Andrew M. Watkins

Publication Activity (10 Years)

Years Active: 2013-2024
Publications (10 Years): 12

Top Topics

Top Venues

Nat. Mac. Intell.

Publications

Samuel Stanton, Robert Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms. CoRR (2024)
Pedro O. Pinheiro, Joshua Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew M. Watkins, Stephen Ra, Vishnu Sresht, Saeed Saremi
3D molecule generation by denoising voxel grids. NeurIPS (2023)
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
OpenProteinSet: Training data for structural biology at scale. CoRR (2023)
Michael Maser, Natasa Tagasovska, Jae Hyeon Lee, Andrew M. Watkins
MoleCLUEs: Optimizing Molecular Conformers by Minimization of Differentiable Uncertainty. CoRR (2023)
Michael Maser, Ji Won Park, Joshua Yao-Yu Lin, Jae Hyeon Lee, Nathan C. Frey, Andrew M. Watkins
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers. CoRR (2023)
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
OpenProteinSet: Training data for structural biology at scale. NeurIPS (2023)
Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew M. Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design. CoRR (2022)
Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, King Yuen Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Rhiju Das
Deep learning models for predicting RNA degradation via dual crowdsourcing. Nat. Mac. Intell. 4 (12) (2022)
Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho
Multi-segment preserving sampling for deep manifold sampler. CoRR (2022)
Hannah K. Wayment-Steele, Wipapat Kladwang, Andrew M. Watkins, Do Soon Kim, Bojan Tunguz, Walter Reade, Maggie Demkin, Jonathan Romano, Roger Wellington-Oguri, John J. Nicol, Jiayang Gao, Kazuki Onodera, Kazuki Fujikawa, Hanfei Mao, Gilles Vandewiele, Michele Tinti, Bram Steenwinckel, Takuya Ito, Taiga Noumi, Shujun He, Keiichiro Ishi, Youhan Lee, Fatih Öztürk, Anthony Chiu, Emin Öztürk, Karim Amer, Mohamed Fares, Eterna Participants, Rhiju Das
Predictive models of RNA degradation through dual crowdsourcing. CoRR (2021)
Julia Koehler Leman, Brian D. Weitzner, P. Douglas Renfrew, Steven M. Lewis, Rocco Moretti, Andrew M. Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W. Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William R. Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland L. Dunbrack Jr., Tanja Kortemme, Andrew Leaver-Fay, Charlie E. M. Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J. Gray, Richard Bonneau
Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS Comput. Biol. 16 (5) (2020)
Gaurav Bhardwaj, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, Surya V. S. R. K. Pulavarti, Quentin Kaas, Alexander Eletsky, Po-Ssu Huang, William A. Johnsen, Per Greisen, Gabriel J. Rocklin, Yifan Song, Thomas W. Linsky, Andrew M. Watkins, Stephen A. Rettie, Xianzhong Xu, Lauren P. Carter, Richard Bonneau, James M. Olson, Evangelos A. Coutsias, Colin E. Correnti, Thomas Szyperski, David J. Craik, David Baker
design of hyperstable constrained peptides. Nat. 538 (7625) (2016)
Christina M. Bergey, Andrew M. Watkins, Paramjit S. Arora
HippDB: a database of readily targeted helical protein-protein interactions. Bioinform. 29 (21) (2013)