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Prediction of Escherichia coli phenotypes through biological networks and machine learning

Grant number: 12/00741-8
Support type:Scholarships in Brazil - Doctorate
Effective date (Start): April 01, 2012
Effective date (End): January 31, 2015
Field of knowledge:Biological Sciences - Biophysics
Principal Investigator:Ney Lemke
Grantee:Esther Camilo dos Reis
Home Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
Associated scholarship(s):12/22395-4 - Visualization of forests of trees, BE.EP.DR


Cell differentiation, carcinogenesis, and gene essentiality are some examples of biological processes that can not be fully explained through the study of individual genes. There is now a concern of researchers in understanding how the various entities of a system interact and produce certain phenotypes using the techniques of systems biology. However, few of these approaches are genome scaled and consider the effects of environment on these networks. In this context, this project aims to predict the phenotypes of the bacterium Escherichia coli, that is, the evaluation of its growth profile in different conditions by metabolic flux balance analysis (FBA) and machine learning. The representation of the system is done by using graph where the interacting elements are represented by nodes and interactions by edges that connect pairs of nodes. From the network it will be extracted centralities data which together with the results of the FBA calculations will be used as attributes of training for the learning algorithm.

Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
ACENCIO, MARCIO LUIS; BOVOLENTA, LUIZ AUGUSTO; CAMILO, ESTHER; LEMKE, NEY. Prediction of Oncogenic Interactions and Cancer-Related Signaling Networks Based on Network Topology. PLoS One, v. 8, n. 10 OCT 25 2013. Web of Science Citations: 5.
CAMILO, ESTHER; BOVOLENTA, LUIZ A.; ACENCIO, MARCIO L.; RYBARCZYK-FILHO, JOSE L.; CASTRO, MAURO A. A.; MOREIRA, JOSE C. F.; LEMKE, NEY. GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks. Bioinformatics, v. 29, n. 19, p. 2505-2506, OCT 1 2013. Web of Science Citations: 3.

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