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Full-Text Articles in Bioinformatics
Validation Of A Multiplex Pcr Assay For The Simultaneous Detection Of Human Papillomavirus And Chlamydia Trachomatis In Cervical Preservcyt Samples., Helen Keegan, Alison Malkin, Mairead Griffin, Fergus Ryan, Helen Lambkin
Validation Of A Multiplex Pcr Assay For The Simultaneous Detection Of Human Papillomavirus And Chlamydia Trachomatis In Cervical Preservcyt Samples., Helen Keegan, Alison Malkin, Mairead Griffin, Fergus Ryan, Helen Lambkin
Articles
No abstract provided.
Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara
Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara
Faculty Publications
Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy …
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
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
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 …
Phylogeny Of Ephemeroptera (Mayflies) Based On Molecular Evidence, T. Heath Ogden
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 …