Rasmus Fonseca

I study efficient computational methods for modeling macromolecules (proteins, RNA and DNA) and computations of geometric properties both in 2, 3, and higher dimensions. I am currently a postdoc at the Department of Computer Science, University of Copenhagen (DIKU). I did my Ph.D. studies at DIKU in Prof. Pawel Winters lab and at University of California, Santa Cruz, in collaboration with Prof. Kevin Karplus. From 2012-2014 I was a postdoc at INRIA Saclay with Dr. Julie Bernauer and at SLAC Stanford with Dr. Henry van den Bedem. From Dec. 2015 I'll be at Stanford University again.

Department of Computer Science University of Copenhagen Universitetsparken 5, 2100 København Office: 01-0-019 HCØ Phone: +45 3044 9717 E-mail: rfonseca@di.ku.dk ORCID profile LinkedIn profile

Links

• Curriculum Vitae - My academic CV
• Various software projects I (co-)authored.
• KGSrna - System for characterizing the conformational flexibility of RNA orders of magnitude faster than traditional MD methods.
• High-dimensional Steiner trees - A C++ library for finding optimal Steiner trees in any dimension.
• ProGAL - Protein Geometric Algorithm Library. A Java library with algorithms and data structures for analyzing and representing protein structures.
• PDBCluster - Small C++ program that performs k-medoids and k-centers clustering of protein/RNA/DNA PDB-files using Partitioning Around Medoids (PAM) and the dRMSD metric.
• KredsDesign - Visual hardware simulator for a machine architecture class. Suitable companion for the book "Computer Organization and Design".
• Useful implementations - Solutions to small problems that I couldn't find implementations to anywhere else
• Java-implementation finding the cartesian coordinates of a regular n-simplex
• Java-implementation that solves the problem of Apollonius (i.e. finding a circle tangent to three other circles)
• Problem of Apollonius in 3D (i.e. finding a sphere tangent to four other spheres. Step-by-step description easily generalized to d-dimensions)
• Installing gnuplot (more importantly xz) on Mac with homebrew.
• Project ideas - Ideas I may never find the time to finish
• Lawsons paper for flip-based Delaunay triangulations - I was unable to google this paper so hopefully this will help someone else.

Publications

• Probing RNA Native Conformational Ensembles with Structural Constraints. R. Fonseca, H. van den Bedem and J. Bernauer. Journal of Computational Biology. May 2016, 23(5): 362-371.
• Coupled Motions in β2AR:Gαs Conformational Ensembles. D.V. Pachov, R. Fonseca, D. Arnol, J. Bernauer, and H. van den Bedem. J. Chem. Theory Comput., 2016, 12 (3), pp 946-956.
• KGSrna: Efficient 3D kinematics-based sampling for nucleic acids. R. Fonseca, H. van den Bedem and J. Bernauer. Research in Computational Molecular Biology (LNCS) volume 9029, pages 80-95. 2015. [Supplementary material] [Video 1] [Video 2]
• Faster Exact Algorithms for Computing Steiner Trees in Higher Dimensional Euclidean Spaces. R. Fonseca, M. Brazil, P. Winter and M. Zachariasen. Pending publication
• Euclidean Steiner Tree Heuristic in d-Space. A.E. Olsen, S.S. Lorenzen, R. Fonseca and P. Winter. Pending publication
• Alpha Complexes in Protein Structure Prediction. P. Winter and R. Fonseca. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Pages 178-182. 2015
• Characterizing RNA dynamics from NMR data with kinematic models. R. Fonseca, D.P. Pachov, J. Bernauer and H. van den Bedem. Nucleic Acids Research. 2014.
• Visualizing and representing the evolution of topological features. R. Fonseca and D. M. S. Jørgensen. Extended abstract for CG:YRF at Symposium of Computational Geometry. 2012. (pdf)
• Bounding Volumes for Proteins: A Comparative Study. R. Fonseca and P. Winter Journal of Computational Biology, 19(10): 1203-1213, 2012
• Ranking Beta Sheet Topologies with Applications to Protein Structure Prediction. R. Fonseca, G. Helles and P. Winter. Journal of Mathematical Modelling and Algorithms, 10(4): 357-369, 2011
• Protein Packing Quality using Delaunay Complexes. R. Fonseca. P. Winter and K. Karplus. Proceedings of ISVD 2011. Pages 117-122. 2011. (pdf)
• Adjustable Chain Trees for Proteins. P. Winter and R. Fonseca. Journal of Computational Biology. 19(1): 83-99. 2012
• Ranking Beta Sheet Topologies of Proteins. R. Fonseca, G. Helles and P. Winter. Proceedings of WCECS, 2:624-628. 2010.
• Protein Structure Prediction using Bee Colony Optimization Metaheuristic. R. Fonseca, M. Paluszewski and P. Winter. Journal of Molecular Modelling and Algorithms, 2010
• Predicting Dihedral Angles of Coil-structure Residues from the Primary Sequence using Neural Networks. R. Fonseca and G. Helles. BMC Bioinformatics 2009, 10:338