IME-USP

Research Areas – Graduate Program in Bioinformatics

Faculty/AdviserResearch Themes
Alan Mitchell DurhamCompiler Development, Bioinformatics, Programming Language Implementation,
Software Engineering, Mobile Computing
Alessandra Alaniz MacedoInformation Extraction, Biomedical Informatics, Ubiquitous Computing
Aline Maria da SilvaRegulation and Function of serine/threonine proteins, phosphatases in microorganisms,
Mechanisms of pathogenicity of Xylella fastidiosa.
Anatoly YambartsevNetwork Modeling in Systems Biology
André FujitaBioinformatics, Microarrays, Regulatory Networks
Angela Kaysel CruzLeishmania genome project; structural aspects of genome organization;
construction of physical maps, analysis of cDNA libraries.
Ariane Machado LimaBioinformatics; Computational identification of non-coding RNAs;
Formal languages
Arthur GruberBiologia Molecular de Microorganismos, Biologia molecular de coccídias,
Desenvolvimento de aplicativos de Bioinformática.
Carlos Alberto de Braganca PereiraBayesian Inference in Engineering, Bayesian Inference
Carlos Alberto LabateGenetic transformation of Eucalyptus, Bioinformatics applied to genomics and proteomics,
Functional Genomics and Proteomics with emphasis on gene expression regulation,
wood formation, rust resistance and water stress resistance
in Eucalyptus plants.
Carlos Frederico Martins MenckDNA Repair Studies and their Biological Consequences
Clever Ricardo Guareis de FariasComponent-based software analysis and design methods, Component-based groupware
systems development, Distributed systems design and development, Conceptual modeling,
Context-aware systems model-based development.
Eduardo Moraes Rego ReisIntegrated analysis of human tumor genomic data.
Fabricio Martins LopesBioinformatics, Pattern Recognition, Computer Vision.
Fernando Luis Barroso da SilvaMolecular Modeling, Structural Bioinformatics, Fundamental Interactions in Molecular Biophysics.
Glaucia Mendes SouzaTransition signal transduction, Growth/development, Sugarcane Signal Transduction (SUCAST), Sugarcane Transcriptome.
Helaine CarrerBiotechnology and Molecular Biology of Organelles, Molecular Biology of Plant-Microorganism Interaction, Genomics and Bioinformatics.
Helder Takashi Imoto NakayaSystems Biology of Long Noncoding RNAs, Systems Immunology
Helena Paula BrentaniGene expression, genomics, Microarray, Bioinformatics, Cancer, Psychiatry, early diagnosis of neurodevelopmental disorders
João Carlos SetubalDevelopment of new bioinformatics tools (suitable for students with a computer science background or good programming experience), and computational analysis of biological data, usually genomics or transcriptomics (suitable for students with a bioscience background)
João Eduardo FerreiraDatabase, Database for knowledge extraction, Information Systems Integration, Database modeling.
João Marcelo Pereira AlvesPhylogeny (traditional and phylogenomics), Genome evolution, Bioinformatics, Human Metagenomics, Transcriptomics of unicellular eukaryotes and bacteria by second generation sequencing, Genomics of unicellular eukaryotes and bacteria.
Julia Maria Pavan SolerGenetic Mapping of Complex Diseases, Genetic mapping of cardiovascular risk factors, Application and development of Statistical Methods in the Analysis of Genetic and Genomic Data
Junior BarreraApplications of Mathematical Morphology in Image Analysis, Development of computational systems for image analysis, Theoretical research on Mathematical Morphology, Identification of gene regulatory networks, Application of morphological operator design to real image analysis problems, Modeling of multi-agent systems, Theoretical research on morphological operator design by computational learning.
Kelly Rosa BraghettoDatabase, Distributed Systems, Bioinformatics
Koichi SameshimaStudy of the mechanisms of temporal information processing in sensory systems: electrophysiological, psychophysical and computational approaches; Psychophysical and neuropsychological approaches applied to the study of sensory systems and cognitive assessment in humans, Functional neuroimaging.
Luciano Antonio DigiampietriWeb 2.0 and Semantic Web, Games in Education, Business Process Management/Scientific Workflows, Database Optimization, Genome Assembly and Annotation, Social Network Analysis and Scientometrics.
Luciano da Fontoura CostaImage Processing and Analysis, Modeling and Simulation of Neural Systems, Bioinformatics, Computational Biology.
Luiz Antonio BaccalaBlind Channel Equalization, Causality among Muiltivariate Time Series, Neural Connectivity.
Marcos Silveira BuckeridgePlant Cell Wall Structure and Metabolism, Plant Responses to Global Climate Change, Ecophysiology of Native Plants, Plant Carbohydrate Biochemistry and Biotechnology.
Odemir Martinez BrunoComputer Vision, Parallel Computing, Image Analysis and Processing, Artificial Vision, Pattern Recognition.
Paolo Marinho de Andrade ZanottoMolecular Biology of Baculoviruses, Insect Tissue Culture, Large-scale viral DNA sequencing, Molecular Virology, Viral gene expression studies by realtime PCR and RLM-RACE, DNA cloning, Cell culture for viral replication, Viral detection by PCR.
Paulo Inácio de Knegt López de PradoInsect-plant interaction ecology, Community ecology, Biodiversity diagnosis, Interdisciplinary environmental research, Multivariate analysis of environmental data, Biodiversity and conservation, Community ecology, Theory and quantification of biological diversity, Insect-plant interactions, Ecology and human societies, Theoretical ecology.
Paulo Sérgio Lopes de OliveiraDevelopment of computational tools for genome analysis, Modeling of transcriptome databases, Computational approach to genetic problems associated with the cardiovascular system, Gene expression analysis, Gene regulation analysis using homology molecular modeling and molecular dynamics, Alternative splicing and protein function: An approach through protein structures, Functional analysis of mutations through computational approach to protein structures, Selection of genetic markers of commercial interest in cattle.
Pedro Alexandre Favoretto GalanteBioinformatics, Molecular Biology, Human and Medical Genetics, Molecular and Microorganism Genetics.
Ricardo Zorzetto Nicoliello VencioApplied Probability and Statistics, Computational Biology, Bioinformatics, Data Analysis.
Roberto Marcondes Cesar JuniorPattern Recognition, Network Modeling, Computer Vision, Image Analysis, Bioinformatics
Ronaldo Fumio HashimotoImage Processing, Pattern Recognition, Mathematical Morphology, Bioinformatics, Probabilistic Boolean Networks, Boolean Networks.
Sergio Russo MatioliEvolutionary Genetics, Quantitative Genetics
Sergio Verjovski-AlmeidaDifferential gene expression in cancer, Large scale gene expression in Schistosoma mansoni – effect of hormones.
Taran GrantAmphibian Systematics, Phylogenetic Inference, Neotropical Herpetology.
Tie KoideSystemic Biology of microorganisms. The Laboratory of Systemic Biology of Microorganisms (LaBiSisMi) has the mission to contribute to the understanding of microorganisms, understood as an integrated dynamical system, searching for quantitative multi-scale models to understand their behavior, guided by Experimental Molecular Biology in synergy with Mathematics/Computing. Currently, we are working with the study of an extremophilic archaea and the influence of non-coding RNAs on global gene regulation.