Two distinct approaches are being used to study complex cellular systems. The first approach automatically searches large datasets for correlations between genes and proteins and represents these as a graph with nodes and edges. The second approach painstakingly crafts detailed models that can be simulated by computer. These approaches have largely been developed separately until now. This project will meld these two approaches into a single framework, thereby allowing fast database searches to augment models that can be simulated. Specifically, the project will 1. Develop fast algorithms to search databases of molecular data to suggest extensions to models of cellular control systems 2. Develop new principles to test how well these extended models match experimental data and 3. Design experimental tests that can validate the predictions made by the first two steps. The project will validate this system by studying the mechanism of cell division, a system involved in the development of cancer. In the long term, the methods developed by this project can be used to study any complex cellular system, e.g., those implicated in infectious diseases.
This project will meld two distinct approaches for studying complex cellular systems, one top-down and the other bottom-up, into a single framework. The project will combine the power of fast database searches with hand-crafted models. The project will validate this system by studying the mechanism of cell division, a system involved in the development of cancer.
| Bharadwaj, Aditya; Singh, Divit P; Ritz, Anna et al. (2017) GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinformatics 33:3134-3136 |
| Ritz, Anna; Avent, Brendan; Murali, T M (2017) Pathway Analysis with Signaling Hypergraphs. IEEE/ACM Trans Comput Biol Bioinform 14:1042-1055 |
| Sam, Sarah A; Teel, Joelle; Tegge, Allison N et al. (2017) XTalkDB: a database of signaling pathway crosstalk. Nucleic Acids Res 45:D432-D439 |
| Gil, Daniel P; Law, Jeffrey N; Murali, T M (2017) The PathLinker app: Connect the dots in protein interaction networks. F1000Res 6:58 |
| Laomettachit, Teeraphan; Chen, Katherine C; Baumann, William T et al. (2016) A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks. PLoS One 11:e0153738 |
| Tegge, Allison N; Sharp, Nicholas; Murali, T M (2016) Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinformatics 32:242-51 |
| Ritz, Anna; Poirel, Christopher L; Tegge, Allison N et al. (2016) Pathways on demand: automated reconstruction of human signaling networks. NPJ Syst Biol Appl 2:16002 |
| Adames, Neil R; Schuck, P Logan; Chen, Katherine C et al. (2015) Experimental testing of a new integrated model of the budding yeast Start transition. Mol Biol Cell 26:3966-84 |
| Tyson, John J; Novák, Béla (2015) Models in biology: lessons from modeling regulation of the eukaryotic cell cycle. BMC Biol 13:46 |
| Kraikivski, Pavel; Chen, Katherine C; Laomettachit, Teeraphan et al. (2015) From START to FINISH: computational analysis of cell cycle control in budding yeast. NPJ Syst Biol Appl 1:15016 |
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