PDB file parser and structure class implemented in Python. - Thomas Hamelryck; Bernard Manderick (Bioinform., 2003)

Evolving hidden Markov models for protein secondary structure prediction. - Kyoung-Jae Won; Thomas Hamelryck; Adam Prügel-Bennett; Anders Krogh (Congress on Evolutionary Computation, 2005)

Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. - Wouter Boomsma; Thomas Hamelryck (BMC Bioinform., 2005)

Reconstructing protein structure from solvent exposure using tabu search. - Martin Paluszewski; Thomas Hamelryck; Pawel Winter (Algorithms Mol. Biol., 2006)

Sampling Realistic Protein Conformations Using Local Structural Bias. - Thomas Hamelryck; John T. Kent; Anders Krogh (PLoS Comput. Biol., 2006)

An evolutionary method for learning HMM structure: prediction of protein secondary structure. - Kyoung-Jae Won; Thomas Hamelryck; Adam Prügel-Bennett; Anders Krogh (BMC Bioinform., 2007)

The Voronoi Diagram of Half-Balls and its Application to the Prediction of the 3D Structure of Proteins. - Francois Anton; Thomas Hamelryck (ISVD, 2009)

Biopython: freely available Python tools for computational molecular biology and bioinformatics. - Peter J. A. Cock; Tiago Rodrigues Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. de Hoon (Bioinform., 2009)

A Probabilistic Model of RNA Conformational Space. - Jes Frellsen; Ida Moltke; Martin Thiim; Kanti V. Mardia; Jesper Ferkinghoff-Borg; Thomas Hamelryck (PLoS Comput. Biol., 2009)

Beyond rotamers: a generative, probabilistic model of side chains in proteins. - Tim Harder; Wouter Boomsma; Martin Paluszewski; Jes Frellsen; Kristoffer E. Johansson; Thomas Hamelryck (BMC Bioinform., 2010)

Mocapy++ - A toolkit for inference and learning in dynamic Bayesian networks. - Martin Paluszewski; Thomas Hamelryck (BMC Bioinform., 2010)

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models. - Kasper Stovgaard; Christian Andreetta; Jesper Ferkinghoff-Borg; Thomas Hamelryck (BMC Bioinform., 2010)

An Efficient Parallel GPU Evaluation of Small Angle X-ray Scattering Profiles. - Lubomir D. Antonov; Christian Andreetta; Thomas Hamelryck (BIOINFORMATICS, 2012)

Parallel GPGPU Evaluation of Small Angle X-Ray Scattering Profiles in a Markov Chain Monte Carlo Framework. - Lubomir D. Antonov; Christian Andreetta; Thomas Hamelryck (BIOSTEC (Selected Papers), 2012)

Fast large-scale clustering of protein structures using Gauss integrals. - Tim Harder; Mikael Borg; Wouter Boomsma; Peter Røgen; Thomas Hamelryck (Bioinform., 2012)

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. - Wouter Boomsma; Jes Frellsen; Tim Harder; Sandro Bottaro; Kristoffer E. Johansson; Pengfei Tian; Kasper Stovgaard; Christian Andreetta; Simon Olsson; Jan B. Valentin; Lubomir D. Antonov; Anders S. Christensen; et al. (J. Comput. Chem., 2013)

A Probabilistic Programming Approach to Protein Structure Superposition. - Lys Sanz Moreta; Ahmad Salim Al-Sibahi; Douglas L. Theobald; William Bullock; Basile Nicolas Rommes; Andreas Manoukian; Thomas Hamelryck (CIBCB, 2019)

Langevin diffusions on the torus: estimation and applications. - Eduardo García-Portugués; Michael Sørensen; Kanti V. Mardia; Thomas Hamelryck (Stat. Comput., 2019)

Bayesian protein superposition using Hamiltonian Monte Carlo. - Lys Sanz Moreta; Ahmad Salim Al-Sibahi; Thomas Hamelryck (BIBE, 2020)

Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model. - Christian B. Thygesen; Christian Skjødt Steenmans; Ahmad Salim Al-Sibahi; Lys Sanz Moreta; Anders Bundgård Sørensen; Thomas Hamelryck (ICML, 2021)

Time-efficient Bayesian Inference for a (Skewed) Von Mises Distribution on the Torus in a Deep Probabilistic Programming Language. - Ola Rønning; Christophe Ley; Kanti V. Mardia; Thomas Hamelryck (MFI, 2021)

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder. - Lys Sanz Moreta; Ola Rønning; Ahmad Salim Al-Sibahi; Jotun Hein; Douglas L. Theobald; Thomas Hamelryck (ICLR, 2022)

AI Implementation and Capability Development in Manufacturing: An Action Research Case. - Jon Eklof; Ulrika Snis; Thomas Hamelryck; Alexander Grima; Ola Rønning (HICSS, 2024)

Abstraction, mimesis and the evolution of deep learning. - Jon Eklof; Thomas Hamelryck; Cadell Last; Alexander Grima; Ulrika Lundh Snis (AI Soc., 2024)

ELBOing Stein: Variational Bayes with Stein Mixture Inference. - Ola Rønning; Eric T. Nalisnick; Christophe Ley; Padhraic Smyth; Thomas Hamelryck (ICLR, 2025)

Unfolding AlphaFold's Bayesian Roots in Probability Kinematics. - Thomas Hamelryck; Kanti V. Mardia (CoRR, 2025)