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Machine learning for molecular systems biology

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


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 (6)
(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)
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. Web of Science Citations: 15.
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. Web of Science Citations: 5.
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. Web of Science Citations: 116.
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. Web of Science Citations: 22.
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. Web of Science Citations: 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.

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