challenge

a partner asked COSBI to determine the pathways involved in adipogenesis under different conditions

network construction
and pathway analysis

identify functional networks affected 
by treatments or phenotypes

solution

by developing a proprietary network-based, functional enrichment algorithm to omics data, we ranked pathways according to their level of involvement at different cellular response time points

proprietary software

COSBI developed a novel network-based, contextual enrichment method

 

 

outcome

a biological interpretation of the results led us to identify important mechanisms affected by the conditions

publications

C. Priami and M.J. Morine. analysis of biological systems. Imperial College Press, 2015

I. Nassiri, R. Lombardo, M. Lauria, M.J. Morine, P. Moyseos, V. Varma, G.T. Nolen, B. Knox, D. Sloper, J. Kaput and C. Priami. Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules, Nat. Sci. Rep., 2016

S. Michelini, B. Balakrishnan, S. Parolo, A. Matone, J. Mullaney, W. Young, O. Gasser, C. Priami, R. Lombardo, M. Kussmann, "A reverse metabolic approach to weaning: In silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space". Microbiome, 2018

L. Marchetti, R. Lombardo, C. Priami HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks. Complexity, 2017.R. Lombardo, C. Priami. Graphical modeling meets systems pharmacology. Gene regulation and systems biology 11, 2017

M. Scott Boyer, S. Lacroix, M. Scotti, M. Morine, J. Kaput, C. Priami. A network analysis of cofactor-protein interactions for analyzing associations between human disease and nutrition, Nat. Sci. Rep., 6:19633, 2016.

T. Nyima, M. Müller, G. Hooiveld, M. Morine, M. Scotti. Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice, BMC Genomics, 17:106, 2016.

A. Matone, C. O’Grada, E.T. Dillon, C. Morris, M.F. Ryan, M. Walsh, E.R. Gibney, L. Brennan, M.J. Gibney, M.J. Morine, H.M. Roche. Body mass index mediates inflammatory response to acute dietary challenges. Mol Nutr Food Res, 2015.

C. O'Grada, M. Morine, C. Morris, M.F. Ryan, E.T. Dillon, M. Walsh, E. Gibney, L. Brennan, M. Gibney, H. Roche. PBMCs reflect the immune component of the WAT transcriptome - Implications as biomarkers of metabolic health in the postprandial state, Mol Nutr Food Res, 2013.