Study of gene regulatory network by stochastic methods and statistical mechanics

• Grant number: 13/14438-8
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: November 01, 2013
• End date: October 31, 2014
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Nestor Felipe Caticha Alfonso
• Grantee: Marcelo Boareto Do Amaral
• Supervisor: José Nelson Onuchic
• Host Institution: Instituto de Física (IF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Rice University, United States
• Associated to the scholarship: 08/10831-9 - Topics in cell signaling and bioinformatics: operating principles of Notch signaling pathway and supervised variational relevance learning, BP.DD

Abstract

After the development of modern molecular biology techniques, more specifically the high-throughput technologies (RNA-seq and microarrays), has been generated a large amount of information on complex biological systems. One of the major challenges of current biology is to use this amount of information to explain and predict behavior in cellular/molecular level. Mathematical modeling of these systems provides an objective approach to test hypotheses about system behavior. More specifically, methods inspired by statistical mechanics ideas appear as an appropriate tool to study these systems since it allows to relate the macroscopic and microscopic interactions effects. The objective of this project is to apply mathematical modeling techniques, especially methods based on statistical physics concepts to biological systems of interest. (AU)

Scientific publications

(9)

(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)

JOLLY, MOHIT KUMAR; BOARETO, MARCELO; LU, MINGYANG; ONUCHIC, JOSE'N; CLEMENTI, CECILIA; BEN-JACOB, ESHEL. Operating principles of Notch-Delta-Jagged module of cell-cell communication. NEW JOURNAL OF PHYSICS, v. 17, MAY 20 2015. (13/14438-8)

BOCCI, FEDERICO; GEARHART-SERNA, LARISA; BOARETO, MARCELO; RIBEIRO, MARIANA; BEN-JACOB, ESHEL; DEVI, GAYATHRI R.; LEVINE, HERBERT; ONUCHIC, JOSE NELSON; JOLLY, MOHIT KUMAR. Toward understanding cancer stem cell heterogeneity in the tumor microenvironment. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 116, n. 1, p. 148-157, JAN 2 2019. (13/14438-8)

JIA, DONGYA; JOLLY, MOHIT KUMAR; BOARETO, MARCELO; PARSANA, PRINCY; MOONEY, STEVEN M.; PIENTA, KENNETH J.; LEVINE, HERBERT; BEN-JACOB, ESHEL. OVOL guides the epithelial-hybrid-mesenchymal transition. ONCOTARGET, v. 6, n. 17, p. 15436-15448, JUN 20 2015. (13/14438-8)

JOLLY, MOHIT KUMAR; BOARETO, MARCELO; HUANG, BIN; JIA, DONGYA; LU, MINGYANG; BEN-JACOB, ESHEL; ONUCHIC, JOSE N.; LEVINE, HERBERT. Implications of the hybrid epithelial/mesenchymal phenotype in metastasis. FRONTIERS IN ONCOLOGY, v. 5, JUL 20 2015. (13/14438-8)

BOARETO, MARCELO; JOLLY, MOHIT KUMAR; BEN-JACOB, ESHEL; ONUCHIC, JOSE N.. Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision. Proceedings of the National Academy of Sciences of the United States of America, v. 112, n. 29, p. E3836-E3844, JUL 21 2015. (13/14438-8)

BOARETO, MARCELO; JOLLY, MOHIT KUMAR; LU, MINGYANG; ONUCHIC, JOSE N.; CLEMENTI, CECILIA; BEN-JACOB, ESHEL. Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype. Proceedings of the National Academy of Sciences of the United States of America, v. 112, n. 5, p. E402-E409, FEB 3 2015. (13/14438-8)

BOARETO, MARCELO; JOLLY, MOHIT KUMAR; GOLDMAN, AARON; PIETILA, MIKA; MANI, SENDURAI A.; SENGUPTA, SHILADITYA; BEN-JACOB, ESHEL; LEVINE, HERBERT; ONUCHIC, JOSE N.. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. Journal of the Royal Society Interface, v. 13, n. 118, MAY 1 2016. (13/14438-8, 08/10831-9)

BOARETO, MARCELO; JOLLY, MOHIT KUMAR; LU, MINGYANG; ONUCHIC, JOSE N.; CLEMENTI, CECILIA; BEN-JACOB, ESHEL. Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 112, n. 5, p. 8-pg., 2015-02-03. (13/14438-8)

BOARETO, MARCELO; JOLLY, MOHIT KUMAR; BEN-JACOB, ESHEL; ONUCHIC, JOSE N.. Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 112, n. 29, p. 9-pg., 2015-07-21. (13/14438-8)