SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. - Joke Reumers; Joost Schymkowitz; Jesper Ferkinghoff-Borg; Francois Stricher; Luis Serrano; Frederic Rousseau 001 (Nucleic Acids Res., 2005)

The FoldX web server: an online force field. - Joost Schymkowitz; Jesper Borg; Francois Stricher; Robby Nys; Frederic Rousseau 001; Luis Serrano (Nucleic Acids Res., 2005)

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm. - Ignacio E. Sánchez; Pedro Beltrão; Francois Stricher; Joost Schymkowitz; Jesper Ferkinghoff-Borg; Frederic Rousseau 001; Luis Serrano (PLoS Comput. Biol., 2008)

Information theoretical quantification of cooperativity in signalling complexes. - Tom Lenaerts; Jesper Ferkinghoff-Borg; Joost Schymkowitz; Frederic Rousseau 001 (BMC Syst. Biol., 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)

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)

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)

Microbial Biofilm as a Smart Material. - Christian Garde; Martin Welch; Jesper Ferkinghoff-Borg; Thomas Sams (Sensors, 2015)

Bayesian Generalised Ensemble Markov Chain Monte Carlo. - Jes Frellsen; Ole Winther; Zoubin Ghahramani; Jesper Ferkinghoff-Borg (AISTATS, 2016)

Bowhead: Bayesian modelling of cell velocity during concerted cell migration. - Mathias Engel; James Longden; Jesper Ferkinghoff-Borg; Xavier Robin; Gaye Saginc; Rune Linding (PLoS Comput. Biol., 2018)

General Protocol for Constructing Molecular Models of Nanodiscs. - Lisbeth Ravnkilde Kjølbye; Leonardo De Maria; Tsjerk A. Wassenaar; Haleh Abdizadeh; Siewert J. Marrink; Jesper Ferkinghoff-Borg; Birgit Schiøtt (J. Chem. Inf. Model., 2021)

Probabilistic thermal stability prediction through sparsity promoting transformer representation. - Yevgen Zainchkovskyy; Jesper Ferkinghoff-Borg; Anja Bennett; Thomas Egebjerg; Nikolai Lorenzen; Per Greisen Jr.; Søren Hauberg; Carsten Stahlhut (CoRR, 2022)

Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P2 Lipids. - Lisbeth Ravnkilde Kjølbye; Lars Sørensen; Jun Yan; Nils A. Berglund; Jesper Ferkinghoff-Borg; Carol V. Robinson; Birgit Schiøtt (J. Chem. Inf. Model., 2022)

Batched Energy-Entropy acquisition for Bayesian Optimization. - Felix Teufel; Carsten Stahlhut; Jesper Ferkinghoff-Borg (NeurIPS, 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)