Jesper Ferkinghoff-Borg

18 papers A* 1A 1Journal 16
YearRankTypeTitle / Venue / Authors
2026 J jnl
MechPert: Mechanistic Consensus as an Inductive Bias for Unseen Perturbation Prediction.
CoRR
Marc Boubnovski Martell, Josefa Lia Stoisser, Lawrence Phillips, Aditya Misra, Robert Kitchen, Jesper Ferkinghoff-Borg, Jialin Yu, Philip Torr, Kaspar Märtens
2025 J jnl
Towards Agents That Know When They Don't Know: Uncertainty as a Control Signal for Structured Reasoning.
CoRR
Josefa Lia Stoisser, Marc Boubnovski Martell, Lawrence Phillips, Gianluca Mazzoni, Lea Mørch Harder, Philip Torr, Jesper Ferkinghoff-Borg, Kaspar Märtens, Julien Fauqueur
2025 J jnl
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation.
CoRR
Jes Frellsen, Maher M. Kassem, Tone Bengtsen, Lars Olsen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Wouter Boomsma
2024 A* conf
Batched Energy-Entropy acquisition for Bayesian Optimization.
NeurIPS
Felix Teufel, Carsten Stahlhut, Jesper Ferkinghoff-Borg
2024 J jnl
Batched Energy-Entropy acquisition for Bayesian Optimization.
CoRR
Felix Teufel, Carsten Stahlhut, Jesper Ferkinghoff-Borg
2022 J jnl
Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P
J. Chem. Inf. Model.
Lisbeth Ravnkilde Kjølbye, Lars Sørensen, Jun Yan, Nils A. Berglund, Jesper Ferkinghoff-Borg, Carol V. Robinson, Birgit Schiøtt
2022 J jnl
Probabilistic thermal stability prediction through sparsity promoting transformer representation.
CoRR
Yevgen Zainchkovskyy, Jesper Ferkinghoff-Borg, Anja Bennett, Thomas Egebjerg, Nikolai Lorenzen, Per Greisen Jr., Søren Hauberg, Carsten Stahlhut
2021 J jnl
General Protocol for Constructing Molecular Models of Nanodiscs.
J. Chem. Inf. Model.
Lisbeth Ravnkilde Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt
2018 J jnl
Bowhead: Bayesian modelling of cell velocity during concerted cell migration.
PLoS Comput. Biol.
Mathias Engel, James Longden, Jesper Ferkinghoff-Borg, Xavier Robin, Gaye Saginc, Rune Linding
2016 A conf
Bayesian Generalised Ensemble Markov Chain Monte Carlo.
AISTATS
Jes Frellsen, Ole Winther, Zoubin Ghahramani, Jesper Ferkinghoff-Borg
2015 J jnl
Microbial Biofilm as a Smart Material.
Sensors
Christian Garde, Martin Welch, Jesper Ferkinghoff-Borg, Thomas Sams
2014 J jnl
Combining Experiments and Simulations Using the Maximum Entropy Principle.
PLoS Comput. Biol.
Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen
2013 J jnl
PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure.
J. Comput. Chem.
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, Mikael Borg, Jan H. Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck
2010 J jnl
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.
BMC Bioinform.
Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg, Thomas Hamelryck
2009 J jnl
A Probabilistic Model of RNA Conformational Space.
PLoS Comput. Biol.
Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck
2009 J jnl
Information theoretical quantification of cooperativity in signalling complexes.
BMC Syst. Biol.
Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, Frederic Rousseau
2008 J jnl
Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm.
PLoS Comput. Biol.
Ignacio E. Sánchez, Pedro Beltrão, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano
2005 J jnl
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs.
Nucleic Acids Res.
Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, Frederic Rousseau