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2008

Selected Works

Bioinformatics

Articles 1 - 9 of 9

Full-Text Articles in Life Sciences

Word Sense Disambiguation In Biomedical Ontologies With Term Co-Occurrence Analysis And Document Clustering, Bill Andreopoulos, Dimitra Alexopoulou, Michael Schroeder Sep 2008

Word Sense Disambiguation In Biomedical Ontologies With Term Co-Occurrence Analysis And Document Clustering, Bill Andreopoulos, Dimitra Alexopoulou, Michael Schroeder

William B. Andreopoulos

With more and more genomes being sequenced, a lot of effort is devoted to their annotation with terms from controlled vocabularies such as the GeneOntology. Manual annotation based on relevant literature is tedious, but automation of this process is difficult. One particularly challenging problem is word sense disambiguation. Terms such as |development| can refer to developmental biology or to the more general sense. Here, we present two approaches to address this problem by using term co-occurrences and document clustering. To evaluate our method we defined a corpus of 331 documents on development and developmental biology. Term co-occurrence analysis achieves an …

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Dioxidobis(2-Oxo-1,2-Dihydropyridin-3-Olato)­Molybdenum(Vi), Manoj Trivedi, Daya Shankar Pandey, Nigam P. Rath Apr 2008

Dioxidobis(2-Oxo-1,2-Dihydropyridin-3-Olato)­Molybdenum(Vi), Manoj Trivedi, Daya Shankar Pandey, Nigam P. Rath

Nigam Rath

In the title compound, [Mo(C5H4NO2)2O2], the MoVI atom exhibits a distorted octa­hedral coordination geometry formed by two terminal oxo ligands and two monoanionic O,O-bidentate pyridinone ligands. The two terminal oxo ligands lie in a cis arrangement, the ketonic O atoms of the pyridinone ligands are coordinated trans to the oxo ligands and the deprotonated hydroxyl O atoms are located trans to each other. The crystal structure contains inter­molecular N-H...O hydrogen bonds, C-H...O contacts and face-to-face [pi]-[pi] stacking inter­actions with an inter­planar separation of 3.25 (1) Å.

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Diethyl 2-[(4-Nitro­Phen­Yl)(4-Phenyl-1,2,3-Selenadiazol-5-Yl)Meth­Yl]Malonate, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam P. Rath Apr 2008

Diethyl 2-[(4-Nitro­Phen­Yl)(4-Phenyl-1,2,3-Selenadiazol-5-Yl)Meth­Yl]Malonate, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam P. Rath

Nigam Rath

In the title compound, C22H21N3O6Se, the heterocyclic ring makes dihedral angles of 50.03 (11) and 67.75 (11)°, respectively, with the benzene and phenyl rings. The terminal C atoms of the ester groups are disordered over two positions: the site occupancies for the C atoms are 0.62 (3)/0.38 (3) and 0.48 (3)/0.52 (3). In the crystal structure, weak intra- and inter­molecular C-H...O inter­actions are observed.

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4-(4-Chlorophenyl)-5-[1-(4-Chlorophenyl)-2-Methyl-2-Nitropropyl]-1,2,3-Selenadiazole, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam P. Rath Feb 2008

4-(4-Chlorophenyl)-5-[1-(4-Chlorophenyl)-2-Methyl-2-Nitropropyl]-1,2,3-Selenadiazole, A. Marx, S. Saravanan, S. Muthusubramanian, V. Manivannan, Nigam P. Rath

Nigam Rath

In the title compound, C18H15Cl2N3O2Se, the selenadiazole ring makes dihedral angles of 49.87 (3) and 55.70 (3)° with the two benzene rings. The dihedral angle between the two benzene rings is 11.90 (5)°. In the crystal structure, intra­molecular C-H...O and C-H...Se inter­actions and inter­molecular C-H...O, C-H...Cl and C-H...N inter­actions are observed.

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Mutual Information Without The Influence Of Phylogeny Or Entropy Dramatically Improves Residue Contact Prediction, Stanley Dunn, Lindi Wahl, Gregory Gloor Dec 2007

Mutual Information Without The Influence Of Phylogeny Or Entropy Dramatically Improves Residue Contact Prediction, Stanley Dunn, Lindi Wahl, Gregory Gloor

Stanley D Dunn

Motivation: Compensating alterations during the evolution of protein families give rise to coevolving positions that contain important structural and functional information. However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions.

Results: We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Removal of this background results in a metric, MIp, that correctly identifies substantially more coevolving positions in protein families than any existing method. A significant fraction of these …

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Tetra-N-Butyl­Ammonium Bis­(2,2-Dicyano­Ethyl­Ene-1,1-Dithiol­Ato)Palladium(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen Dec 2007

Tetra-N-Butyl­Ammonium Bis­(2,2-Dicyano­Ethyl­Ene-1,1-Dithiol­Ato)Palladium(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen

Daron E Janzen, Ph.D.

No abstract provided.

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Tetra-N-Butyl-Ammonium Bis-(1,1-Dicyano-Ethyl-Ene-2,2-Dithiol-Ato)Platinum(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen Dec 2007

Tetra-N-Butyl-Ammonium Bis-(1,1-Dicyano-Ethyl-Ene-2,2-Dithiol-Ato)Platinum(Ii), Nyasha Kanganga, Kent R. Mann, Daron E. Janzen

Daron E Janzen, Ph.D.

No abstract provided.

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Pisciforma, Setisura, And Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based On 18s Rdna Sequences: A Reply To Sun Et Al. (2006), T. Heath Ogden Dec 2007

Pisciforma, Setisura, And Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based On 18s Rdna Sequences: A Reply To Sun Et Al. (2006), T. Heath Ogden

T. Heath Ogden

No abstract provided.

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Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden Dec 2007

Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden

T. Heath Ogden

We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher-level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non-monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta …

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