Conferences

Conference participation

2017


Sep 26-28, 2017:
5th International Conference on Particle-based Methods (PARTICLES2017), IACM + ECCOMAS, Hanover, Germany.
Talk and Paper: S. Karol, T. Nett, P. Incardona, N. Khouzami, J. Castrillon, I. F. Sbalzarini: "A Language and Development Environment for Parallel Particle Methods"

Sep 14, 2017:
5th Swiss Microscopy Core Facility Day, Fribourg, Switzerland.
Talk: U Günther, L. Royer, I. F. Sbalzarini: "Smart Microscopy with ClearVolume, Scenery, and AutoPilot"

Jun 26-28, 2017:
ACM PASC, Platform for Advanced Scientific Computing Conference, Lugano, Switzerland.
Poster: A. Huebl, R. Lehe, J.-L. Vay, D.P. Grote, I. F. Sbalzarini, S. Kuschel, M. Bussmann: "Open Science with openPMD"
(Poster PDF, InsideHPC News Flash)

May 29 - Jun 2, 2017:
International Workshop "Future Trends in DNA-based Nanotechnology", Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
Invited Talk: I. F. Sbalzarini: "Optimal reconstruction of sub-resolution structures in fluorescence microscopy images"

2016


Sep 3-7, 2016:
European Conference on Computational Biology (ECCB), The Hague, The Netherlands.
Poster: V. Andriasyan, A. Yakimovich, R. Witte, F. Georgi, I. F. Sbalzarini, U. Greber: "Computational Modeling of Human Adenovirus Egress"

May 8-12, 2016:
SIAM Conference on Mathematical Aspects of Materials Science, Workshop on Active Matter, Philadelphia, PA, USA.
Talk: Ivo F. Sbalzarini and Rajesh Ramaswamy: "A Hybrid Particle-Mesh Method for Active Polar Gels"
Talk: Rajesh Ramaswamy: "Mechano-Chemical Pattern Formation on Surfaces"

Apr 6-8, 2016:
Systems Biology of Mammalian Cells (SBMC), Munich, Germany.
Session organizer and chair: Ivo F. Sbalzarini: "Image-based Systems Biology"

Mar 9-11, 2016:
Visualization in Biology (VizBi), Heidelberg, Germany.
Poster: Loic Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W. Myers: "ClearVolume - microscope to visualization in seconds"

Mar 6-11, 2016:
Spring Meeting of the German Physical Society (DPG), Regensburg, Germany.
Talk: Jens Karschau, Ulrik Günther, Alessandro de Moura: "Stochasticity in DNA Replication of Archaea"

Feb 24, 2016:
Intersectional Max Planck Symposium on Networks in Biology, Harnack House, Berlin, Germany.

Feb 22-24, 2016:
Trends in Microscopy, Dresden, Germany.

2015


Oct 22-24, 2015:
17th EMBL PhD Symposium: Just by Chance? Randomness and Variability Shaping Biology, EMBL, Heidelberg, Germany.

Oct 14-16, 2015:
BioImage Informatics Conference, National Institute of Standards and Technology (NIST), Gaitherburg, MD, USA.
Keynote Lecture: I. F. Sbalzarini, "Model-based Image Analysis for Fluorescence Microscopy"

Jul 5-10, 2015:
29th European Conference on Object-Oriented Programming (ECOOP), Workshop DSLDI, Prague, Czech Republic (paper acceptance rate: 31/136).
Talk and Paper: Sven Karol, Pietro Incardona, Yaser Afshar, Ivo F. Sbalzarini and Jerónimo Castrillón "Towards a Next-Generation Parallel Particle- Mesh Language"

Jun 26-30, 2015:
30th Congress of the International Society for the Advancement of Cytometry (CYTO2015), Glasgow, Scotland, UK.
Invited Plenary Talk: I. F. Sbalzarini, "Model-Based Image Analysis: Towards Versatile and Robust Microscopy Image Qualification"

Jun 2-3, 2015:
10th Annual OME Users Meeting, Institut Pasteur, Paris, France.
Poster: Alessandro Rigano, Vanni Galli, Raffaello Giulietti, Tiziano Leidi, Mario Valle, Ivo F. Sbalzarini and Caterina Strambio-De-Castillia, "OMEGA: an open source environment to facilitate the execution of motion analysis workflows, to estimate error and to share results"

Apr 16-17, 2015:
Circle Meeting Biological Physics 2015, FOM Institute AMOLF, Amsterdam, The Netherlands.


Mar 29- Apr 1, 2015:
Focus on Microscopy, Göttingen, Germany.
Poster: L. A. Royer, M. Weigert, U. Günther, N. Maghelli, I. F. Sbalzarini & E. W. Myers, "ClearVolume - Light sheet microscopy deserves to be experienced live and in 3D"


Mar 16-20, 2015:
DPG Spring Meeting, TU Berlin, Berlin, Germany.


Jan 7-9, 2015:
Quantitative BioImaging Conference (QBI), Institute Pasteur, Paris, France.
Talk: I. F. Sbalzarini, "Globally optimal image segmentation over continuous Bayesian models"
Poster: P. Incardona and I. F. Sbalzarini, "The MOSAICsuite for Fiji and ImageJ."


Jan 5-6, 2015:
European BioImage Analysis Symposium (EuBIAS) 2015, Institute Curie, Paris, France.
Talk: I. F. Sbalzarini, "Bioimaging requires novel computer vision approaches and open software."


2014


Nov 24-25, 2014:
MPI-MDC Systems Biology Symposium, Berlin, Germany.
Talk: I. F. Sbalzarini, "Developments in Scientific Computing for Image-based Systems Biology."


Nov 1-5, 2014:
12th Asian Conference on Computer Vision (ACCV), Singapore. Workshop on Emerging Topics in Image Restoration and Enhancement.
Talk and Paper: Y. Gong and I. F. Sbalzarini, "Image Enhancement by Gradient Distribution Specification." (Paper PDF, Supplementary Material ZIP, Talk Slides PDF, Software Download)


Oct 8-10, 2014:
Bio-Image Informatics Conference, Leuven, Belgium.
Talk: B. Cheeseman and I. F. Sbalzarini, "Forget pixels: adaptive particle representation for efficient storage and processing of fluorescence microscopy images."
Poster: Y. Gong and I. F. Sbalzarini, "Making Microscopy Images more Natural."
Poster: Ö. Demirel, I. Smal, E. Meijering, and I. F. Sbalzarini, "A Parallel Particle Filtering Framework for Multi-Object Tracking in Bioimaging."
Poster: P. Incardona and I. F. Sbalzarini, "The MOSAICsuite for Fiji and ImageJ."
Poster: S. Schneider and I. F. Sbalzarini, "Towards a fully automated representation of epithelial tissues as 3D graphs."
Poster: X. Xiao, V. Geyer, H. Bowne-Anderson, J. Howard, and I. F. Sbalzarini, "Optimal Sub-pixel Filament Segmentation using a B-Spline Vector Level-Set."
Poster: Y. Afshar and I. F. Sbalzarini, "A parallel distributed-memory particle method enables segmenting very large images."
Poster: U. Guenther and I. F. Sbalzarini, " Dive into data: Immersive visualization of 3D particle image representations."


Sep 25-26, 2014:
2nd International Workshop on Image-based Systems Biology, Jena, Germany.


Sep 2-5, 2014:
German Conference on Pattern Recognition (GCPR), Münster, Germany.


Aug 25-28, 2014:
Conference on Early Events in Virus Infection, Monte Verita, Ascona, Switzerland.
Invited Talk: I. F. Sbalzarini, "From Prototypes to Workhorses: Computational Methods Help Dissect Viral Dynamics."


Aug 18-29, 2014:
EMBO Course on Lightsheet Microscopy, Dresden, Germany.
Tutor: U. Günther


Aug 18-22, 2014:
European Conference on Artificial Intelligence (ECAI), Prague, Czech Republic.
Paper and Talk: J. Asmus, D. Borchmann, I. F. Sbalzarini, D. Walther, "Towards an FCA-based Recommender System for Black-Box Optimization."


May 4 - 9, 2014:
IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Florence, Italy.
Paper and Talk: Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini, "An Adaptive Distributed Resampling Algorithm with Non-Proportional Allocation." (PDF, Software Download)


April 29 - May 2, 2014:
IEEE International Symposium on Biomedical Imaging (ISBI), Beijing, China.
Paper and Poster: Xun Xiao and I. F. Sbalzarini, "Globally Optimal Geometric Segmentation of Filaments." (PDF)


April 30, 2014:
IET Data Fusion & Target Tracking Conference, Liverpool, UK. 2 Papers and 2 Talks:
Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini, "PPF – A Parallel Particle Filtering Library." (PDF, Software Download)
Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini, "Piecewise Constant Sequential Importance Sampling for Fast Particle Filtering." (PDF, Software Download)


Mar 18 - 21, 2014:
International Meeting of the German Society for Cell Biology, Regensburg, Germany.
Invited Talk: Ivo F. Sbalzarini, "Uniting image reconstruction and segmentation for fluorescence microscopy".
Chairman and Organizer of the session "Quantitative imaging of cell dynamics" (PDF, Software Download)


2013


Sep 18-20, 2013:
3rd International Conference on Particle-Based Methods: Fundamentals and Applications, Stuttgart, Germany.
Talk and Paper: Omar Awile, Milan Mitrovic, Sylvain Reboux, and Ivo F. Sbalzarini, "A Domain-Specific Programming Language for Particle Simulations on Distributed-Memory Parallel Computers". (PDF, Abstract PDF)


Sep 15-18, 2013:
IEEE International Conference on Image Processing (ICIP), Melbourne, Australia.
Talk and Paper: Yuanhao Gong and Ivo F. Sbalzarini, "Local Weighted Gaussian Curvature for Image Processing". (PDF)


Aug 30 - Sep 3, 2013:
14th International Conference on Systems Biology (ICSB), Copenhagen, Denmark.
Poster: Sophie Schneider, Stephan Daetwyler, Jan Huisken, and Ivo F. Sbalzarini, "3D Computer Reconstruction of the Developing Zebrafish Vasculature".


Jul 21-23, 2013:
21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), Berlin, Germany.
Poster: Sophie Schneider, Stephan Daetwyler, Jan Huisken, and Ivo F. Sbalzarini, "3D Computer Reconstruction of the Developing Zebrafish Vasculature".
Poster: Yuanhao Gong and Ivo F. Sbalzarini, " Reconstructing high-resolution images from multiple low-resolution views".


Jul 6-10, 2013:
Genetic and Evolutionary Computation Conference (GECCO), Amsterdam, The Netherlands.


Jun 16-20, 2013:
International Supercomputing Conference (ISC’13), Leipzig, Germany.


May 13, 2013:
All SystemsX Day 2013, Bern, Switzerland.
Poster: Chiara Gabella, E. Bertseva, Celine Bottier, Ivo F. Sbalzarini, and A. B. Verkhovsky, "Contact angle at the leading edge controls cell protrusion rate".


Feb 8, 2013:
National Competence Center on Biomedical Imaging, Annual Meeting, Paul-Scherrer Institute, Villigen, Switzerland.
Talk: M. E. Ambühl, F. Raynaud, J.-J. Meister, I. F. Sbalzarini, A. B. Verkhovsky, "Cell shape transformation: from observation to analysis".


2012


Dec 15-19, 2012:
Annual Meeting of the American Society for Cell Biology (ACSB), San Francisco, California.
Poster: C. Gabella, E. Bertseva, C. Bottier, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky, "Interplay between cytoskeletal forces, membrane tension and hydrostatic pressure in rapidly migrating cells".
Poster: M. E. Ambühl, F. Raynaud, J.-J. Meister, I. F. Sbalzarini, A. B. Verkhovsky, "How Protrusion/retraction switch controls cell shape and motion".


Dec 6-7, 2012:
Biotec Forum Dresden, Dresden, Germany.
Invited talk: Ivo F. Sbalzarini, "Image-based Systems Biology: Modeling and Simulation in Image-derived Geometries".


Oct 15-17, 2012:
IUTAM Symposium on Particle Methods in Fluid Mechanics, Copenhagen, Denmark.
Talk and Abstract: Ivo F. Sbalzarini, Christoph Häcki, and Sylvain Reboux, "Anisotropic kernels for self-organizing Lagrangian particles". (PDF)


Sep 19, 2012:
Workshop on Image-based Systems Biology, Jena, Germany.
Invited talk: Ivo F. Sbalzarini, "Image-based Systems Biology: Modeling and Simulation in Image-derived Geometries". (PDF)


Sep 16-19, 2012:
BioImage Informatics Conference 2012, Dresden, Germany.
Talk: Ivo F. Sbalzarini, "Flexible multi-region bio-image segmentation including prior knowledge".
Poster: A. Yakimovich, Y. Yakimovich, M. Schmid, L. Pelkmans, I. F. Sbalzarini, U. Greber, "A computational multi-scale hybrid framework for modeling virus transmission".
Conference co-organizer: Ivo F. Sbalzarini

>>Conference web page...

Sep 9-12, 2012:
European Conference on Computational Biology (ECCB), Basel, Switzerland.
Poster: A. Yakimovich, Y. Yakimovich, M. Schmid, L. Pelkmans, I. F. Sbalzarini, U. Greber, "A computational multi-scale hybrid framework for modeling virus transmission".


Jul 9-11, 2012:
2012 Conference on Systems Biology of Mammalian Cells (SBMC), Leipzig, Germany.
Invited keynote lecture: Ivo F. Sbalzarini, "Image-based Systems Biology of Mammalian Cells: Watching Closely".


Jun 18-20, 2012:
PDEsoft: 1st Intl. Workshop on PDE Software Frameworks, Münster, Germany.
Talk and abstract: O. Awile, M. Mitrović, and I. F. Sbalzarini, "PPM: A scalable software framework for parallel particle-mesh simulations". (PDF)


Jun 13-17, 2012:
10th International Adenovirus Meeting. Umeå, Sweden.
Poster: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, U. F. Greber, "Multi-scale hybrid dynamics modeling and passive mass transfer reveal cell-free virus transmission". (Best Poster Award)


Jun 14-15, 2012:
Insel Symposium Konstanz "The Roots of Future Biology", Konstanz, Germany.
Invited talk: Ivo F. Sbalzarini, "My Life and My Science".


May 2-5, 2012:
IEEE International Symposium on Biomedical Imaging (ISBI), Barcelona, Spain.
Talk and paper: Yuanhao Gong, Grégory Paul & Ivo F. Sbalzarini, "Coupled signed-distance functions for implicit surface reconstruction" (PDF) (best paper award);
Workshop Talk: Yuanhao Gong, "Fast Particle Tracking for Prior-free Motion".


May 2-3, 2012:
6th Workshop on Theory of Randomized Search Heuristics (ThRaSH'2012), Lille, France.
2 Talks and Abstracts: Christian L. Müller and Ivo F. Sbalzarini, "Variable-metric randomized black-box optimization over the cone of positive definite matrices" (PDF);
Sebastian U. Stich, "Convergence of local search".
(PDF)


Mar 28 - Apr 1, 2012:
105th International Titisee Conference "Lipids as Organizers of Cell Membranes", Titisee, Germany.
Invited talk: Ivo F. Sbalzarini, "Imaging and simulation of intracellular membrane dynamics".


Feb 25-29, 2012:
56th annual meeting of the Biophysical Society, San Diego, California, USA.
Talk and Abstract: C. Gabella, C. Bottier, E. Bertseva, I. F. Sbalzarini, and A. B. Verkhovsky, "Interplay Between Cytoskeletal Forces, Membrane Tension and Hydrostatic Pressure in Rapidly Migrating Cells".
Abstract published in: Biophysical Journal, vol. 102(3), p. 704a, 2012.


Feb 13, 2012:
Swiss Soft Days 7, Lausanne, Switzerland.
Talk: M. E. Ambühl, C. Brepsant, J.-J. Meister, A. B. Verkhovsky, I. F. Sbalzarini, "Cell shape transformation: from observation to analysis".


Jan 30-31, 2012:
Swiss Institute of Bioinformatics Annual Meeting (SIB Days). Biel/Bienne, Switzerland.
2 Posters: Arun Shivanandan, Aleksandra Radenovic & Ivo F. Sbalzarini, “Super-resolution imaging and image analysis of protein-protein interactions in membranes”;
Yuanhao Gong, Grégory Paul & Ivo F. Sbalzarini, “Coupled signed-distance functions for implicit surface reconstruction”;

2 Talks: Grégory Paul, Janick Cardinale & Ivo F. Sbalzarini: "Seeing is believing - quantifying is convincing: Advances in image processing for modern biological images";
Christian L. Müller, Rajesh Ramaswamy & Ivo F. Sbalzarini: "Parameter estimation and approximate Bayesian computation in deterministic and stochastic biological networks" (Slides PDF) (Springer Link)


Jan 15-20, 2012:
Biophysics LEB meeting, Monte Verita, Switzerland.
Poster: M. E. Ambühl, C. Brepsant, J.-J. Meister, A. B. Verkhovsky, I. F. Sbalzarini, "Accurate cell outline segmentation and tracking from phase-contrast microscopy images and applications for investigating the mechanism of cell motility". (Best Poster Award 2nd place)


2011


Dec 13, 2011:
3rd Cell Shape Changes Course, Paris, France.
Talk and poster: C. Gabella, E. Bertseva, C. Bottier, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky, "Correlation between membrane tension, 3D shape and cell migration"


Dec 3-7, 2011:
American Society for Cell Biology (ASCB) Meeting, Denver, USA.
Poster: C. Gabella, E. Bertseva, C. Bottier, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky, "Correlation between membrane tension, three-dimensional shape and cell migration"


Nov 6-9, 2011:
45th IEEE Asilomar Conference on Signals, Systems and Computers, Pacific Grove, CA, USA.
Invited talk and invited paper: Grégory Paul, Janick Cardinale, Ivo F. Sbalzarini, "Flexible and Efficient Multi-Region Segmentation Using Active Contours"


Oct 24-26, 2011:
1st International SystemsX.ch Conference on Systems Biology, Basel, Switzerland.
2 Posters: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, and U. F. Greber, "Adenoviral Infection Spread in Two-Dimensional Cell Arrays Characterized by Hybrid Spatial Dynamics Modeling";
C. Gabella, C. Bottier, E. Bertseva, J.-J. Meister, I. F. Sbalzarini, and A. B. Verkhovsky, "Correlation between membrane tension, three-dimensional shape and cell migration velocity".


Oct 17-19, 2011:
4th European Cell Mechanics Meeting (CellMech 2011), Amsterdam, The Netherlands.
Poster: C. Gabella, C. Bottier, B. Vianay, L. Buscemi, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky, "Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique"


Sep 18-21, 2011:
BioImage Informatics Conference, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn (VA), USA.
Invited talk: Ivo F. Sbalzarini, “Coupling image restoration and segmentation: a generalized linear model approach” (invited).


Sep 14-16, 2011:
International Conference on Evolutionary and Deterministic Methods
for Design, Optimization and Control (EuroGen2011), Capua, Italy.
Invited paper and invited talk: C. L. Müller and I. F. Sbalzarini, "Gaussian Adaptation for Robust Design Centering".


Aug 30-Sep 2, 2011:
International Conference on Operations Research (OR'11), Zurich, Switzerland.
Talk: C. L. Müller, "Continuous gradient-free optimization over convex domains based on Gibbs sampling".


Aug 29, 2011:
NCCBI meeting of the National Competence Center for Biomedical Imaging, Zurich, Switzerland.
Talk: M. Ambühl, A. Verkhovsky and I. F. Sbalzarini, "Cell shape transformations: from observations to analysis".
Poster: Arun Shivanandan, Alkeksandra Radenovic, and Ivo F. Sbalzarini, "Super-resolution imaging and image analysis of protein-protein interactions in membranes"


Aug 28-Sep 1, 2011:
International Conference on Systems Biology (ICSB), Mannheim, Germany.
Invited talk: I. F. Sbalzarini, "From images to 3D simulations of cellular dynamics using particles".


Aug 29-30, 2011:
Swiss Fundamental Virology workshop, Thun, Switzerland.
Poster: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, and U. F. Greber, "Adenoviral Infection Spread in Two-Dimensional Cell Arrays Characterized by Hybrid Spatial Dynamics Modeling".


Aug 29, 2011:
National Competence Center on Biomedical Imaging, Annual Meeting, ETH Zurich, Zurich, Switzerland.
Poster: M. E. Ambühl, C. Brepsant, J.-J. Meister, I. F. Sbalzarini, A. B. Verkhovsky, "Cell shape transformation: from observation to analysis".


Jul 8-9, 2011:
5th Workshop on Theory of Randomized Search Heuristics (ThRaSH'2011), Copenhagen, Denmark.
2 Talks: Christian L. Müller, "Evolution Strategies in linearly constrained domains using efficient Gibbs sampling";
Sebastian U. Stich, Christian L. Müller, and Bernd Gärtner, "Random derivative-free optimization of convex functions using a line search oracle".


Jun 23-24, 2011:
Basel Computational Biology Conference (BC2), Basel, Switzerland.
Poster: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, and U. F. Greber, "Adenoviral Infection Spread in Two-Dimensional Cell Arrays Characterized by Hybrid Spatial Dynamics Modeling".


Jun 9-11, 2011:
Workshop on Computational Geometric Learning, Institut Henri Poincare, Paris, France.
Talk: Christian L. Müller, "Variable-metric randomized search heuristics for gradient-free black-box optimization".


May 25-27, 2011:
EVOLVE, workshop on Probability, Set Oriented Numerics, and Evolutionary Computation, Bourglinster Castle, Luxembourg.
Talks and Papers: Grégory Paul, Christian L. Müller, and Ivo F. Sbalzarini, "Sensitivity analysis from evolutionary algorithm search paths";
Christian L. Müller, "Continuous black-box optimization in linearly constrained domains using efficient Gibbs sampling".


May 3-5, 2011:
6th International Symposium on Health Informatics and Bioinformatics, (HIBIT 2011), Izmir, Turkey.
Talk and Paper: Omer Demirel, Birte Schrader, and Ivo F. Sbalzarini, "A parallel particle method for solving the EEG source localization forward problem".


Apr 27-29, 2011:
EvoStar Joint European Conference on Evolutionary Computation, Torino, Italy.
Talk and Paper: C. L. Müller and I. F. Sbalzarini, "Global characterization of the CEC 2005 fitness landscapes using fitness-distance analysis".


Mar 28-30, 2011:
27th European Workshop on Computational Geometry (EuroCG), Morschach, Switzerland.
Talk and Paper: C. L. Müller and I. F. Sbalzarini, "A conjecture about an upper bound of the RMSD between linear chains".


Mar 5-9, 2011:
55th annual meeting of the Biophysical Society, Baltimore, Maryland, USA.
Talk and Abstract: M. E. Ambühl, C. Brepsant, J.-J. Meister, I. F. Sbalzarini, A. B. Verkhovsky, "Cell edge dynamics during polarization".
Abstract published in: Biophysical Journal, vol. 100(3), p. 307a-308a, 2011.
Talk and Abstract: M. F. Fournier, C. Gabella, J.-J. Meister, I. F. Sbalzarini, A. B. Verkhovsky, "Dynamics of Wound Repair in the Lamellipodia".
Abstract published in: Biophysical Journal, vol. 100(3), p. 303a, 2011.
Poster: M. E. Ambühl, C. Brepsant, J.-J. Meister, A. B. Verkhovsky, I. F. Sbalzarini, "Accurate cell outline segmentation and tracking from phase-contrast microscopy images and applications for investigating the mechanism of cell motility".


Jan 27-28, 2011:
USGEB meeting, Union of Swiss Societies for Experimental Biology, Zurich, Switzerland.
Talk: I. F. Sbalzarini, "Image-based Systems Biology: Modeling and Simulation in Image-derived Geometries" (invited).
Poster: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, U. F. Greber, "Spatial dynamics and modeling of viral infection in two-dimensional cell arrays" (Best Poster Award).


2010


Nov 29-30, 2010:
NCCBI meeting of the National Competence Center for Biomedical Imaging, Lausanne, Switzerland.
Talk: M. E. Ambühl, C. Brepsant, J.-J. Meister, A. Verkhovsky and I. F. Sbalzarini, "Cell Edge Dynamics during Polarization".


Sep 30-Oct 1, 2010:
SystemsX.ch PhD Student Retreat, Murten, Switzerland.
Poster: Chiara Gabella, Elena Bertseva, J. Jacques Meister, Ivo F. Sbalzarini and Alexander B. Verkhovsky, ”Plasma membrane tension and actin-dependent protrusion forces in migrating cells”.


Sep 19-25, 2010:
8th International Conference on Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece.
Talk and Paper: R. Ramaswamy and I. F. Sbalzarini, "Efficient simulation of coupled chemical reaction networks using partial-propensity methods"


Sep 13-16, 2010:
8th Euromech Fluid Mechanics Conference (EFMC8), Bad Reichenhall, Germany.
Talk and Paper: B. Schrader, S. Reboux, and I. F. Sbalzarini, "Discretization-Corrected PSE Operators for Particle Methods".


Sep 2-4, 2010:
Molecular Life Science graduate school retreat, Chandolin, Switzerland.
Talk: Ivo F. Sbalzarini, "My Life and Science".


Sep 2-4, 2010:
Life Science Symposium 2010, EPFL, Lausanne, Switzerland.
Poster: M. Ambühl, C. Brepsant, J.-J. Meister, A. Verkhovsky, I. F. Sbalzarini, "Computational method for investigating the mechanisms of cell motility".


Jul 18-23, 2010:
IEEE Congress on Evolutionary Computation (CEC) 2010, Barcelona, Spain.
Talk and Paper: C. L. Müller and I. F. Sbalzarini, “Gaussian Adaptation as a unifying framework for continuous black-box optimization and adaptive Monte Carlo sampling”.


Jun 23-25, 2010:
Basel Computational Biology Conference (BC2), Basel, Switzerland.
Talk: R. Ramaswamy, “A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks” (invited SIB best paper award talk).


Jun 23, 2010:
Swiss Soft Day 2, Conference on soft matter physics, EPFL, Lausanne, Switzerland.
Talk: Chiara Gabella, Elena Bertseva, J. Jacques Meister, Ivo F. Sbalzarini and Alexander B. Verkhovsky, "Plasma membrane tension and actin-dependent protrusion forces in migrating cells"


Jun 20-27, 2010:
International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia.
Poster and Abstract: A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, and U. F. Greber, “Spatial dynamics modeling of viral infection in two-dimensional cell arrays”.


May 9-12, 2010:
Turning Images to Knowledge: Large-Scale 3D Image Annotation, Management and Visualization, Janelia Farm, Howard Hughes Medical Institute, Ashburn (VA), USA.
Invited talk: Ivo F. Sbalzarini, "Including prior knowledge in segmentation and tracking algorithms" (invited).


Apr 7-9, 2010:
EvoStar Joint European Conference on Evolutionary Computation, Istanbul, Turkey.
Talk and Paper: C. L. Müller and I. F. Sbalzarini, “Gaussian adaptation revisited — an entropic view on covariance matrix adaptation”. (Best paper award)


Feb 14-20, 2010:
Studying biomolecules by experiment and theory: a biophysicist's view, Crans Montana, Switzerland.
Poster: M. E. Ambühl, C.Brepsant, J.-J. Meister, A. Verkhovsky, and I. F. Sbalzarini, "Computational method for investigating the mechanisms of cell motility".


2009


Dec 5-9, 2009:
The American Society for Cell Biology Annual Meeting (ASCB), San Diego, USA.
Poster: A. Rauch, J. Cardinale, I. F. Sbalzarini, K. Jaqaman, G. Szekely, Y. Barral, "Dissecting the Mechanism of Nuclear Migration in S. cerevisiae".


Nov 30 - Dec 2, 2009:
International Symposium on Visual Computing (ISVC), Las Vegas, USA.
Talk and Paper: J. A. Helmuth and I. F. Sbalzarini, "Deconvolving active contours for fluorescence microscopy images".


Nov 18, 2009:
All-SystemsX.ch day, Bern, Switzerland.
Poster: R. Ramaswamy and I. F. Sbalzarini, “A new class of highly effi-cient exact stochastic simulation algorithms for chemical reaction net-works”.


Oct 19-20, 2009:
3rd Workshop on Theory of Randomized Search Heuristics (TRSH), Birmingham, UK.
Talk: C. L. Müller and I. F. Sbalzarini, "Gaussian Adaptation revisited - an entropic view on Covariance Matrix Adaptation".


Oct 5-7, 2009:
International Conference on Evolutionary Computation (ICEC), Funchal, Madeira (Portugal).
Talk and Paper: C. L. Müller and I. F. Sbalzarini, "A tunable real-world multi-funnel benchmark problem for evolutionary optimization (and why parallel island models might remedy the failure of CMA-ES on it)".


Sep 7-9, 2009:
CCP5 Conference on Structure Prediction, London, UK.
Talk: C. L. Müller, G. Ofenbeck, and I. F. Sbalzarini, "Searching potential energy surfaces with the Covariance Matrix Adaptation Evolution Strategy".


Aug 2-9, 2009:
FEBS Course on Computational Biology, Split, Croatia.
Poster: M. E. Ambuhl, A. B. Verkhovsky, and I. F. Sbalzarini, "Computational methods for investigating the mechanism of cell motility".


Jul 8-12, 2009:
ACM Genetic and Evolutionary Computing Conference (GECCO) 2009, Montréal, Canada.
Talk and Paper: C. L. Müller, B. Baumgartner, G. Ofenbeck, B. Schrader, and I. F. Sbalzarini, “pCMALib: a Parallel FORTRAN 90 Library for the Evolution Strategy with Covariance Matrix Adaptation”.


Jun 27-Jul 1, 2009:
IEEE International Symposium on Biomedical Imaging (ISBI) 2009, Boston, USA.
Poster and Paper: J. Cardinale, A. Rauch, Y. Barral, G. Székely, and I. F. Sbalzarini, “Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking”.


Jun 23-26, 2009:
CECAM workshop on Computational Systems Biology, Lausanne, Switzerland.
Invited talk: I. F. Sbalzarini, “A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks” (invited).


May 18-21, 2009:
IEEE Congress on Evolutionary Computation (CEC) 2009, Trondheim, Norway.
Talk and Paper: C. L. Müller, B. Baumgartner, and I. F. Sbalzarini, “Particle swarm CMA evolution strategy for the optimization of multi-funnel landscapes”.


Apr 5-9, 2009:
International Conference on Information Processing in Cells and Tissues (IPCAT) 2009, Locarno, Switzerland.
Poster: Oliwia Szklarczyk, Nélido González-Segredo, Helge Ewers & Ivo F. Sbalzarini, “Binding dynamics of SV40 virus capsids to GM1 glycolipid-receptor membranes”.


Apr 5-8, 2009:
BioImage Informatics Conference, Janelia Farm, Howard Hughes Medical Institute, Ashburn (VA), USA.
Invited talk: Ivo F. Sbalzarini, “Reconstruction and characterization of the shapes and dynamics of sub-cellular structures in live cells” (invited).


Feb 2 - 3, 2009:
Swiss Institute of Bioinformatics Scientific Meeting. Fribourg, Switzerland.
5 Posters: Christian L. Müller, Benedikt Baumgartner & Ivo F. Sbalzarini, “Particle Swarm CMA Evolution Strategy for the Optimization of Multi-Funnel Landscapes”;
Janick Cardinale, Alex Rauch, Yves Barral, Gabor Szekely & Ivo F. Sbalzarini, “Bayesian image analysis for tracking of astral microtubules with confidence estimation”;
Rajesh Ramaswamy, Nélido González-Segredo, Ruth Kroschewski & Ivo F. Sbalzarini, “A biophysical model describing the growth dynamics and size distribution of protein domains in biological membranes”;
Jo A. Helmuth, Gregory Paul & Ivo F. Sbalzarini, “Using spatial point patterns to extend colocalization analysis to interaction analysis”;
Nélido González-Segredo, Regula Gehrig & Ivo F. Sbalzarini, “Role of lipid composition on the hydration barrier to mixed-lipid-membrane fusion”.


2008


Nov 25 - 27, 2008:
Joint Scottish-Swiss Forum for Bioinformatics, Edinburgh, UK.
Invited talk: Ivo F. Sbalzarini, "Spatiotemporal Modelling and Simulation in Biology" (invited).


Oct 27 - 30, 2008:
5th international congress of Nano-Bio & Clean Tech, San Francisco, USA.
Talk and Abstract: H. A. Zambrano, J. H. Walther, P. Koumoutsakos & I. F. Sbalzarini, "Atomistic simulations of thermophoresis in carbon nanotubes".


Oct 16 - 17, 2008:
21st Nordic Seminar on Computational Mechanics, Trondheim, Norway.
Talk and Paper: H. A. Zambrano, J. H. Walther, P. Koumoutsakos & I. F. Sbalzarini, "Atomistic simulations of thermophoretic motion of water nanodroplets in carbon nanotubes".


Oct 16, 2008:
All SystemsX.ch day, Basel, Switzerland.
Poster: Rajesh Ramaswamy, Nélido González-Segredo, Ruth Kroschewski & Ivo F. Sbalzarini, "A biophysical model describing the growth dynamics and size distribution of protein domains in biological membranes" (Best poster award).


Sep 08 - 10, 2008:
CCP5 Annual Meeting, Surfaces and Interfaces, London, UK.
Talk: Nélido González-Segredo, "A molecular dynamics study of supercooled Newton black films".


Jul 27 - Aug 01, 2008:
Water and Aqueous Solutions Gordon Research Conference, New Hampshire, USA.
Poster presentation: Nélido González-Segredo, "A molecular dynamics study of supercooled biological water".


Jul 26, 2008:
pre-Gordon Conference Water Meeting 2008, Centre for Polymer Studies, Boston University, USA.
Invited talk: Nélido González-Segredo, "A supercooled perspective of the hydration force between biological surfaces" (invited).


Jun 2 - 4, 2008:
D-BIOL Symposium, Davos, Switzerland.
Invited talk: Ivo F. Sbalzarini, “Automated analysis and large-scale computer simulations of dynamic processes in biology” (invited).
Poster: Rajesh Ramaswamy, Nelido Gonzalez-Segredo, Ruth Kroschewski & Ivo F. Sbalzarini, “A model to describe the growth kinetics and distribution of multimeric protein domains on plasma membranes: Towards biophysical understanding of the establishment of the preapical patch during lumen formation in MDCK cells.”


May 27 - 30, 2008:
European Light Microscopy Conference (ELMI08), Davos, Switzerland.
Invited talk: Ivo F. Sbalzarini, “Nanometer-precision computational reconstruction of sub-cellular shapes in live cell light microscopy” (invited).


April 5, 2008:
Scientific Advisory Board Meeting, Mediterranean Institute for Life Sciences, Split, Croatia.
Poster: Nela Nikolic, Zlatko Smole, Ivo F. Sbalzarini & Anita Krisko, “Bringing Science to Society”
Poster: Nela Nikolic, Zlatko Smole, Ivo F. Sbalzarini & Anita Krisko, “Adaptation of prokaryotic proteomes to different lifestyles”


Mar 10-12, 2008:
12th Sandia, Oak Ridge, Switzerland conference on supercomputing (SOS12), Wildhaus, Switzerland.
Session chair: Ivo F. Sbalzarini, “What new science due to peta/exaflops?”.


2007


Sept 24 - 25, 2007:
Swiss Institute of Bioinformatics Scientific Meeting, Grindelwald, Switzerland.
Talk: Ivo F. Sbalzarini, "Computational Biophysics"
Poster: Christian L. Müller, Grégory Paul & Ivo F. Sbalzarini, "Sensitivities for free: CMA-ES based Sensitivity Analysis".


Sept 17, 2007:
SystemsX meeting, Lausanne, Switzerland.
Poster: Maren Vens, Alexey Veligodskiy, Ivo F. Sbalzarini & Ruth Kroschewski, "A model to predict maturity and morphological changes during epithelial cyst development".


Sept 4 - 9, 2007:
2nd Opatija Meeting On Computational Solutions in the Life Sciences, Opatija, Croatia.
Poster: Zlatko Smole, Nela Nikolić, Ivo F. Sbalzarini & Anita Kriško, "Adaptation to extreme environments - looking for the proteome patterns".


Aug 27 - 29, 2007:
International Conference on Discrete Element Methods (DEM07), Brisbane, Australia.
Talk: Jens H. Walther & Ivo F. Sbalzarini, "Large-scale Parallel Discrete Element Simulations of Granular Flow".


Jun 27 - 30, 2007:
The American Society for Cell Biology Summer Meeting (ASCB-ECF), Dijon, France.
Talk: C. J. Burckhardt, P. Schönenberger, J. A. Helmuth, P. Koumoutsakos, I. F. Sbalzarini, U. F. Greber, "Computational Dissection of Adenovirus Cell Surface Motion Reveals Receptor Mediated Virus Drifting on Filopodia".


Jun 18 - 22, 2007:
Fifth International Conference on Sensitivity Analysis of Model Output (SAMO07), Eötvös University (ELTE), Budapest, Hungary.
Poster: Christian L. Müller, Grégory Paul & Ivo F. Sbalzarini, "Sensitivities for free: CMA-ES based Sensitivity Analysis".


Jun 11 - 14, 2007:
11th Sandia, Oak Ridge, Switzerland Conference on Supercomputing (SOS11), Key West, Florida, USA.
Talk: Ivo F. Sbalzarini, "Software Chellenges for Petaflop Computing". (invited).


Mar 13 - 14, 2007:
Basel Computational Biology Conference (BC2), Basel, Switzerland.
Talk: C. Burckhardt, P. Schönenberger, J. A. Helmuth, H. Ewers, P. Koumoutsakos, I. F. Sbalzarini & U. F. Greber, "Computational dissection of adenovirus cell surface motion reveals receptor mediated virus drifting on filopodia".


2006


Dec 9-13, 2006:
46th annual meeting of the American Society for Cell Biology (ASCB), San Diego, California, USA.
Poster: C. J. Burckhardt, I. F. Sbalzarini, J. A. Helmuth, H. Ewers, P. Koumoutsakos, U. F. Greber, "Computational Dissection of Adenovirus Motion on the Cell Surface".


Oct 5, 2006:
50th anniversary of the Institute of Biochemistry at ETH Zurich.
Poster: Ivo F. Sbalzarini, Jo Helmuth, Christoph Burckhardt, Urs Greber & Petros Koumoutsakos, "Single-Particle Tracking and Automated Trajectory Analysis from Image Data".


Aug 29 - Sept 1, 2006:
European Conference on Parallel Computing (Euro-Par). Dresden, Germany.
Talk: Ivo F. Sbalzarini, “A software framework for portable parallelization of particle-mesh simulations”.


2004


Oct 9-13, 2004:
5th International Conference on Systems Biology (ICSB). Heidelberg, Germany.


2003


Nov 5-9, 2003:
4th International Conference on Systems Biology (ICSB). Washington
University, St. Louis, USA.
Posters: Ivo F. Sbalzarini, Cosima Luedeke & Yves Barral, “Model-based quantitative evaluation of FLIP experiments in budding Yeast”,
Ivo F. Sbalzarini, Anna Mezzacasa, Ari Helenius & Petros Koumoutsakos, “Measuring Diffusion in Intracellular Compartments: Computer Simulations reveal Influence of Organelle Geometry”.


Organizer of workshop #2: Large scale simulations of biological systems (9 speakers).
Talk: Ivo F. Sbalzarini, “Automated virus trajectory acquisition”.


Sept 20-24, 2003:
European Life Scientists Organization (ELSO) Meeting. Dresden, Germany.


Organizer of sub-group meeting #8: Computational Science in Cell Biology (7 speakers).
Talk: Ivo F. Sbalzarini, “Automated virus trajectory acquisition”.


March 18, 2003:
Joining Forces: Intersections between Biology, Chemistry, Engineering and Informatics. ETH Zurich, Switzerland.
Talk: Ivo F. Sbalzarini, “Automated virus trajectory acquisition and classification”.


2002


Dec 11-15, 2002:
3rd International Conference on Systems Biology (ICSB). Karolinska Institutet, Stockholm, Sweden.


June 29–July 7, 2002:
European Life Scientists Organization (ELSO) Meeting. Nice, France. Poster: Ivo F. Sbalzarini, Anna Mezzacasa, Ari Helenius, Petros Koumoutsakos, “Diffusion in the Endoplasmic Reticulum – Computer Simulations and Models”.