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ORCIDAndrew M. Watkins
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- affiliation (PhD): New York University, Department of Chemistry, New York City, NY, USA
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2020 – today
- 2024
[i11]Samuel Stanton, Robert G. Alberstein, Nathan C. Frey, Andrew M. Watkins, Kyunghyun Cho:
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms. CoRR abs/2407.00236 (2024)- [i10]Ewa M. Nowara, Pedro O. Pinheiro, Sai Pooja Mahajan, Omar Mahmood, Andrew Martin Watkins, Saeed Saremi, Michael Maser:
NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries. CoRR abs/2407.03428 (2024) - [i9]Natasa Tagasovska, Ji Won Park, Matthieu Kirchmeyer, Nathan C. Frey, Andrew Martin Watkins, Aya Abdelsalam Ismail, Arian Rokkum Jamasb, Edith Lee, Tyler Bryson, Stephen Ra, Kyunghyun Cho:
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design. CoRR abs/2407.21028 (2024) - [i8]Angelica Chen, Samuel Don Stanton, Robert G. Alberstein, Andrew M. Watkins, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Nathan C. Frey:
LLMs are Highly-Constrained Biophysical Sequence Optimizers. CoRR abs/2410.22296 (2024) - 2023
- [c2]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 - [c1]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 - [i7]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 abs/2302.07754 (2023) - [i6]Pedro O. Pinheiro, Joshua Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew Martin Watkins, Stephen Ra, Vishnu Sresht, Saeed Saremi:
3D molecule generation by denoising voxel grids. CoRR abs/2306.07473 (2023) - [i5]Michael Maser, Natasa Tagasovska, Jae Hyeon Lee, Andrew M. Watkins:
MoleCLUEs: Optimizing Molecular Conformers by Minimization of Differentiable Uncertainty. CoRR abs/2306.11681 (2023) - [i4]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 abs/2308.05326 (2023) - 2022
- [j4]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): 1174-1184 (2022) - [i3]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 abs/2205.04259 (2022) - [i2]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 abs/2210.04096 (2022) - 2021
- [i1]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 abs/2110.07531 (2021) - 2020
- [j3]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)
2010 – 2019
- 2016
- [j2]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:
Accurate de novo design of hyperstable constrained peptides. Nat. 538(7625): 329-335 (2016) - 2013
- [j1]Christina M. Bergey, Andrew M. Watkins, Paramjit S. Arora:
HippDB: a database of readily targeted helical protein-protein interactions. Bioinform. 29(21): 2806-2807 (2013)
Coauthor Index
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