New International Collaboration to Study Viral Recombination Flaviviruses and Coronaviruses
Artificial Intelligence for Recombination Identification and Surveillance in Epidemiology in HPC Environment
The Phyloinformatics lab is happy to announce that we have finalized the submission of a new proposal to Brazil’s National Council for Scientific and Technological Development (CNPq), CNPq/MCTI/FNDCT No. 22/2024 (“Programa Conhecimento Brasil – Apoio a Projetos em Rede com Pesquisadores Brasileiros no Exterior”). Our proposal is entitled “ARISE in HPC: Artificial Intelligence for Recombination Identification and Surveillance in Epidemiology in HPC Environment.”
Our Proposal
The rapid evolution of viral infectious diseases like Zika, Dengue, and Yellow Fever poses significant public health challenges worldwide. These viruses undergo frequent recombination, a process where they exchange genetic material, potentially creating new strains that can evade existing diagnostics, vaccines, and treatments. Detecting viral recombination is critical to understanding the emergence of new variants and responding swiftly to epidemiological threats. However, current recombination detection tools are limited by the volume of data they can process, especially in next-generation sequencing analyses.
Our project, ARISE in HPC, integrates high-performance computing (HPC), artificial intelligence (AI), and phylogenomics to develop advanced solutions for detecting viral recombination. Leveraging AI models such as neural networks, deep learning, decision trees, and ensemble learning, the project aims to optimize computational resource allocation and improve the analysis of large viral databases using the Santos Dumont (SDumont) supercomputer. This approach will enhance bioinformatics workflows, bolster disease detection and control strategies, and support the development of new diagnostics, vaccines, and therapeutics in Brazil.
Our Collaborators
Our core team is composed of 9 researchers from 7 institutions in five countries. Here is the core team, organized alphabetically by their first names:
- Carla Osthoff Ferreira de Barros (Researcher, LNCC, Brazil)
- Denis Jacob Machado (Assistant Professor, UNC Charlotte, U.S.A.)
- Diego Moreira de Araújo Carvalho (Associate Professor, Cefet/RJ, Brazil)
- Douglas de Oliveira Cardoso (Assistant Professor, UC, Portugal)
- Francieli Zanon Boito (Associate Professor, University of Bordeaux, France)
- Kary Ann del Carmen Ocaña Gautherot (Researcher, LNCC, Brazil)
- Luan Teylo (Researcher, Inria, France)
- Luiz Manoel Rocha Gadelha Júnior (Researcher, DKFZ, Germany)
- Marcelo Trindade dos Santos (Researcher, LNCC, Brazil)
Participating Institutions
This is the list of participating institutions in alphabetical order:
- Computational Intelligence for Predicting Health and Environmental Risks (CIPHER), UNC Charlotte, USA
- Department of Bioinformatics and Genomics (BiG), College of Computing and Informatics (CCI), University of North Carolina at Charlotte (UNC Charlotte), USA
- Federal Center for Technological Education Celso Suckow da Fonseca (Cefet/RJ), Brazil
- German Cancer Research Center (DKFZ) and German Human Genome and Phenome Archive (GHGA), Germany
- Inria Center, University of Bordeaux, France
- National Laboratory for Scientific Computing (LNCC), Brazil
- University of Coimbra, Portugal
Previous post
The Phyloinformatics Lab is a Safety Champion