Diogo Borges Lima


I hold a Bachelor's degree in Computer Science from the Federal University of Rio de Janeiro (UFRJ) and an M.Sc. in Computer Science with a focus on Artificial Intelligence from UFRJ's Systems Engineering and Computer Science Program. I also have a Ph.D. in Biosciences and Biotechnology from the Carlos Chagas Institute / Fiocruz, where I developed a search tool called SIM-XL for complex scenarios involving cross-linked peptides, aiding structural proteomics and protein-protein interaction studies. During my first post-doc in computational proteomics at Institut Pasteur in Paris, in the Mass Spectrometry for Biology Unit, I have developed new bioinformatics solutions for analyzing top-down proteomics data. In my second post-doc at the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), in the Liu Lab, I focused on cross-linking mass spectrometry using cleavable reagents. There, we have developed an innovative software called Scout, designed to identify cross-linked peptides on a large scale, employing efficient machine learning methods and robust algorithm design patterns to achieve reliable identifications in a shorter processing time.

I have experience in Proteomics Data Analysis (Bottom-up & Top-down) and Quantitative Mass Spectrometry, Structural Mass Spectrometry, Natural Optimization (e.g., Genetic Algorithms, Particle Swarm Optimization, Ant Colony Optimization, Simulated Annealing), Statistical Classifiers (e.g., Support Vector Machines, Bayesian Classifiers etc.), Artificial Neural Networks (e.g., Feed Forward with back propagation), Statistical Inference and advanced experience in Python, Java, C# and C++.