Machine learning for molecular systems biology

• Grant number: 09/10382-2
• Support Opportunities: Regular Research Grants
• Start date: August 01, 2010
• End date: July 31, 2012
• Field of knowledge: Physical Sciences and Mathematics - Physics - Condensed Matter Physics
• Principal Investigator: Ney Lemke
• Grantee: Ney Lemke
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

The development of high-throughput techniques in biology is transforming biology in a data-rich discipline. We will consider in this project integrated biological networks: these networks deal with all the gene interactions mediated by metabolism, regulation and protein-protein interactions. We will deploy machine learning tools that will use topological data from these graphs, expression data, genomic organization and cellular localization to extract relevant biological information such as detection of drug target genes, morbid genes for humans or essential genes for bacteria. We will also investigate the community structure of these networks and we will detect topological motifs aiming the characterization of the large scale topological organization of gene interactions on biological cells. (AU)

Scientific publications

(7)

(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)

COSTA, PEDRO RAFAEL; ACENCIO, MARCIO LUIS; LEMKE, NEY. Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation. PLoS One, v. 8, n. 2, FEB 21 2013. (09/10382-2, 10/20684-3, 10/03338-4)

BOVOLENTA‚ L.; ACENCIO‚ M.; LEMKE‚ N.. The development of an open-access database for human transcriptional regulation interactions. BMC Bioinformatics, v. 12, n. Suppl 11, p. A10, 2011. (09/10382-2, 10/20684-3)

LEMKE, N.; CAMPBELL, IAN A.. Stretched-exponential behavior and random walks on diluted hypercubic lattices. Physical Review E, v. 84, n. 4, p. 6-pg., 2011-10-18. (09/10382-2)

LEMKE, N.; CAMPBELL, IAN A.. Stretched-exponential behavior and random walks on diluted hypercubic lattices. Physical Review E, v. 84, n. 4, 1, OCT 18 2011. (09/10382-2)

CARVALHO, DIEGO Z.; GERHARDT, GUENTHER J. L.; DELLAGUSTIN, GUILHERME; DE SANTA-HELENA, EMERSON L.; LEMKE, NEY; SEGAL, ALAN Z.; SCHOENWALD, SUZANA V.. Loss of sleep spindle frequency deceleration in Obstructive Sleep Apnea. CLINICAL NEUROPHYSIOLOGY, v. 125, n. 2, p. 306-312, FEB 2014. (09/10382-2)

BOVOLENTA, LUIZ A.; ACENCIO, MARCIO L.; LEMKE, NEY. HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. BMC Genomics, v. 13, AUG 17 2012. (09/10382-2, 10/20684-3)

SCHOENWALD, SUZANA V.; CARVALHO, DIEGO Z.; DE SANTA-HELENA, EMERSON L.; LEMKE, NEY; GERHARDT, GUENTHER J. L.. Topography-specific spindle frequency changes in Obstructive Sleep Apnea. BMC NEUROSCIENCE, v. 13, JUL 31 2012. (09/10382-2)