selected scholarly activity
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chapters
- Theory and Applications of Proteomics. 461-469. 2011
- Theory and Applications of Proteomics. 448-455. 2011
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conferences
- Functional Characterization Of Dbf4 Interactions With DNA Replication And Checkpoint Factors. The FASEB Journal. 2013
- Discrimination of Insoluble-Carbohydrate Binding Proteins and Their Binding Sites Using a 3D Motif Detection Method. Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. 207-213. 2008
- Occurrence and Toxicity of Photomodified Polycyclic Aromatic Hydrocarbon Mixtures Present in Contaminated Sediments. ASTM Special Technical Publication. 211-220. 2000
- Use of Artificial Lighting in Environmental Assessment Studies. ASTM Special Technical Publication. 55-70. 1996
- QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS FOR THE PHOTOCHEMICAL STRESS OF POLYCYCLIC AROMATIC-HYDROCARBONS TO HIGHER-PLANTS. Plant Physiology. 158-158. 1993
- Quantitative Structure Activity Relationships for the Photoinduced Toxicity of Polycyclic Aromatic Hydrocarbons to Duckweed — A Preliminary Model. ASTM Special Technical Publication. 369-378. 1993
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journal articles
- Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog.. Virus Evolution. 10:veae082. 2024
- Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. Scientific Reports. 12:6180. 2022
- Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds. Applied and Environmental Microbiology. 87:e02914-e02920. 2021
- Slr4, a newly identified S‐layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Molecular Microbiology. 114:979-990. 2020
- Effect of long-acting β-agonists/glucocorticoids on human airway epithelial cell cytokine, transcriptomic and oxidative stress responses to cannabis smoke. ERJ Open Research. 6:00265-2019. 2020
- Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke. Physiological Reports. 7:e14249. 2019
- The GRHL2/ZEB Feedback Loop-A Key Axis in the Regulation of EMT in Breast Cancer. Journal of Cellular Biochemistry. 118:2559-2570. 2017
- Nutritional characteristics of the potential aquaculture feed species Boekelovia hooglandii. Annual Review of Fish Diseases. 474:113-120. 2017
- Assessing the bioremediation potential of algal species indigenous to oil sands process-affected waters on mixtures of oil sands acid extractable organics. Ecotoxicology and Environmental Safety. 133:373-380. 2016
- An omics approach to rational feed: Enhancing growth in CHO cultures with NMR metabolomics and 2D-DIGE proteomics. - PubMed - NCBI. Journal of Biotechnology. 234:127-138. 2016
- Comparative assessment of microalgal fatty acids as topical antibiotics. Journal of Applied Phycology. 28:1695-1704. 2016
- Pollux: platform independent error correction of single and mixed genomes. BMC Bioinformatics. 16:10. 2015
- Effects of 1-aminocyclopropane-1-carboxylate (ACC) deaminase-overproducing Sinorhizobium meliloti on plant growth and copper tolerance of Medicago lupulina. Plant and Soil. 391:383-398. 2015
- Pathogen-secreted proteases activate a novel plant immune pathway. Nature. 521:213-216. 2015
- Optimization of culturing conditions for toxicity testing with the algaOophilasp. (Chlorophyceae), an amphibian endosymbiont. Environmental Toxicology and Chemistry. 33:2566-2575. 2014
- Modeling of cell culture damage and recovery leads to increased antibody and biomass productivity in CHO cell cultures. Biotechnology journal. 9:1152-1163. 2014
- Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities. mBio. 5:e01157-e01114. 2014
- A Novel Non-canonical Forkhead-associated (FHA) Domain-binding Interface Mediates the Interaction between Rad53 and Dbf4 Proteins. Journal of Biological Chemistry. 289:2589-2599. 2014
- New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance. PLoS ONE. 9:e99168-e99168. 2014
- Modeling the coupled extracellular and intracellular environments in mammalian cell culture. Metabolic Engineering. 19:57-68. 2013
- Prediction of molecular mimicry candidates in human pathogenic bacteria. Virulence. 4:453-466. 2013
- Identification of plant growth-promoting bacteria-responsive proteins in cucumber roots under hypoxic stress using a proteomic approach. Journal of Proteomics. 84:119-131. 2013
- Investigating the Role of Protein UnkG from the Pseudomonas putida UW4 in the Ability of the Bacterium to Facilitate Plant Growth. Current Microbiology. 66:331-336. 2013
- Serum Immune-Related Proteins are Differentially Expressed during Hibernation in the American Black Bear. PLoS ONE. 8:e66119-e66119. 2013
- A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. BMC Systems Biology. 6:78. 2012
- The evolution of the class A scavenger receptors. BMC Ecology and Evolution. 12:227. 2012
- Toxic effects of oil sand naphthenic acids on the biomass accumulation of 21 potential phytoplankton remediation candidates. Ecotoxicology and Environmental Safety. 86:156-161. 2012
- Combined effects of the plant growth-promoting bacterium Pseudomonas putida UW4 and salinity stress on the Brassica napus proteome. Applied Soil Ecology. 61:255-263. 2012
- Effects of Bacterial ACC Deaminase onBrassica napusGene Expression. Molecular Plant-Microbe Interactions. 25:668-676. 2012
- Population‐based modeling of the progression of apoptosis in mammalian cell culture. Biotechnology and Bioengineering. 109:1193-1204. 2012
- Horizontal Gene Transfer Contributed to the Evolution of Extracellular Surface Structures: The Freshwater Polyp Hydra Is Covered by a Complex Fibrous Cuticle Containing Glycosaminoglycans and Proteins of the PPOD and SWT (Sweet Tooth) Families. PLoS ONE. 7:e52278-e52278. 2012
- Modular Evolution and the Origins of Symmetry: Reconstruction of a Three-Fold Symmetric Globular Protein. Folding and Design. 20:161-171. 2012
- Nuclear Targeting of Methyl-Recycling Enzymes in Arabidopsis thaliana Is Mediated by Specific Protein Interactions. Molecular Plant. 5:231-248. 2012
- Differential chromatin proteomics of the MMS-induced DNA damage response in yeast. Proteome Science. 9:62. 2011
- Proteomics analysis of chinese hamster ovary cells undergoing apoptosis during prolonged cultivation. Cytotechnology. 63:663-677. 2011
- Development of a mathematical model for evaluating the dynamics of normal and apoptotic Chinese hamster ovary cells. Biotechnology Progress. 27:1197-1205. 2011
- Dynamic Modeling of Apoptosis and its Interaction with Cell Growth in Mammalian Cell Culture. IFAC-PapersOnLine. 44:9691-9696. 2011
- Characterization of Plant-Bacterial Interactions Using Proteomic Approaches. Current Proteomics. 7:244-257. 2010
- Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC Molecular and Cell Biology. 10:23. 2010
- Proteomic studies of plant–bacterial interactions. Soil Biology and Biochemistry. 42:1673-1684. 2010
- Apoptosis induction by eIF5A1 involves activation of the intrinsic mitochondrial pathway. Journal of Cellular Physiology. 223:798-809. 2010
- Metabolic flux and nutrient uptake modeling of normal and apoptotic CHO cells. IFAC-PapersOnLine. 43:395-400. 2010
- Modeling the progression of apoptosis in Chinese Hamster Ovary cells. IFAC-PapersOnLine. 43:467-472. 2010
- Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress. Proteome Science. 7:18. 2009
- Identification of Myopia-Related Marker Proteins in Tilapia Retinal, RPE, and Choroidal Tissue following Induced Form Deprivation. Current Eye Research. 34:966-975. 2009
- Proteome reference map for the plant growth‐promoting bacterium Pseudomonas putida UW4. Proteomics. 9:4271-4274. 2009
- Identification of Bacterial Proteins Mediating the Interactions Between Pseudomonas putida UW4 and Brassica napus (Canola). Molecular Plant-Microbe Interactions. 22:686-694. 2009
- The origin recognition complex protein family. Genome Biology. 10:214-214. 2009
- Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. BMC Ecology and Evolution. 8:316. 2008
- TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis. Nature Genetics. 40:572-574. 2008
- Assessing the evolution of gene expression using microarray data. Evolutionary Bioinformatics. 2008:139-152. 2008
- Transcriptional regulation of ACC deaminase gene expression inPseudomonas putidaUW4. Canadian Journal of Microbiology. 54:128-136. 2008
- Assessing the Evolution of Gene Expression Using Microarray Data. Evolutionary Bioinformatics. 4:EBO.S628-EBO.S628. 2008
- Systems level modeling of the cell cycle using budding yeast.. Cancer Informatics. 3:357-370. 2007
- Promotion of Plant Growth by Bacterial ACC Deaminase. Critical Reviews in Plant Sciences. 26:227-242. 2007
- Functional Divergence in the Arabidopsis -1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States. Molecular Biology and Evolution (MBE). 24:1045-1055. 2007
- Systems Level Modeling of the Cell Cycle Using Budding Yeast. Cancer Informatics. 3:117693510700300-117693510700300. 2007
- Cold-Active Winter Rye Glucanases with Ice-Binding Capacity. Plant Physiology. 141:1459-1472. 2006
- Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Nature Biotechnology. 24:852-855. 2006
- Discrimination of native protein structures using atom–atom contact scoring. Proceedings of the National Academy of Sciences of the United States of America. 100:3215-3220. 2003
- The performance of current methods in ligand-protein docking. Current Science. 83:845-856. 2002
- Quantification of protein surfaces, volumes and atom–atom contacts using a constrained Voronoi procedure. Bioinformatics. 18:1365-1373. 2002
- Measurement of Short- and Long-Term Toxicity of Polycyclic Aromatic Hydrocarbons Using Luminescent Bacteria. Ecotoxicology and Environmental Safety. 51:12-21. 2002
- Natural sunlight induced photooxidation of naphthalene in aqueous solution. Water, Air, and Soil Pollution. 136:347-359. 2002
- Fractional Simplex Designs for Interaction Screening in Complex Mixtures. Biometrics. 56:824-832. 2000
- Impacts of Structural Photomodification on the Toxicity of Environmental Contaminants: Anthracene Photooxidation Products. Ecotoxicology and Environmental Safety. 43:204-212. 1999
- MECHANISMS OF PHOTOINDUCED TOXICITY OF PHOTOMODIFIED ANTHRACENE TO PLANTS: INHIBITION OF PHOTOSYNTHESIS IN THE AQUATIC HIGHER PLANT LEMNA GIBBA (DUCKWEED). Environmental Toxicology and Chemistry. 16:1707-1707. 1997
- MECHANISTIC QUANTITATIVE STRUCTURE–ACTIVITY RELATIONSHIP MODEL FOR THE PHOTOINDUCED TOXICITY OF POLYCYCLIC AROMATIC HYDROCARBONS: II. AN EMPIRICAL MODEL FOR THE TOXICITY OF 16 POLYCYCLIC AROMATIC HYDROCARBONS TO THE DUCKWEED LEMNA GIBBA L. G-3. Environmental Toxicology and Chemistry. 16:2296-2296. 1997
- TOXICITY OF A PAH PHOTOOXIDATION PRODUCT TO THE BACTERIA PHOTOBACTERIUM PHOSPHOREUM AND THE DUCKWEED LEMNA GIBBA: EFFECTS OF PHENANTHRENE AND ITS PRIMARY PHOTOPRODUCT, PHENANTHRENEQUINONE. Environmental Toxicology and Chemistry. 16:892-892. 1997
- Photoinduced Toxicity of Three Polycyclic Aromatic Hydrocarbons (Fluoranthene, Pyrene, and Naphthalene) to the Duckweed Lemna gibba L. G-3. Ecotoxicology and Environmental Safety. 28:160-171. 1994