Project 1 focuses on the fundamental challenge of integrating different levels of information comprising different molecular species and operating across different time scales. In particular, two model systems (yeast and halobacterium) will be exploited to develop approaches for understanding the principles and rules governing how information from the environment is propagated to coordinate multiple responses and complex phenotypes. We will use models that traverse across signaling, gene regulatory and metabolic networks. Tools and insights developed through this project will be applicable to all biological system developmental, physiological and structural. Moreover, the malfunction of signaling processes leads to phenotypic and metabolic changes underlying human disease, including cancers, neuropathies, myopathies and diabetes. Understanding the dynamic nature of these networks is a window into understanding disease states and rational strategies for effective interventions the basis of a systems view of medicine.
| Lee, Joon-Yong; Choi, Hyungwon; Colangelo, Christopher M et al. (2018) ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data. J Biomol Tech 29:39-45 |
| Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda et al. (2018) Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep 22:3251-3264 |
| Maixner, Frank; Turaev, Dmitrij; Cazenave-Gassiot, Amaury et al. (2018) The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals. Curr Biol 28:2348-2355.e9 |
| Holden, Jennifer M; Koreny, Ludek; Obado, Samson et al. (2018) Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell 29:1100-1110 |
| Hoopmann, Michael R; Winget, Jason M; Mendoza, Luis et al. (2018) StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline. J Proteome Res 17:1314-1320 |
| Slama, Patrick; Hoopmann, Michael R; Moritz, Robert L et al. (2018) Robust determination of differential abundance in shotgun proteomics using nonparametric statistics. Mol Omics 14:424-436 |
| Jabbari, Neda; Glusman, Gustavo; Joesch-Cohen, Lena M et al. (2018) Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1. PLoS One 13:e0198135 |
| Trachana, Kalliopi; Bargaje, Rhishikesh; Glusman, Gustavo et al. (2018) Taking Systems Medicine to Heart. Circ Res 122:1276-1289 |
| Shao, Wenguang; Pedrioli, Patrick G A; Wolski, Witold et al. (2018) The SysteMHC Atlas project. Nucleic Acids Res 46:D1237-D1247 |
| Kazantsev, Fedor; Akberdin, Ilya; Lashin, Sergey et al. (2018) MAMMOTh: A new database for curated mathematical models of biomolecular systems. J Bioinform Comput Biol 16:1740010 |
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