Carlos Oliver Homepage

Starting January 2025, I will be joining Vanderbilt University as Assistant Professor in the Department of Molecular Physiology and Biophysics and core member of the Center for Applied AI in Protein Dynamics in Nashville, Tennessee. Previously, I led the Molecular Pattern Mining Project Group at the Department of Machine Learning and Systems Biology at the Max Planck Institute of Biochemistry, postdoc at ETH Zurich and a member of the labs of Jérôme Waldispühl and William L. Hamilton during my PhD studies in Computer Science.

I build algorithms that extract knowledge from complex biological systems. More on my research here.

Contact

• Academic: carlos.oliver@vanderbilt.edu
• Business & Personal: cgoliver@protonmail.com
• GitHub: @cgoliver

Updates

• 30.06.24 - GMSM accepted at ICML 2024 Workshop on Differentiable Almost Everything
• 27.06.24 - Tim Kucera wins Max Planck Junior Scientist Award for his work on ProteinShake!
• 27.06.24 - Major update to RNAmigos2 preprint.
• 19.05.24 - Structure and function aware substitution matrices paper appears in RECOMB 2024 proceeding.
• 04.05.24 - A letter in support of Prof. Provost and of academic freedom.
• 14.03.24 - Book chapter on using rnaglib for RNA function prediction on ArXiV [ArXiV].
• 20.01.24 - Preprint on injecting structural language to large protein language models posted [ArXiV].
• 15.01.24 - PhD student, Luis Wyss joins Molecular Pattern Mining Group. Welcome Luis.
• 20.12.23 - Paper on conditional structure-aware substitution matrices accepted at RECOMB 2024! Preprint coming soon..
• Updates archive

Fields of study

• RNA and protein computational structural biology
• Structural bioinformatics
• Network motif mining
• Graph representation learning
• Drug discovery

Activities

• Google Scholar
• Consulting at Ozeki Inc.
• Pear Review
• Former Lead Scientist in Residence at Next AI
• Member of The Heterodox Academy

Reviewing (by topic)

• Bio(informatics): OUP Bioinformatics, ISMB, RECOMB, Nucleic Acids Research, eLife, Cell
• Machine Learning: Journal of Machine Learning Research, AAAI, NeurIPS
• Data Mining: KDD, IEEE Transactions on Emerging Topics in Computing, SIAM International Conference on Data Mining
• Cheminformatics: Nature Communications Chemistry, Journal of Cheminformatics

Software

• rnaglib: analysis and deep learning on RNA 2.5D and 3D models (Homepage, Source Code)
• proteinshake: deep learning on protein 3D structures (Homepage, Source Code)

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