Affiliation: University of Toronto
- Network-based characterization of drug-regulated genes, drug targets, and toxicityMax Kotlyar
The Campbell Family Institute for Cancer Research, Ontario Cancer Institute, University Health Network, IBM Life Sciences Discovery Centre, Toronto Medical Discovery Tower, 9 305, 101 College Street, Toronto, Ontario, M5G 1L7, Canada
Methods 57:499-507. 2012..Finally, network centrality of a drug's differentially regulated genes correlated significantly with drug toxicity...
- The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cellsJulia Petschnigg
Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
Nat Methods 11:585-92. 2014..MaMTH is a powerful tool for investigating the dynamic interactomes of human integral membrane proteins. ..
- Prioritizing therapeutics for lung cancer: an integrative meta-analysis of cancer gene signatures and chemogenomic dataKristen Fortney
Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
PLoS Comput Biol 11:e1004068. 2015..Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain. ..
- In silico drug screen in mouse liver identifies candidate calorie restriction mimeticsKristen Fortney
Department of Medical Biophysics, University of Toronto, Ontario, Canada
Rejuvenation Res 15:148-52. 2012..Here we integrate these data with gene expression signatures of CR in mouse liver to generate a prioritized list of candidate CR mimetics. We identify 14 drugs that reproduce the effects of CR at the transcriptional level...
- CHIP-MYTH: a novel interactive proteomics method for the assessment of agonist-dependent interactions of the human β₂-adrenergic receptorSaranya Kittanakom
Donnelly Centre, University of Toronto, Ontario, Canada
Biochem Biophys Res Commun 445:746-56. 2014....
- Integration, visualization and analysis of human interactomeChiara Pastrello
Princess Margaret Cancer Centre, University Health Network and TECHNA Institute for the Advancement of Technology for Health, TMDT, Room 11 314, 101 College Street, Toronto, ON M5G 1L7, Canada
Biochem Biophys Res Commun 445:757-73. 2014..Finally, we present an example integration to demonstrate the value of the network approach in cancer research, and highlight the importance of dynamic data in the specific context of signaling pathways...
- NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiaeKristen Fortney
Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
Nucleic Acids Res 41:D720-7. 2013..We demonstrate with use case examples how NetwoRx can be applied to target specific phenotypes, repurpose drugs using mode of action analysis, investigate bipartite networks and predict new drugs that affect yeast aging...
- Integrated interactions database: tissue-specific view of the human and model organism interactomesMax Kotlyar
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
Nucleic Acids Res 44:D536-41. 2016..IID is available at http://ophid.utoronto.ca/iid. ..
- Fundamentals of protein interaction network mappingJamie Snider
Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
Mol Syst Biol 11:848. 2015..We hope that this review serves as both a useful overview of the field and a guide to help more scientists actively employ these powerful approaches in their research. ..
- Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans agingKristen Fortney
Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, M5G 2M9, Canada
Genome Biol 11:R13. 2010..We apply these modular biomarkers to assign novel aging-related functions to poorly characterized longevity genes...
- Uninterrupted Sedentary Behavior Downregulates BRCA1 Gene ExpressionRachael Pettapiece-Phillips
Women s College Research Institute, Women s College Hospital, Toronto, Ontario, Canada Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
Cancer Prev Res (Phila) 9:83-8. 2016..Whether this translates into a potentially more harmful effect in BRCA1 mutation carriers warrants further investigation. Cancer Prev Res; 9(1); 83-88. ©2015 AACR. ..
- In silico prediction of physical protein interactions and characterization of interactome orphansMax Kotlyar
Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
Nat Methods 12:79-84. 2015..We provide an online database of annotated PPI predictions (http://ophid.utoronto.ca/fpclass/) and the prediction software (http://www.cs.utoronto.ca/~juris/data/fpclass/)...
- Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathologyBrian Cox
The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, Ontario, Canada
Mol Syst Biol 5:279. 2009..The entire data are available as a web-accessible database to guide the informed development of mouse models to study human disease...