sp., a deep-branching relative of diplomonads.

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Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. g., n. sp., a deep-branching relative of diplomonads.
J Eukaryot Microbiol. 2009 Jul-Aug;56(4):373-84
Auth…

Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction.

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Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction.
J Hered. 2009 Sep-Oct;100(5):582-90
Authors: Archibald JM, Lane CE
Abstract
Nucleomorphs are the relic …

GenGIS: A geospatial information system for genomic data.

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GenGIS: A geospatial information system for genomic data.
Genome Res. 2009 Oct;19(10):1896-904
Authors: Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG
Abstract

Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept".

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Reconciling ecological and genomic divergence among lineages of listeria under an “extended mosaic genome concept”.
Mol Biol Evol. 2009 Nov;26(11):2605-15
Authors: Dunn KA, Bielawski JP, Ward TJ, Urquhart C,…

Eradicating typological thinking in prokaryotic systematics and evolution.

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Eradicating typological thinking in prokaryotic systematics and evolution.
Cold Spring Harb Symp Quant Biol. 2009;74:197-204
Authors: Doolittle WF
Abstract
In 1982, John Maynard Smith called f…

Nucleomorph genomes.

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Nucleomorph genomes.
Annu Rev Genet. 2009;43:251-64
Authors: Moore CE, Archibald JM
Abstract
Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes…

General heterotachy and distance method adjustments.

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General heterotachy and distance method adjustments.
Mol Biol Evol. 2009 Dec;26(12):2689-97
Authors: Wu J, Susko E
Abstract
Heterotachy is a general term to describe positions in a sequence t…

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis.

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PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis.
BMC Evol Biol. 2009;9:225
Authors: Wang HC, Susko E, Roger AJ
Abstract

Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.

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Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.
Bioinformatics. 2009 Dec 1;25(23):3093-8
Authors: Blouin C, Perry S, Lavell A, Susko E, Roger AJ
Abstract

Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.

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Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.
Mol Biol Evol. 2010 Feb;27(2):311-24
Authors: Hug LA, Stechmann A, Roger AJ
Abstract