An alternative model of amino acid replacement. - Gavin E. Crooks; Steven E. Brenner (Bioinform., 2005)

Pairwise alignment incorporating dipeptide covariation. - Gavin E. Crooks; Richard E. Green; Steven E. Brenner (Bioinform., 2005)

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap. - Gavin A. Price; Gavin E. Crooks; Richard E. Green; Steven E. Brenner (Bioinform., 2005)

A high level interface to SCOP and ASTRAL implemented in Python. - James A. Casbon; Gavin E. Crooks; Mansoor A. S. Saqi (BMC Bioinform., 2006)

The thermodynamics of prediction - Susanne Still; David A. Sivak; Anthony J. Bell; Gavin E. Crooks (CoRR, 2012)

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. - Josh Fass; David A. Sivak; Gavin E. Crooks; Kyle Beauchamp; Benedict J. Leimkuhler; John D. Chodera (Entropy, 2018)

Thermodynamic Computing. - Tom Conte 001; Erik DeBenedictis; Natesh Ganesh; Todd Hylton; John Paul Strachan; R. Stanley Williams; Alexander A. Alemi; Lee Altenberg; Gavin E. Crooks; James P. Crutchfield; Lídia del Rio; Josh Deutsch; et al. (CoRR, 2019)

Two-Qubit Circuit Depth and the Monodromy Polytope. - Eric C. Peterson; Gavin E. Crooks; Robert S. Smith (Quantum, 2020)

Measuring Analytic Gradients of General Quantum Evolution with the Stochastic Parameter Shift Rule. - Leonardo Banchi; Gavin E. Crooks (Quantum, 2021)

Thermodynamic Linear Algebra. - Maxwell Aifer; Kaelan Donatella; Max Hunter Gordon; Thomas Ahle; Daniel Simpson; Gavin E. Crooks; Patrick J. Coles (CoRR, 2023)

Thermodynamic Matrix Exponentials and Thermodynamic Parallelism. - Samuel Duffield; Maxwell Aifer; Gavin E. Crooks; Thomas Ahle; Patrick J. Coles (CoRR, 2023)

Thermodynamic Computing System for AI Applications. - Denis Melanson; Mohammad Abu Khater; Maxwell Aifer; Kaelan Donatella; Max Hunter Gordon; Thomas Ahle; Gavin E. Crooks; Antonio J. Martinez; Faris M. Sbahi; Patrick J. Coles (CoRR, 2023)

Thermodynamic Bayesian Inference. - Maxwell Aifer; Samuel Duffield; Kaelan Donatella; Denis Melanson; Phoebe Klett; Zach Belateche; Gavin E. Crooks; Antonio J. Martinez; Patrick J. Coles (ICRC, 2024)

Error Mitigation for Thermodynamic Computing. - Maxwell Aifer; Denis Melanson; Kaelan Donatella; Gavin E. Crooks; Thomas Ahle; Patrick J. Coles (CoRR, 2024)

Thermodynamic Natural Gradient Descent. - Kaelan Donatella; Samuel Duffield; Maxwell Aifer; Denis Melanson; Gavin E. Crooks; Patrick J. Coles (CoRR, 2024)

Scalable Thermodynamic Second-order Optimization. - Kaelan Donatella; Samuel Duffield; Denis Melanson; Maxwell Aifer; Phoebe Klett; Rajath Salegame; Zach Belateche; Gavin E. Crooks; Antonio J. Martinez; Patrick J. Coles (CoRR, 2025)

Solving the compute crisis with physics-based ASICs. - Maxwell Aifer; Zach Belateche; Suraj Bramhavar; Kerem Yunus Çamsari; Patrick J. Coles; Gavin E. Crooks; Douglas J. Durian; Andrea J. Liu; Anastasia Marchenkova; Antonio J. Martinez; Peter L. McMahon; Faris M. Sbahi; et al. (CoRR, 2025)