Diogo Borges Lima


I have a bachelor's degree in Computer Science from the Federal University of Rio de Janeiro (UFRJ) and a M.Sc. in Computer Science in Artificial Intelligence from the Systems Engineering and Computer Science Program also from UFRJ. I hold a PhD in Biosciences and Biotechnology from Carlos Chagas Institute / Fiocruz supervised by Dr. Paulo Costa Carvalho and Dr. Fabio Cesar Gozzo. We have developed a search tool, called SIM-XL, to work with complex scenarios of cross-linked peptides for aiding in structural proteomics or protein-protein interactions studies. I had a Post-doc in computational proteomics at Institut Pasteur - Paris, in the Mass Spectrometry for Biology Unit, supervised by Dr. Julia Chamot-Rooke, where I have worked on the developments of new bioinformatics solutions for the analyses of top-down proteomics data. Currently, I'm post-doc also in computational proteomics, but now tailored toward cross-linking mass spectrometry, at Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), in the Liu Lab, supervised by Dr. Fan Liu, where I have been working on the development of algorithms for identifying and quantifying cross-linked peptides.

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++.