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Papers by Brigitte Tuekam

Research paper thumbnail of PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine

BMC bioinformatics, Jan 27, 2003

The majority of experimentally verified molecular interaction and biological pathway data are pre... more The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND. Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high t...

Research paper thumbnail of The Biomolecular Interaction Network Database and related tools 2005 update

Nucleic Acids Research, 2005

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular inter... more The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machinereadable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.

Research paper thumbnail of Primary Epitopes of Chicken Egg Yolk Antibodies to Peptidophosphogalactomannan

Egg yolks from hens immunized with peptidophosphogalactomannan (pPGalMan(ii)), which contains 10 ... more Egg yolks from hens immunized with peptidophosphogalactomannan (pPGalMan(ii)), which contains 10 phosphocholine diester residues and is secreted by Penicillium fellutanum, contain antibodies against 5-O-beta-D-galactofuranosyl epitopes. These epitopes were the only significant determinants in pPGalMan(ii). Approximately 60-fold less pPGalMan(ii) (1.6 microM galactofuran chains) was required for 50% inhibition than galactofurano-oligosaccharides or pPGalMan containing two galactofuranosyl residues per chain.

Research paper thumbnail of Relationship of Exo- -D-Galactofuranosidase Kinetic Parameters to the Number of Phosphodiesters in Penicillium fellutanum Peptidophosphogalactomannan: Enzyme Purification and Kinetics of Glycopeptide and Galactofuran Chain Hydrolysis

Applied and Environmental Microbiology, 2001

Extracellular Penicillium fellutanum exo-␤-D-galactofuranosidase, with a mass of 70 kDa, was puri... more Extracellular Penicillium fellutanum exo-␤-D-galactofuranosidase, with a mass of 70 kDa, was purified to apparent homogeneity. The enzyme was used to investigate the influence of phosphodiesters of the peptidophosphogalactomannans pP 2 GM ii and pP 25 GM ii (containing 2 and 25 phosphodiester residues, respectively, per mol of polymer) on the kinetic parameters of galactofuranosyl hydrolysis of these two polymers, of 1-O-methyl-␤-D-galactofuranoside, and of two galactofuranooligosaccharides. The enzyme did not hydrolyze phosphorylated galactose residues of pP 2 GM ii or pP 25 GM ii . The k cat /K m value for pP 25 GM ii is 1.7 ؋ 10 3 M ؊1 s ؊1 , that for 1-O-methyl-␤-D-galactofuranoside is 1.1 ؋ 10 4 M ؊1 s ؊1 , that for pP 2 GM ii is 1.7 ؋ 10 4 M ؊1 s ؊1 , and those for 5-O-␤-D-galactofuranooligosaccharides with degrees of polymerization of 3.4 and 5.5 are 1.7 ؋ 10 5 and 4.1 ؋ 10 5 M ؊1 s ؊1 , respectively. Variability in the k cat /K m values is due primarily to differences in K m values; the k ؊1 /k 1 ratio likely provides the most influence on K m . k cat increases as the degree of polymerization of galactofuranosyl residues increases. Most of the galactofuranosyl and phosphocholine residues were removed by day 8 in vivo from pP x GM ii added to day 3 cultures initiated in medium containing 2 mM phosphate but not from those initially containing 20 mM phosphate. The filtrates from day 9 cultures initiated in 2 mM inorganic phosphate in modified Raulin-Thom medium contained 0.2 mM inorganic phosphate and 2.2 U of galactofuranosidase ml ؊1 h ؊1 . No galactofuranosidase activity but 15 mM inorganic phosphate was found in filtrates from day 9 cultures initiated in 20 mM phosphate. In vivo the rate of galactofuranosyl hydrolysis of pP x GM ii and of related polymers is proportional to the k cat /K m value of each polymer. The kinetic data show that the k cat /K m value increases as the number of phosphodiesters of pP x GM ii decreases, also resulting in an increase in the activity of exo-␤-D-galactofuranosidase.

Research paper thumbnail of PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine

BMC Bioinformatics, 2003

The majority of experimentally verified molecular interaction and biological pathway data are pre... more The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND.

Research paper thumbnail of Generation of Glyphs for Conveying Complex Information, with Application to Protein Representations

We present a method to generate glyphs which convey complex information in graphical form. A glyp... more We present a method to generate glyphs which convey complex information in graphical form. A glyph has a linear geometry which is specified using geometric operations, each represented by characters nested in a string. This format allows several glyph strings to be concatenated, resulting in more complex geometries. We explore automatic generation of a large number of glyphs using a genetic algorithm. To measure the visual distinctness between two glyph geometries, we use the iterative closest point algorithm. We apply these methods to create two different types of representations for biological proteins, transforming the rich data describing their various characteristics into graphical form. The representations are automatically built from a finite set of glyphs, which have been created manually or using the genetic algorithm.

Research paper thumbnail of PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine

BMC bioinformatics, Jan 27, 2003

The majority of experimentally verified molecular interaction and biological pathway data are pre... more The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND. Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high t...

Research paper thumbnail of The Biomolecular Interaction Network Database and related tools 2005 update

Nucleic Acids Research, 2005

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular inter... more The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machinereadable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.

Research paper thumbnail of Primary Epitopes of Chicken Egg Yolk Antibodies to Peptidophosphogalactomannan

Egg yolks from hens immunized with peptidophosphogalactomannan (pPGalMan(ii)), which contains 10 ... more Egg yolks from hens immunized with peptidophosphogalactomannan (pPGalMan(ii)), which contains 10 phosphocholine diester residues and is secreted by Penicillium fellutanum, contain antibodies against 5-O-beta-D-galactofuranosyl epitopes. These epitopes were the only significant determinants in pPGalMan(ii). Approximately 60-fold less pPGalMan(ii) (1.6 microM galactofuran chains) was required for 50% inhibition than galactofurano-oligosaccharides or pPGalMan containing two galactofuranosyl residues per chain.

Research paper thumbnail of Relationship of Exo- -D-Galactofuranosidase Kinetic Parameters to the Number of Phosphodiesters in Penicillium fellutanum Peptidophosphogalactomannan: Enzyme Purification and Kinetics of Glycopeptide and Galactofuran Chain Hydrolysis

Applied and Environmental Microbiology, 2001

Extracellular Penicillium fellutanum exo-␤-D-galactofuranosidase, with a mass of 70 kDa, was puri... more Extracellular Penicillium fellutanum exo-␤-D-galactofuranosidase, with a mass of 70 kDa, was purified to apparent homogeneity. The enzyme was used to investigate the influence of phosphodiesters of the peptidophosphogalactomannans pP 2 GM ii and pP 25 GM ii (containing 2 and 25 phosphodiester residues, respectively, per mol of polymer) on the kinetic parameters of galactofuranosyl hydrolysis of these two polymers, of 1-O-methyl-␤-D-galactofuranoside, and of two galactofuranooligosaccharides. The enzyme did not hydrolyze phosphorylated galactose residues of pP 2 GM ii or pP 25 GM ii . The k cat /K m value for pP 25 GM ii is 1.7 ؋ 10 3 M ؊1 s ؊1 , that for 1-O-methyl-␤-D-galactofuranoside is 1.1 ؋ 10 4 M ؊1 s ؊1 , that for pP 2 GM ii is 1.7 ؋ 10 4 M ؊1 s ؊1 , and those for 5-O-␤-D-galactofuranooligosaccharides with degrees of polymerization of 3.4 and 5.5 are 1.7 ؋ 10 5 and 4.1 ؋ 10 5 M ؊1 s ؊1 , respectively. Variability in the k cat /K m values is due primarily to differences in K m values; the k ؊1 /k 1 ratio likely provides the most influence on K m . k cat increases as the degree of polymerization of galactofuranosyl residues increases. Most of the galactofuranosyl and phosphocholine residues were removed by day 8 in vivo from pP x GM ii added to day 3 cultures initiated in medium containing 2 mM phosphate but not from those initially containing 20 mM phosphate. The filtrates from day 9 cultures initiated in 2 mM inorganic phosphate in modified Raulin-Thom medium contained 0.2 mM inorganic phosphate and 2.2 U of galactofuranosidase ml ؊1 h ؊1 . No galactofuranosidase activity but 15 mM inorganic phosphate was found in filtrates from day 9 cultures initiated in 20 mM phosphate. In vivo the rate of galactofuranosyl hydrolysis of pP x GM ii and of related polymers is proportional to the k cat /K m value of each polymer. The kinetic data show that the k cat /K m value increases as the number of phosphodiesters of pP x GM ii decreases, also resulting in an increase in the activity of exo-␤-D-galactofuranosidase.

Research paper thumbnail of PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine

BMC Bioinformatics, 2003

The majority of experimentally verified molecular interaction and biological pathway data are pre... more The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND.

Research paper thumbnail of Generation of Glyphs for Conveying Complex Information, with Application to Protein Representations

We present a method to generate glyphs which convey complex information in graphical form. A glyp... more We present a method to generate glyphs which convey complex information in graphical form. A glyph has a linear geometry which is specified using geometric operations, each represented by characters nested in a string. This format allows several glyph strings to be concatenated, resulting in more complex geometries. We explore automatic generation of a large number of glyphs using a genetic algorithm. To measure the visual distinctness between two glyph geometries, we use the iterative closest point algorithm. We apply these methods to create two different types of representations for biological proteins, transforming the rich data describing their various characteristics into graphical form. The representations are automatically built from a finite set of glyphs, which have been created manually or using the genetic algorithm.