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Life Sciences Commons™

Open Access. Powered by Scholars. Published by Universities.®

2008

Selected Works

Computer Sciences

Articles 1 - 16 of 16

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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Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder Jul 2008

Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

William B. Andreopoulos

Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we …

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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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Brain Bases Of Individual Differences In Cognition, Chantel Prat, Marcel Just Dec 2007

Brain Bases Of Individual Differences In Cognition, Chantel Prat, Marcel Just

Marcel Adam Just

No abstract provided.

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A Decrease In Brain Activation Associated With Driving When Listening To Someone Speak, Marcel Just, Timothy Keller, Jacquelyn Cynkar Dec 2007

A Decrease In Brain Activation Associated With Driving When Listening To Someone Speak, Marcel Just, Timothy Keller, Jacquelyn Cynkar

Marcel Adam Just

No abstract provided.

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Fmri Investigation Of Working Memory For Faces In Autism: Visual Coding And Underconnectivity With Frontal Areas, Hideya Koshino, Rajesh Kana, Timothy Keller, Vladimir Cherkassky, Nancy Minshew, Marcel Just Dec 2007

Fmri Investigation Of Working Memory For Faces In Autism: Visual Coding And Underconnectivity With Frontal Areas, Hideya Koshino, Rajesh Kana, Timothy Keller, Vladimir Cherkassky, Nancy Minshew, Marcel Just

Marcel Adam Just

No abstract provided.

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Using Fmri Brain Activation To Identify Cognitive States Associated With Perception Of Tools And Dwellings, Svetlana V. Shinkareva, Robert A. Mason, Vicente L. Malave, Wei Wang, Tom M. Mitchell, Marcel Adam Just Dec 2007

Using Fmri Brain Activation To Identify Cognitive States Associated With Perception Of Tools And Dwellings, Svetlana V. Shinkareva, Robert A. Mason, Vicente L. Malave, Wei Wang, Tom M. Mitchell, Marcel Adam Just

Marcel Adam Just

No abstract provided.

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Modifying The Brain Activation Of Poor Readers During Sentence Comprehension With Extended Remedial Instruction: A Longitudinal Study Of Neuroplasticity, Ann Meyler, Timothy A. Keller, Vladimir L. Cherkassky, John D. E. Gabrieli, Marcel Adam Just Dec 2007

Modifying The Brain Activation Of Poor Readers During Sentence Comprehension With Extended Remedial Instruction: A Longitudinal Study Of Neuroplasticity, Ann Meyler, Timothy A. Keller, Vladimir L. Cherkassky, John D. E. Gabrieli, Marcel Adam Just

Marcel Adam Just

No abstract provided.

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What Brain Imaging Can Tell Us About Embodied Meaning, Marcel Adam Just Dec 2007

What Brain Imaging Can Tell Us About Embodied Meaning, Marcel Adam Just

Marcel Adam Just

No abstract provided.

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Theory Of Mind Disruption And Recruitment Of The Right Hemisphere During Narrative Comprehension In Autism, Robert A. Mason, Diane L. Williams, Rajesh K. Kana, Nancy J. Minshew, Marcel Adam Just Dec 2007

Theory Of Mind Disruption And Recruitment Of The Right Hemisphere During Narrative Comprehension In Autism, Robert A. Mason, Diane L. Williams, Rajesh K. Kana, Nancy J. Minshew, Marcel Adam Just

Marcel Adam Just

No abstract provided.

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Predicting Human Brain Activity Associated With The Meanings Of Nouns, Tom M. Mitchell, Svetlana V. Shinkareva, Andrew Carlson, Kai-Min Chang, Vicente L. Malave, Robert A. Mason, Marcel Adam Just Dec 2007

Predicting Human Brain Activity Associated With The Meanings Of Nouns, Tom M. Mitchell, Svetlana V. Shinkareva, Andrew Carlson, Kai-Min Chang, Vicente L. Malave, Robert A. Mason, Marcel Adam Just

Marcel Adam Just

No abstract provided.

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The Plant Ontology Database: A Community Resource For Plant Structure And Developmental Stages Controlled Vocabulary And Annotations, Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware Dec 2007

The Plant Ontology Database: A Community Resource For Plant Structure And Developmental Stages Controlled Vocabulary And Annotations, Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware

Peter Stevens

The Plant Ontology Consortium (POC, http://www.plantontology.org ) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC …

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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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