Selected publications
Computational Biology
Willis, J.R. et al (2024). Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans, to appear in Science.Hahn, W.O. et al (2024). HIV BG505 SOSIP.664 trimer with 3M-052-AF/alum induces human autologous tier-2 neutralizing antibodies. medRxiv 2024.05.08.24306957
Van Nostrand, E.L., et al (2020) A Large-Scale Binding and Functional Map of Human RNA Binding Proteins, Nature 583, pp. 711–719, July 29.
Garren, S., Kondaveeti, Y., Duff, M.O., & Carmichael, G. (2015) Global analysis of mouse polyomavirus infection reveals dynamic regulation of viral and host gene expression and promiscuous viral RNA editing. PLOS Pathogens, 11(9), September 25.
Duff, M.O., Olson, S, Wei, X., Osman, A., Plocik, A., Bolisetty, M. Celniker, S. & Graveley, B.R. (2015) Genome-wide Identification of Zero Nucleotide Recursive Splicing in Drosophila. Nature 521, May 21, 376-9.
Yang L., Duff M.O., Graveley B.R., Carmichael G.G. and Chen L-L. (2011) Genomewide characterization of long nonpolyadenylated RNAs. Genome Biology, Feb 16.
Graveley,B.R, Brooks,A.N., Carlson,J.W., Duff,M.O., Landolin,J.M., Yang,L., et al (2010). The developmental transcriptome of Drosophila melanogaster. Nature, Dec 22.
Reinforcement Learning Theory
Duff, M.O. (2003) Design for an optimal probe. Proceedings of the 20th International Conference on Machine Learning 131-138.
Duff, M.O. (2001) Monte-Carlo Algorithms for the Improvement of Finite-State Stochastic Controllers. Eighth International Workshop on Artificial Intelligence and Statistics, Key West FL.
Duff, M.O. (1995) Q-learning for bandit problems. Proceedings of the 12th International Conference on Machine Learning, 209-217.
Duff, M.O. (1994) Solving Bellman's equation by the method of continuation. Proceedings of the American Control Conference, 2671-2682.