Modeling, analysis, and inference of biological networks

• Grant number: 21/09070-8
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: September 01, 2021
• End date: October 31, 2023
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
• Principal Investigator: Ronaldo Fumio Hashimoto
• Grantee: Shantanu Gupta
• Host Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 15/22308-2 - Intermediate representations in Computational Science for knowledge discovery, AP.TEM

Abstract

The Institute of Mathematics and Statistics of Universidade de São Paulo (IME-USP), offers a postdoctoral position for scientists interested in working with Systems Biology approach to model and analyze biological phenomena. The project focuses on modeling, analysis, and inference of biological networks to better understand how the interactions of their components (network topology or architecture structure) give rise to the function or behavior of those systems (network dynamics or phenotypes). The postdoctoral fellow will specifically work in modeling biological networks as dynamical systems: topology, stability, robustness, inference, and simulation. Candidates with knowledge in complex networks, boolean networks and Markov Chain are desirable. The PD researcher will be responsible to propose and implement models for intermediate network representations and analyze them for knowledge discovery. The research will take into account various data sources, such as genomics, transcriptomics, proteomics, metabolomics, and also knowledge found in the literature (e.g., gene interactions in published papers) or in online databases (e.g., KEGG, GO, STRING). Of particular interest is to incorporate machine learning methods to this approach. The candidate is expected to have programming knowledge. (AU)

Scientific publications

(5)

(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)

GUPTA, SHANTANU; HASHIMOTO, RONALDO F.. Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer. BIOMOLECULES, v. 12, n. 3, p. 19-pg., 2022-03-01. (15/22308-2, 21/09070-8)

GUPTA, SHANTANU; SILVEIRA, DANER A.; HASHIMOTO, RONALDO E.; MOMBACH, JOSE CARLOS M.. A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells. BIOLOGY-BASEL, v. 11, n. 4, p. 14-pg., 2022-04-01. (15/22308-2, 21/09070-8)

GUPTA, SHANTANU; PANDA, PRITAM KUMAR; HASHIMOTO, RONALDO F.; SAMAL, SHAILESH KUMAR; MISHRA, SUMAN; VERMA, SURESH KR; MISHRA, YOGENDRA KUMAR; AHUJA, RAJEEV. Dynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells. SCIENTIFIC REPORTS, v. 12, n. 1, p. 13-pg., 2022-03-22. (21/09070-8, 15/22308-2)

GUPTA, SHANTANU; PANDA, PRITAM KUMAR; SILVEIRA, DANER A.; AHUJA, RAJEEV; HASHIMOTO, RONALDO F.. Quadra-Stable Dynamics of p53 and PTEN in the DNA Damage Response. CELLS, v. 12, n. 7, p. 17-pg., 2023-04-01. (21/09070-8, 15/22308-2)

GUPTA, SHANTANU; SILVEIRA, DANER A.; HASHIMOTO, RONALDO F.. A Boolean model of the oncogene role of FAM111B in lung adenocarcinoma. COMPUTATIONAL BIOLOGY AND CHEMISTRY, v. 106, p. 6-pg., 2023-10-01. (21/09070-8, 15/22308-2)