Jesper Ferkinghoff-Borg

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Thomas HamelryckProfessor in Machine Learning, BIO/DIKU, University of CopenhagenVerified email at bio.ku.dk
Wouter BoomsmaProfessor, Department of Computer Science, University of CopenhagenVerified email at di.ku.dk
Jes FrellsenAssociate Professor, Technical University of Denmark (DTU)Verified email at dtu.dk
Kresten Lindorff-LarsenLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenVerified email at bio.ku.dk
Kanti MardiaSENIOR RESARCH PROFESSOR ,UNIVERSITY OF LEEDS AND UNIVERSITY OF OXFORDVerified email at leeds.ac.uk
Mogens H. JensenProfessor of Complex Systems, Niels Bohr InstituteVerified email at nbi.dk
Dr. Rune LindingHumboldt-Universität zu BerlinVerified email at hu-berlin.de
Christian AndreettaUniv. of Copenhagen, Denmark, and Uni Computing, Uni Research, NorwayVerified email at uni.no
Thomas SamsTechnical University of DenmarkVerified email at dtu.dk
Poul OlesenEmeritus Professor of Theoretical Physics, Niels Bohr InstituteVerified email at nbi.dk
Kim SneppenProfessor at Niels Bohr Institute, Copenhagen UniversityVerified email at nbi.dk
Simon OlssonChalmers University of TechnologyVerified email at chalmers.se
Guido TianaUniversity of MilanoVerified email at unimi.it
Pengfei TianPrincipal Scientist, Lila SciencesVerified email at nih.gov
Kristoffer Enøe JohanssonDepartment of Biology, University of CopenhagenVerified email at bio.ku.dk
Tim HarderResearch Scientist at Philips ResearchVerified email at philips.com
Pedro BeltraoAssociate Professor, ETH ZurichVerified email at ethz.ch
Michael GivskovProfessor of Microbiology, Costerton Biofilm Center ISIM, University of CopenhagenVerified email at sund.ku.dk
Thomas BjarnsholtProfessor in Biofilms and Chronic InfectionsVerified email at sund.ku.dk
Thomas R. CoxGarvan Institute of Medical ResearchVerified email at garvan.org.au

Jesper Ferkinghoff-Borg

Associate Professor, Research Director, Novo Nordisk A/S

Verified email at novonordisk.com

Machine Learning Deep Learning protein dynamics - protein interaction networks - cellular communication - automatisation


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The FoldX web server: an online force field J Schymkowitz, J Borg, F Stricher, R Nys, F Rousseau, L Serrano Nucleic acids research 33 (suppl_2), W382-W388, 2005	2843	2005
Prediction of water and metal binding sites and their affinities by using the Fold-X force field JWH Schymkowitz, F Rousseau, IC Martins, J Ferkinghoff-Borg, F Stricher, ... Proceedings of the National Academy of Sciences 102 (29), 10147-10152, 2005	401	2005
A generative, probabilistic model of local protein structure W Boomsma, KV Mardia, CC Taylor, J Ferkinghoff-Borg, A Krogh, ... Proceedings of the National Academy of Sciences 105 (26), 8932-8937, 2008	212	2008
Combining experiments and simulations using the maximum entropy principle W Boomsma, J Ferkinghoff-Borg, K Lindorff-Larsen PLoS computational biology 10 (2), e1003406, 2014	203	2014
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs J Reumers, J Schymkowitz, J Ferkinghoff-Borg, F Stricher, L Serrano, ... Nucleic acids research 33 (suppl_1), D527-D532, 2005	187	2005
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks M Ander, P Beltrao, B Di Ventura, J Ferkinghoff-Borg, M Foglierini, ... IEE Proceedings-Systems Biology 1 (1), 129-138, 2004	184	2004
Kinome-wide decoding of network-attacking mutations rewiring cancer signaling P Creixell, EM Schoof, CD Simpson, J Longden, CJ Miller, HJ Lou, ... Cell 163 (1), 202-217, 2015	181	2015
A probabilistic model of RNA conformational space J Frellsen, I Moltke, M Thiim, KV Mardia, J Ferkinghoff-Borg, T Hamelryck PLoS computational biology 5 (6), e1000406, 2009	133	2009
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations C Kiel, S Wohlgemuth, F Rousseau, J Schymkowitz, J Ferkinghoff-Borg, ... Journal of molecular biology 348 (3), 759-775, 2005	133	2005
Potentials of mean force for protein structure prediction vindicated, formalized and generalized T Hamelryck, M Borg, M Paluszewski, J Paulsen, J Frellsen, C Andreetta, ... PloS one 5 (11), e13714, 2010	100	2010
Similarity measures for protein ensembles K Lindorff-Larsen, J Ferkinghoff-Borg PloS one 4 (1), e4203, 2009	94	2009
Experimental parameterization of an energy function for the simulation of unfolded proteins AB Norgaard, J Ferkinghoff-Borg, K Lindorff-Larsen Biophysical journal 94 (1), 182-192, 2008	90	2008
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models K Stovgaard, C Andreetta, J Ferkinghoff-Borg, T Hamelryck BMC bioinformatics 11, 1-14, 2010	70	2010
Quorum sensing regulation in Aeromonas hydrophila C Garde, T Bjarnsholt, M Givskov, TH Jakobsen, M Hentzer, A Claussen, ... Journal of molecular biology 396 (4), 849-857, 2010	63	2010
Bayesian methods in structural bioinformatics T Hamelryck, K Mardia, J Ferkinghoff-Borg Springer, 2012	59	2012
Stop-and-go kinetics in amyloid fibrillation J Ferkinghoff-Borg, J Fonslet, CB Andersen, S Krishna, S Pigolotti, H Yagi, ... Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 82 (1 …, 2010	57	2010
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm IE Sánchez, P Beltrao, F Stricher, J Schymkowitz, J Ferkinghoff-Borg, ... PLoS computational biology 4 (4), e1000052, 2008	52	2008
PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure W Boomsma, J Frellsen, T Harder, S Bottaro, KE Johansson, P Tian, ... Journal of computational chemistry 34 (19), 1697-1705, 2013	48	2013
Optimized Monte Carlo analysis for generalized ensembles J Ferkinghoff-Borg The European Physical Journal B-Condensed Matter and Complex Systems 29, 481-484, 2002	48	2002
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure T Lenaerts, J Ferkinghoff-Borg, F Stricher, L Serrano, JWH Schymkowitz, ... BMC structural biology 8, 1-15, 2008	45	2008

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