moduff.github.io/selected_publications.html at master · moduff/moduff.github.io · GitHub

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<title>Michael O. Duff</title>

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<h4>Selected publications</h4>

<h5>Computational Biology</h5>


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Willis, J.R. et al (2025). <a href = "https://www.science.org/doi/10.1126/science.adr8382">Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans</a>, Science 0,eadr8382DOI:10.1126/science.adr8382

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Tom G. Caniels et al (2025). <a href = "https://www.science.org/doi/10.1126/science.adv5572">Precise targeting of HIV broadly neutralizing antibody precursors in humans</a>.Science 0,eadv5572DOI:10.1126/science.adv5572
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Hahn, W.O. et al (2024). <a href = "https://doi.org/10.1101/2024.05.08.24306957">HIV BG505 SOSIP.664 trimer with 3M-052-AF/alum induces human autologous tier-2 neutralizing antibodies</a>. medRxiv 2024.05.08.24306957

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Van Nostrand, E.L., et al (2020) <a href="https://www.nature.com/articles/s41586-020-2077-3">A Large-Scale Binding and Functional Map of Human RNA
	Binding Proteins</a>, Nature 583, pp. 711–719, July 29.

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Garren, S., Kondaveeti, Y., Duff, M.O., & Carmichael, G. (2015) <a
href="http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005166">Global
analysis of mouse polyomavirus infection reveals dynamic regulation of
viral and host gene expression and promiscuous viral RNA
editing</a>. PLOS Pathogens, 11(9), September 25.

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Duff, M.O., Olson, S, Wei, X., Osman, A., Plocik, A., Bolisetty, M. Celniker, S. & Graveley, B.R. (2015) <a href="https://www.nature.com/articles/nature14475">Genome-wide Identification of Zero Nucleotide Recursive Splicing in Drosophila</a>. Nature 521, May 21, 376-9.


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Yang L., Duff M.O., Graveley B.R., Carmichael G.G. and Chen L-L. (2011) <a
href="http://genomebiology.com/2011/12/2/R16">Genomewide
characterization of long nonpolyadenylated RNAs</a>. Genome Biology,
  Feb 16.


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Graveley,B.R, Brooks,A.N., Carlson,J.W., Duff,M.O., Landolin,J.M., Yang,L., et al (2010). <a href="https://www.nature.com/articles/nature09715">The developmental transcriptome of Drosophila melanogaster</a>. Nature, Dec 22.


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<h5>Reinforcement Learning Theory</h5>

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Duff, M.O. (2003) <a
href="http://www.aaai.org/Papers/ICML/2003/ICML03-020.pdf">Design for
an optimal probe<a/>. Proceedings of the 20th International Conference
on Machine Learning 131-138.

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Duff, M.O. (2001)<a href="duff_ai_stat_2001.pdf">
Monte-Carlo Algorithms for the Improvement of Finite-State Stochastic Controllers</a>.
Eighth International Workshop on Artificial Intelligence and
Statistics, Key West FL.

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Duff, M.O. (1995)<a
href="Duff_1995_q_learning_bandits.pdf">
Q-learning for bandit problems</a>. Proceedings of the 12th International Conference on Machine Learning, 209-217.

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Duff, M.O. (1994) <a href="solving-bellmans-equation-by-solving-method-of-continuity.pdf">Solving Bellman's equation by the method of continuation</a>. Proceedings of the American Control Conference, 2671-2682.<br><p>


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