Introductory Programming

About

I received a PhD degree in Computer Science with emphasis in Bioinformatics in 2017 from McGill University. During my doctoral studies, I worked under the supervision of Professor Jérôme Waldispühl. From 2018 to 2020, I was a post-doctoral fellow under the supervision of Professor Philip Kim in the Terrence Donnelly Centre for Cellular & Biomolecular Research. I recieved my undergrad and master degrees from the Universidad Nacional de Colombia, where I developed my master thesis and undergrad capstone project under the supervision of Professor Luis Niño I joined the School of CS at McGill in 2020 as a Faculty Lecturer. I really enjoy researching and teaching courses in bioinformatics and algorithms. I am also highly interested in programming competitions.

Selected publications

• JG Carvajal-Patiño*, V Mallet*, David Becerra, LF Niño Vasquez, Carlos Oliver and J. Waldispühl. RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning. Nature Communications 16 (1), March 2025.
• Alexey Strokach*, David Becerra, Carles Corbi, Albert Perez-Riba and Philip M. Kim. Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver. Star protocols 12 (2), June 2021.
• Alexey Strokach*, David Becerra, Carles Corbi, Albert Perez-Riba and Philip M. Kim. Fast and flexible design of novel proteins using graph neural networks. Cell Systems 11 (4), 402-411, August 2020.
• Pedro Alberto Valiente*, David Becerra, Philip M. Kim. A method to calculate the relative binding free energy differences of α-helical stapled peptides. J Org Chem, 2020.
• David Becerra*, A. Butyaev, J. Waldispühl. Predicting Protein Folding Pathways using Ensemble Modelling and Evolutionary Sequence Variation. Oxford Bioinformatics, 2019, btz743.
• Zheng Dai*, David Becerra, J. Waldispühl. On Stable States in a Topologically Driven Protein Folding Model. Journal of Computational Biology, 2017, 24,9.
• David Becerra*, Juan Mendivelso, Yoan Pinzon. A Multiobjective Optimization Algorithm for the Weighted LCS, Journal of Discrete Applied Mathematics, 2015,11,005.
• Wilson Soto*, David Becerra*. A Multi-Objective Evolutionary Algorithm for Improving Multiple Sequence Alignments. Advances in Bioinformatics and Computational Biology, 73-82 (Brasil, 2015).
• D. Kwak*, A. Kam*, David Becerra*, Q. Zhou, A. Hops, E. Zarour, A. Kam, L. Sarmenta, J. Waldispühl. Open-Phylo: A customizable crowd-computing platform for multi sequence alignment. Genome Biology, 2013, 14:R116.
• Angelica Sandoval*, David Becerra*, Daniel Restrepo-Montoya, Diana Vanegas, Luis F. Nino. A Multi-objective Optimization Energy Approach to Predict the Ligand Conformation and Configuration in a Docking Process. European Conference on Evolutionary Computation, Machine Learning and Data Mining in Computational Biology, EvoStar 2013, (Vienna, Austria. 2013).