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Bioinformatics

Selected Works

2005

Articles 1 - 5 of 5

Full-Text Articles in Life Sciences

Cgkb-Cyanogroup Genomics Knowledge Base, Tin-Chun Chu, Lee Lee, Shankar Srinivasan, John Gaynor, Quinn Vega, Bonnie Lustigman May 2005

Cgkb-Cyanogroup Genomics Knowledge Base, Tin-Chun Chu, Lee Lee, Shankar Srinivasan, John Gaynor, Quinn Vega, Bonnie Lustigman

Tin-Chun Chu, Ph.D.

No abstract provided.

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Bioinformatic Analysis Of The Metal-Binding Protein Families And Heavy Metal Resistance Amongst Cyanobacteria, Tin-Chun Chu, Lee Lee, Shankar Srinivasan Dec 2004

Bioinformatic Analysis Of The Metal-Binding Protein Families And Heavy Metal Resistance Amongst Cyanobacteria, Tin-Chun Chu, Lee Lee, Shankar Srinivasan

Tin-Chun Chu, Ph.D.

No abstract provided.

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Plant Ontology (Po): A Controlled Vocabulary Of Plant Structures And Growth Stages, Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Doreen Ware, Felipe Zapata Dec 2004

Plant Ontology (Po): A Controlled Vocabulary Of Plant Structures And Growth Stages, Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Doreen Ware, Felipe Zapata

Peter Stevens

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, …

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Poor Taxon Sampling, Poor Character Sampling, And Non-Repeatable Analyses Of A Contrived Dataset Do Not Provide A More Credible Estimate Of Insect Phylogeny: A Reply To Kjer., T. Heath Ogden Dec 2004

Poor Taxon Sampling, Poor Character Sampling, And Non-Repeatable Analyses Of A Contrived Dataset Do Not Provide A More Credible Estimate Of Insect Phylogeny: A Reply To Kjer., T. Heath Ogden

T. Heath Ogden

The wealth of data available for phylogenetic analysis of the insect orders, from both morphological and molecular sources, is steadily increasing. However, controversy exists among the methodologies one can use to reconstruct ordinal relationships. Recently, Kjer (2004) presented an analysis of insect ordinal relationships based exclusively on a single source of information: 18S rDNA sequence data. Kjer claims that his analysis resulted in a more ‘‘credible’’ phylogeny for the insect orders and strongly criticized our previous phylogenetic results. However, Kjer only used a subset of the data that are currently available for insect ordinal phylogeny, misrepresented our analyses, and omitted …

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Phylogeny Of Ephemeroptera (Mayflies) Based On Molecular Evidence, T. Heath Ogden Dec 2004

Phylogeny Of Ephemeroptera (Mayflies) Based On Molecular Evidence, T. Heath Ogden

T. Heath Ogden

This study represents the Wrst molecular phylogeny for the Order Ephemeroptera. The analyses included 31 of the 37 families, representing »24% of the genera. Fifteen families were supported as being monophyletic, Wve families were supported as nonmonophyletic, and 11 families were only represented by one species, and monophyly was not testable. The suborders Furcatergalia and Carapacea were supported as monophyletic while Setisura and Pisciforma were not supported as monophyletic. The superfamilies Ephemerelloidea and Caenoidea were supported as monophyletic while Baetoidea, Siphlonuroidea, Ephemeroidea, and Heptagenioidea were not. Baetidae was recovered as sister to the remaining clades. The mayXy gill to wing …

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