Using adaptive operator scheduling on problem domains with an operator manifold: applications to the travelling salesman problem. - Wouter Boomsma (IEEE Congress on Evolutionary Computation, 2003)

A Comparison of Adaptive Operator Scheduling Methods on the Traveling Salesman Problem. - Wouter Boomsma (EvoCOP, 2004)

Multiple Sequence Alignment Using SAGA: Investigating the Effects of Operator Scheduling, Population Seeding, and Crossover Operators. - René Thomsen; Wouter Boomsma (EvoWorkshops, 2004)

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

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)

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)

Combining Experiments and Simulations Using the Maximum Entropy Principle. - Wouter Boomsma; Jesper Ferkinghoff-Borg; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2014)

ENCORE: Software for Quantitative Ensemble Comparison. - Matteo Tiberti; Elena Papaleo; Tone Bengtsen; Wouter Boomsma; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2015)

Spherical convolutions and their application in molecular modelling. - Wouter Boomsma; Jes Frellsen (NIPS, 2017)

3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data. - Maurice Weiler; Mario Geiger; Max Welling; Wouter Boomsma; Taco Cohen (NeurIPS, 2018)

(q, p)-Wasserstein GANs: Comparing Ground Metrics for Wasserstein GANs. - Anton Mallasto; Jes Frellsen; Wouter Boomsma; Aasa Feragen (CoRR, 2019)

What is a meaningful representation of protein sequences? - Nicki Skafte Detlefsen; Søren Hauberg; Wouter Boomsma (CoRR, 2020)

Adaptive Cholesky Gaussian Processes. - Simon Bartels; Kristoffer Stensbo-Smidt; Pablo Moreno-Muñoz; Wouter Boomsma; Jes Frellsen; Søren Hauberg (AISTATS, 2023)

Implicit Variational Inference for High-Dimensional Posteriors. - Anshuk Uppal; Kristoffer Stensbo-Smidt; Wouter Boomsma; Jes Frellsen (NeurIPS, 2023)

Kernel-Matrix Determinant Estimates from stopped Cholesky Decomposition. - Simon Bartels; Wouter Boomsma; Jes Frellsen; Damien Garreau (J. Mach. Learn. Res., 2023)

BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks. - Frederikke Isa Marin; Felix Teufel; Marc Horlacher; Dennis Madsen; Dennis Pultz; Ole Winther; Wouter Boomsma (ICLR, 2024)

A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences. - Miguel González Duque; Richard Michael; Simon Bartels; Yevgen Zainchkovskyy; Søren Hauberg; Wouter Boomsma (NeurIPS, 2024)

Kermut: Composite kernel regression for protein variant effects. - Peter Mørch Groth; Mads Herbert Kerrn; Lars Olsen; Jesper Salomon; Wouter Boomsma (NeurIPS, 2024)

A Continuous Relaxation for Discrete Bayesian Optimization. - Richard Michael; Simon Bartels; Miguel González Duque; Yevgen Zainchkovskyy; Jes Frellsen; Søren Hauberg; Wouter Boomsma (CoRR, 2024)

A systematic analysis of regression models for protein engineering. - Richard Michael; Jacob Kæstel-Hansen; Peter Mørch Groth; Simon Bartels; Jesper Salomon; Pengfei Tian; Nikos S. Hatzakis; Wouter Boomsma (PLoS Comput. Biol., 2024)

Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters. - Marloes Arts; Jes Frellsen; Wouter Boomsma (Trans. Mach. Learn. Res., 2024)

Zero-shot protein stability prediction by inverse folding models: a free energy interpretation. - Jes Frellsen; Maher M. Kassem; Tone Bengtsen; Lars Olsen; Kresten Lindorff-Larsen; Jesper Ferkinghoff-Borg; Wouter Boomsma (CoRR, 2025)