Research Groups

2018

Alejandro Vignoni, Anna Bajur, Elisabeth Knust, Ivo F. Sbalzarini
Multi-objective identification from fluorescence recovery after photobleaching experiments: Understanding morphogenetic regulation of epithelial polarity
IFAC-PapersOnLine, 51(19) 8-11 (2018)
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Ivo F. Sbalzarini, Urs F Greber
How Computational Models Enable Mechanistic Insights into Virus Infection.
Methods Mol Biol, 1836 609-631 (2018)
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Michael Hecht, Ivo F. Sbalzarini
Fast interpolation and Fourier transform in high-dimensional spaces
In: Intelligent Computing, Proc. 2018 IEEE Computing Conf., Vol. 2 (2018) Advances in Intelligent Systems and Computing, Dordrecht, Springer (2018), 53-75
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Sven Karol, Tobias Nett, Jeronimo Castrillon, Ivo F. Sbalzarini
A domain-specific language and editor for parallel particle methods
ACM Trans Math Softw, 44(3) Art. No. 34 (2018)

2017

Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini
pSSAlib: The partial-propensity stochastic chemical network simulator.
PLoS Comput Biol, 13(12) Art. No. e1005865 (2017)
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Bevan Cheeseman
The Adaptive Particle Representation (APR) for Simple and Efficient Adaptive Resolution Processing, Storage and Simulations
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2017)
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Yadira Boada, Alejandro Vignoni, Jesús Picó
Multi-objective optimization for gene expression noise reduction in a synthetic gene circuit
IFAC-PapersOnLine, 50(1) 4472-4477 (2017)
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Yadira Boada, Alejandro Vignoni, Jesús Picó
Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise.
ACS Synth Biol, 6(10) 1903-1912 (2017)
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Maj Svea Grieb, Aleksandra Nivina, Bevan Cheeseman, Andreas Hartmann, Didier Mazel, Michael Schlierf
Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality.
Nucleic Acids Res, 45(18) 10555-10563 (2017)
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Karl Hoffmann, Anja Voss-Böhme, Jochen Rink, Lutz Brusch
A dynamically diluted alignment model reveals the impact of cell turnover on the plasticity of tissue polarity patterns.
J R Soc Interface, 14(135) Art. No. 20170466 (2017)
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Sven Karol, Tobias Nett, Pietro Incardona, Nesrine Khouzami, Jeronimo Castrillon, Ivo F. Sbalzarini
A Language and Development Environment for Parallel Particle Methods
In: V. International Conference on Particle-based Methods : Fundamentals and Applications ; PARTICLES 2017 (2017)(Eds.) Peter Wriggers, Barcelona, International Center for Numerical Methods in Engineering (CIMNE) (2017), 564-575
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Josefine Asmus, Christian L Müller, Ivo F. Sbalzarini
Lp-Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems.
Sci Rep, 7(1) Art. No. 6660 (2017)
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Yadira Boada, Alejandro Vignoni, Jesús Picó
Multi-objective identification of synthetic circuits stochastic models using flow flcytometry data
In: 2017 25TH MEDITERRANEAN CONFERENCE ON CONTROL AND AUTOMATION (MED) : July 3-6, 2017, University of Malta, Valetta Campus, Malta (2017) Mediterranean Conference on Control and Automation, Piscataway, N.J., IEEE (2017), 1077-1082
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Gerald Hempel, Goens Andres, Josefine Asmus, Jeronimo Castrillon, Ivo F. Sbalzarini
Robust Mapping of Process Networks to Many-Core Systems Using Bio-Inspired Design Centering
In: Proceedings of the 20th International Workshop on Software and Compilers for Embedded Systems - SCOPES '17 (2017)(Eds.) Sander Stuijk , New York, ACM (2017), 21-30
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Yuanhao Gong, Ivo F. Sbalzarini
Curvature Filters Efficiently Reduce Certain Variational Energies.
IEEE Trans Image Process, 26(4) 1786-1798 (2017)
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Kirstin Meyer, Oleksandr Ostrenko, George Bourantas, Hernán Morales-Navarrete, Natalie Porat-Shliom, Fabián Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo F. Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial
A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.
Cell Syst, 4(3) 277-290 (2017)
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Donald F Newgreen, Dongcheng Zhang, Bevan Cheeseman, Benjamin J Binder, Kerry A Landman
Differential Clonal Expansion in an Invading Cell Population: Clonal Advantage or Dumb Luck?
Cells Tissues Organs , 203(2) 105-113 (2017)
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Josefine Asmus
An efficient randomized approximation algorithm for volume estimation and design centering
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2017)

2016

Yadira Boada, Alejandro Vignoni, Gilberto Reynoso-Meza, Jesús Picó
Parameter identification in synthetic biological circuits using multi-objective optimization
IFAC-PapersOnLine, 49(26) 77-82 (2016)
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Enric Picó-Marco, Yadira Boada, Jesús Picó, Alejandro Vignoni
Contractivity of a genetic circuit with internal feedback and cell-to-cell communication
IFAC-PapersOnLine, 49(26) 213-218 (2016)
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Yaser Afshar
Parallel distributed-memory particle methods for acquisition-rate segmentation and uncertainty quantifications of large fluorescence microscopy images.
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2016)
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George Bourantas, Bevan Cheeseman, Rajesh Ramaswamy, Ivo F. Sbalzarini
Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries
Computers & Fluids, 136 285-300 (2016)
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Ivo F. Sbalzarini
Seeing Is Believing: Quantifying Is Convincing: Computational Image Analysis in Biology
In: Focus on Bio-Image Informatics. (Eds.) Winnok, H. De Vos (Advances in Anatomy, Embryology and Cell Biology ; 219).,Cham,Springer International Publishing (2016),1-39 Ch. 1
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Janko Kajtez, Anastasia Solomatina, Maja Novak, Bruno Polak, Kruno Vukušić, Jonas Rüdiger, Gheorghe Cojoc, Ana Milas, Ivana Šumanovac Šestak, Patrik Risteski, Federica Tavano, Anna Klemm, Emanuele Roscioli, Julie Welburn, Daniela Cimini, Matko Glunčić, Nenad Pavin, Iva M Tolić
Overlap microtubules link sister k-fibres and balance the forces on bi-oriented kinetochores.
Nat Commun, 7 Art. No. 10298 (2016)
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Yadira Boada, José Luis Pitarch, Alejandro Vignoni, Gilberto Reynoso-Meza, Jesús Picó
Optimization Alternatives for Robust Model-based Design of Synthetic Biological Circuits
IFAC-PapersOnLine, 49(7) 821-826 (2016)
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Franck Raynaud, Mark E. Ambühl, Chiara Gabella, Alicia Bornert, Ivo F. Sbalzarini, J-J Meister, A B Verkhovsky
Minimal model for spontaneous cell polarization and edge activity in oscillating, rotating and migrating cells
Nat Phys, 12 367-373 (2016)
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Artur Yakimovich, Yauhen Yakimovich, Michael Schmid, Jason Mercer, Ivo F. Sbalzarini, Urs F Greber
Infectio: a Generic Framework for Computational Simulation of Virus Transmission between Cells.
mSphere, 1(1) Art. No. e00078-15 (2016)
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Xun Xiao, Veikko Geyer, Hugo Bowne-Anderson, Jonathon Howard, Ivo F. Sbalzarini
Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets
Med Image Anal, 32 157-172 (2016)
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Yaser Afshar, Ivo F. Sbalzarini
A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images
PLoS ONE, 11(4) Art. No. e0152528 (2016)
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Yuanhao Gong, Ivo F. Sbalzarini
A Natural-Scene Gradient Distribution Prior and its Application in Light-Microscopy Image Processing
IEEE J Sel Top Signal Process, 10(1) 99-114 (2016)

2015

Sven Karol, Pietro Incardona, Yaser Afshar, Ivo F. Sbalzarini, Jeronimo Castrillon
Towards a Next-Generation Parallel Particle-Mesh Language.
In: Proceedings of the 3rd Workshop on Domain-Specific Language Design and Implementation DSLDI’15 at 29th European Conference on Object-Oriented Programming (ECOOP 2015), Prague, Czech Republic, July 7, 2015 (2015)(Eds.) Sebastian Erdweg, Tijs van der Storm, Cornell University Library, arXiv (2015)
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Loic Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W Myers
ClearVolume: open-source live 3D visualization for light-sheet microscopy.
Nat Methods, 12(6) 480-481 (2015)
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Yuanhao Gong, Ivo F. Sbalzarini
Image Enhancement by Gradient Distribution Specification
In: Proceedings ACCV, 12th Asian Conference on Computer Vision, Workshop on Emerging Topics in Image Enhancement and Restoration (2015) Lecture Notes in Computer Science, New York, Springer (2015), 47-62
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Yuanhao Gong
Spectrally Regularized Surfaces
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2015)
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Christoph Häcki, Sylvain Reboux, Ivo F. Sbalzarini
A Self-Organizing Adaptive-Resolution Particle Methods with Anisotropic Kernels
Proc IUTAM, 18 40-55 (2015)
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Rajesh Ramaswamy, George Bourantas, Frank Jülicher, Ivo F. Sbalzarini
A hybrid particle-mesh method for incompressible active polar viscous gels
J Comput Phys, 291 334-361 (2015)

2014

Ömer Demirel, Ihor Smal, Wiro J. Niessen, Erik Meijering, Ivo F. Sbalzarini
An adaptive distributed resampling algorithm with non-proportional allocation
In: IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP) : Florence, Italy, 4-9 May 2014 (2014), Piscataway, N.J., IEEE (2014), 1635-1639
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Aurelien Rizk, Gregory Paul, Pietro Incardona, Milica Bugarski, Maysam Mansouri, Axel Niemann, Urs Ziegler, Philipp Berger, Ivo F. Sbalzarini
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.
Nat Protoc, 9(3) 586-596 (2014)
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Josefine Asmus, Daniel Borchmann, Ivo F. Sbalzarini, Dirk Walther
Towards an FCA-based Recommender System for Black-Box Optimization
In: Proceedings of the 3rd International Workshop "What can FCA do for Artificial Intelligence"? co-located with the European Conference on Artificial Intelligence (ECAI 2014) Prague, Czech Republic, August 19, 2014 (2014), Aachen, CEUR Workshop Proceedings (2014), 35-42
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Christian Bläsche
Setting Young’s modulus in the subcellular element model
Diploma Thesis,Technische Universität Dresden, Dresden, Germany (2014)
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Nicolas Chenouard, Ihor Smal, Fabrice de Chaumont, Martin Maška, Ivo F. Sbalzarini, Yuanhao Gong, Janick Cardinale, Craig Carthel, Stefano Coraluppi, Mark Winter, Andrew R Cohen, William J. Godinez, Karl Rohr, Yannis Kalaidzidis, Liang Liang, James Duncan, Hongying Shen, Yingke Xu, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Perrine Paul-Gilloteaux, Philippe Roudot, Charles Kervrann, Francois Waharte, Jean-Yves Tinevez, Spencer L Shorte, Joost Willemse, Katherine Celler, Gilles P van Wezel, Han-Wei Dan, Yuh-Show Tsai, Carlos Ortiz de Solórzano, Jean-Christophe Olivo-Marin, Erik Meijering
Objective comparison of particle tracking methods.
Nat Methods, 11(3) 281-289 (2014)
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Ömer Demirel
Dynamic Load Balancing in Parallel Particle Methods
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2014)
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Chiara Gabella, Elena Bertseva, Céline Bottier, Niccolo Piacentini, Alicia Bornert, Sylvia Jeney, Laszlo Forro, Ivo F. Sbalzarini, J-J Meister, A B Verkhovsky
Contact Angle at the Leading Edge Controls Cell Protrusion Rate
Curr Biol, 24(10) 1126-1132 (2014)
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Fabian Multrus
Calculation of the Electric Potential for a Neuronal Activity Model in the Brain
Diploma Thesis,Technische Universität Dresden, Dresden, Germany (2014)
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Omar Awile, Ivo F. Sbalzarini
A pthreads wrapper for Fortran 2003
ACM Trans Math Softw, 40(3) Art. No. 19 (2014)
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Yuri K. Shestopaloff, Ivo F. Sbalzarini
A method for modeling growth of organs and transplants based on the general growth law: application to the liver in dogs and humans.
PLoS ONE, 9(6) Art. No. e99275 (2014)

2013

Ivo F. Sbalzarini
Modeling and simulation of biological systems from image data.
Bioessays, 35(5) 482-490 (2013)
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Ferit Büyükkeçeci, Omar Awile, Ivo F. Sbalzarini
A portable OpenCL implementation of generic particle-mesh and mesh-particle interpolation 2D and 3D
Parallel Comput, 39(2) 94-111 (2013)
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Janick Cardinale
Unsupervised Segmentation and Shape Posterior Estimation under Bayesian Image Models
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2013)
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Oliwia M. Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F. Sbalzarini, Helge Ewers
Receptor Concentration and Diffusivity Control Multivalent Binding of SV40 to Membrane Bilayers
PLoS Comput Biol, 9(11) Art. No. e1003310 (2013)
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Katharina Philipp
Piecewise smooth deconvolving segmentation
Diploma Thesis,Technische Universität Dresden, Dresden, Germany (2013)
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Ali Ghaemi
Numerical simulations of bile flow in realistic image-derived bile canalicular geometries
Diploma Thesis,Technische Universität Dresden, Dresden, Germany (2013)
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Arun Shivanandan, Aleksandra Radenovic, Ivo F. Sbalzarini
MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis
BMC Bioinformatics, 14 Art. No. 349 (2013)
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Yuanhao Gong, Ivo F. Sbalzarini
Local weighted Gaussian curvature for image processing
In: 2013 IEEE International Conference on Image Processing (ICIP 2013) : Melbourne, Australia, 15 - 18 September (2013), Piscataway, N.J., IEEE (2013), 534-538
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Gregory Paul, Janick Cardinale, Ivo F. Sbalzarini
Coupling Image Restoration and Segmentation: A Generalized Linear Model/Bregman Perspective
Int J Comput Vis, 104(1) 69-93 (2013)
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Nicolas Fietier, Ömer Demirel, Ivo F. Sbalzarini
A meshless particle method for Poisson and diffusion problems with discontinuous coefficients and inhomogeneous boundary conditions
SIAM J Sci Comput, 35(6) 2469-2493 (2013)
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Omar Awile, Milan Mitrovic, Sylvain Reboux, Ivo F. Sbalzarini
A domain-specific programming language for particle simulations on distributed-memory parallel computers
In: Particle-based methods III : fundamentals and applications ; proceedings of the III International Conference on Particle-Based Methods, Fundamentals and Applications (Particles 2013), Stuttgart, 18 - 20 September (2013), Barcelona, International Center for Numerical Methods in Engineering (CIMNE) (2013), 436-447
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Omar Awile
A Domain-Specific Language and Scalable Middleware for Particle-Mesh Simulations on Heterogeneous Parallel Computers
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2013)

2012

Artur Yakimovich, Heidi Gumpert, C J Burckhardt, Verena A Lütschg, Andreas Jurgeit, Ivo F. Sbalzarini, U F Greber
Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model.
J Virol, 86(18) 10123-10137 (2012)
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Janick Cardinale, Gregory Paul, Ivo F. Sbalzarini
Discrete region competition for unknown numbers of connected regions
IEEE Trans Image Process, 21(8) 3531-3545 (2012)
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Ivo F. Sbalzarini
Active flows cluster cell surface proteins.
Dev Cell, 22(6) 1121-1122 (2012)
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Sylvain Reboux, Birte Schrader, Ivo F. Sbalzarini
A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations
J Comput Phys, 231(9) 3623-3646 (2012)
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Mark E. Ambühl, C Brepsant, J-J Meister, A B Verkhovsky, Ivo F. Sbalzarini
High-resolution cell outline segmentation and tracking from phase-contrast microscopy images.
J Microsc, 245(2) 161-170 (2012)
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Sebastian Stich, Christian L. Müller
On spectral invariance of Randomized Hessian and Covariance Matrix Adaptation Schemes
In: Proc. Parallel Problem Solving From Nature (PPSN) (2012) Lecture Notes in Computer Science, Berlin;Heidelberg, Springer (2012), 1-1
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Christian L. Müller, Rajesh Ramaswamy, Ivo F. Sbalzarini
Global parameter identification of stochastic reaction networks from single trajectories.
Adv Exp Med Biol, 736 477-498 (2012)
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Omar Awile, Ferit Büyükkeçeci, Sylvain Reboux, Ivo F. Sbalzarini
Fast neighbor lists for adaptive-resolution particle simulations
Comput Phys Commun, 183(5) 1073-1081 (2012)
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Christian L. Müller, Ivo F. Sbalzarini
Energy landscapes of atomic clusters as black box optimization benchmarks.
Evol Comput, 20(4) 543-573 (2012)
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Rajesh Ramaswamy, Nélido González-Segredo, Ivo F. Sbalzarini, Ramon Grima
Discreteness-induced concentration inversion in mesoscopic chemical systems
Nat Commun, 3 Art. No. 779 (2012)
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Yuanhao Gong, Gregory Paul, Ivo F. Sbalzarini
Coupled signed-distance functions for implicit surface reconstruction
In: Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI) (2012), Piscataway, N.J., IEEE (2012), 1000-1003
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Birte Schrader, Sylvain Reboux, Ivo F. Sbalzarini
Choosing the best kernel: performance models for diffusion operators in particle methods
SIAM J Sci Comput, 34(3) 1607-1634 (2012)

2011

Jo A. Helmuth, Sylvain Reboux, Ivo F. Sbalzarini
Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors
J Comput Sci, 2(4) 324-334 (2011)
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Rajesh Ramaswamy, Ivo F. Sbalzarini
Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods
J Chem Phys, 135(24) Art. No. 244103 (2011)
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Céline Bottier, Chiara Gabella, Benoît Vianay, Lara Buscemi, Ivo F. Sbalzarini, J-J Meister, A B Verkhovsky
Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique.
Lab on a chip, 11(22) 3855-3863 (2011)
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Yohei Yamauchi, Heithem Boukari, Indranil Banerjee, Ivo F. Sbalzarini, Peter Horvath, Ari Helenius
Histone deacetylase 8 is required for centrosome cohesion and influenza A virus entry
PLoS Pathog, 7(10) 1002316-1002316 (2011)
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Gregory Paul, Christian L. Müller, Ivo F. Sbalzarini
Sensitivity analysis from evolutionary algorithm search paths
In: Proc. EVOLVE (2011), Luxembourg, EVOLVE (2011), 1-4
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Zlatko Smole, Nela Nikolic, Fran Supek, Tomislav Šmuc, Ivo F. Sbalzarini, Anita Krisko
Proteome sequence features carry signatures of the environmental niche of prokaryotes.
BMC Evol Biol, 11 26-26 (2011)
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Rajesh Ramaswamy
Partial-propensity simulation algorithms for stochastic chemical kinetics and the role of fluctuations in mesoscopic reaction systems
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2011)
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Rajesh Ramaswamy, Ivo F. Sbalzarini, Nélido González-Segredo
Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks
PLoS ONE, 6(1) Art. No. e16045 (2011)
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Rajesh Ramaswamy, Ivo F. Sbalzarini
Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems
Sci Rep, 1 Art. No. 154 (2011)
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Christian L. Müller, Ivo F. Sbalzarini
Global characterization of the CEC 2005 fitness landscapes using fitness-distance analysis
In: Proc. EvoStar (2011) Leture Notes in Computer Science, New York, Springer (2011), 294-303
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Christian L. Müller, Ivo F. Sbalzarini
Gaussian Adaptation for robust design centering
In: Proc. EuroGen (2011), Italy, CIRA (2011), 736-742
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Birte Schrader
Discretization-Corrected PSE Operators for Adaptive Multiresolution Particle Methods
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2011)
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Christian L. Müller
Continuous black-box optimization in linearly constrained domains using efficient Gibbs sampling
In: Proc. EVOLVE (2011), Luxembourg, EVOLVE (2011), 1-4
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Rajesh Ramaswamy, Ivo F. Sbalzarini
A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays
J Chem Phys, 134(1) Art. No. 014106 (2011)
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Ömer Demirel, Birte Schrader, Ivo F. Sbalzarini
A parallel particle method for solving the EEG source localization forward problem
In: Proc. 6th Intl. Symp. Health Informatics and Bioinformatics (HIBIT) (2011), Piscataway, N.J., IEEE (2011), 154-158
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Gregory Paul, Janick Cardinale, Ivo F. Sbalzarini
An alternating split Bregman algorithm for multi-region segmentation
In: Proc. 45th IEEE Asilomar Conf. Signals, Systems, and Computers (2011), Piscataway, N.J., IEEE (2011), 426-430
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Christian L. Müller, Ivo F. Sbalzarini
A conjecture about an upper bound of the RMSD between linear chains
In: Proc. EuroCG (2011), Brussels, EuroCG (2011), 31-34

2010

M. Bergdorf, Ivo F. Sbalzarini, Petros Koumoutsakos
A Lagrangian particle method for reaction-diffusion systems on deforming surfaces.
J Math Biol, 61(5) 649-663 (2010)
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Omar Awile, Ömer Demirel, Ivo F. Sbalzarini
Toward an Object-Oriented Core of the PPM Library
In: Numerical Analysis and Applied Mathematics : International Conference on Numerical Analysis and Applied Mathematics ; Rhodes, Greece, 19 - 25 September 2010 ; ICNAAM 2010 (2010)(Eds.) Theodore E. Simos AIP conference proceedings ; 1281, Melville, N.Y., AIP (2010), 1313-1316
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Omar Awile, Anita Krisko, Ivo F. Sbalzarini, Bojan Zagrovic
Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.
PLoS Comput Biol, 6(7) 1000854-1000854 (2010)
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Christian L. Müller, Ivo F. Sbalzarini
Gaussian adaptation revisited — an entropic view on covariance matrix adaptation
In: Proc. EvoStar (2010) Lecture Notes in Computer Science, Berlin;Heidelberg, Springer (2010), 432-441
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Christian L. Müller, Ivo F. Sbalzarini
Gaussian Adaptation as a unifying framework for continuous black-box optimization and adaptive Monte Carlo sampling
In: Proc. IEEE Congress on Evolutionary Computation (CEC) (2010), Piscataway, N.J., IEEE (2010), 2594-2601
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Rajesh Ramaswamy, Ivo F. Sbalzarini
Fast exact stochastic simulation algorithms using partial propensities
In: Proc. ICNAAM (2010), Melville, N.Y., AIP (2010), 1338-1341
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Birte Schrader, Sylvain Reboux, Ivo F. Sbalzarini
Discretization correction of general integral PSE Operators for particle methods
J Comput Phys, 229 4159-4182 (2010)
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Birte Schrader, Sylvain Reboux, Ivo F. Sbalzarini
Discretization-Corrected PSE Operators for Particle Methods
In: Proc. 8th Euromech Fluid Mechanics Conference (EFMC8) (2010), EuroMech EFMC (2010), 1-1
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Jo A. Helmuth
Computational Methods for Analyzing and Simulating Intra-Cellular Transport Processes
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2010)
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Christian L. Müller
Black-box Landscapes: Characterization, Optimization, Sampling, and Application to Geometric Configuration Problems
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2010)
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Jo A. Helmuth, Gregory Paul, Ivo F. Sbalzarini
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images
BMC Bioinformatics, 11 Art. No. 372 (2010)
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Rajesh Ramaswamy, Ivo F. Sbalzarini
A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks
J Chem Phys, 132(4) Art. No. 044102 (2010)
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Anton A. Polyansky, Rajesh Ramaswamy, Pavel E. Volynsky, Ivo F. Sbalzarini, Siewert J. Marrink, Roman G. Efremov
Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane
J Phys Chem Lett, 1 3108-3111 (2010)
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Ivo F. Sbalzarini
Abstractions and middleware for petascale computing and beyond
Intl J Dist Sys & Technol, 1(2) 40-56 (2010)

2009

Jo A. Helmuth, C J Burckhardt, U F Greber, Ivo F. Sbalzarini
Shape reconstruction of subcellular structures from live cell fluorescence microscopy images
J Struct Biol, 167(1) 1-10 (2009)
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Christian L. Müller, Ivo F. Sbalzarini, Wilfred F van Gunsteren, Bojan Zagrović, Philippe H Hünenberger
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble
J Chem Phys, 130(21) Art. No. 214904 (2009)
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Rajesh Ramaswamy, Nélido González-Segredo, Ivo F. Sbalzarini
A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks
J Chem Phys, 130(24) Art. No. 244104 (2009)
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Harvey A Zambrano, Jens H. Walther, Petros Koumoutsakos, Ivo F. Sbalzarini
Thermophoretic motion of water nanodroplets confined inside carbon nanotubes.
Nano Lett, 9(1) 66-71 (2009)
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Ivo F. Sbalzarini
Spatiotemporal Modeling and Simulation in Biology
In: Bioinformatics.,Hackensack, USA,World Scientific (2009),381-432 Ch. 14
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Christian L. Müller, Benedikt Baumgartner, Georg Ofenbeck, Birte Schrader, Ivo F. Sbalzarini
pCMALib: a parallel FORTRAN 90 library for the evolution strategy with covariance matrix adaptation
In: Proc. ACM Genetic and Evolutionary Computation Conference (GECCO’09) (2009), New York, ACM (2009), 1-8
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Christian L. Müller, Benedikt Baumgartner, Ivo F. Sbalzarini
Particle Swarm CMA Evolution Strategy for the Optimization of Multi-Funnel Landscapes
In: IEEE Congress on Evolutionary Computation : CEC 2009 ; Trondheim, Norway, 18 - 21 May 2009 (2009), Piscataway, N.J., IEEE (2009), 2685-2692
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Jens H. Walther, Ivo F. Sbalzarini
Large-scale parallel discrete element simulations of granular flows
Eng Comput, 26(6) 688-697 (2009)
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Jo A. Helmuth, Ivo F. Sbalzarini
Deconvolving Active Contours for Fluorescence Microscopy Images
In: Advances in Visual Computing : 5th International Symposium Visual Computing ISVC 2009, Las Vegas, NV; USA, Nov. 30-Dec. 02, 2009 ; Poceedings, Part 1 (2009)(Eds.) George Bebis Lecture Notes in Computer Science ; 5875, Berlin;Heidelberg, Springer (2009), 544-553
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Jo A. Helmuth, Ivo F. Sbalzarini
Deconvolving active contours for fluorescence microscopy images
In: Proc. Intl. Symp. Visual Computing (ISVC) (2009) Lecture Notes in Computer Science, Berlin;Heidelberg, Springer (2009), 544-553
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Janick Cardinale, Alexander Rauch, Yves Barral, Gabor Szekely, Ivo F. Sbalzarini
Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking
In: In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI) (2009), Piscataway, N.J., IEEE (2009), 1091-1094
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Christian L. Müller, Ivo 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)
In: Proc. Intl. Joint Conf. Computational Intelligence (IJCCI) (2009), INSTICC Press (2009), 248-253
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Ivo F. Sbalzarini
Analysis, Modeling & Simulation of Diffusion Processes in Cell Biology
Heidelberg, Germany, VDM Verlag (2009), 388 S.

2007

Jo A. Helmuth, C J Burckhardt, Petros Koumoutsakos, U F Greber, Ivo F. Sbalzarini
A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells
J Struct Biol, 159(3) 347-358 (2007)
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Jens H. Walther, Ivo F. Sbalzarini
Large-scale parallel discrete element simulations of granular flow
In: Proceedings of the International Conference on Discrete Element Modelling (DEM07) (2007), Amsterdam, Netherlands, Academic Press (2007), 1-8
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Ivo F. Sbalzarini
Informatik und Biologie – Eine Symbiose ermöglicht neue Entdeckungen
Vierteljahresschrift der Naturforschenden Gesellschaft in Zurich, 152(3) 63-70 (2007)

2006

Ivo F. Sbalzarini, Arnold Hayer, Ari Helenius, Petros Koumoutsakos
Simulations of (an)isotropic diffusion on curved biological surfaces.
Biophys J, 90(3) 878-885 (2006)
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Ivo F. Sbalzarini, J. Walther, M. Bergdorf, Simone E. Hieber, Evangelos M. Kotsalis, Petros Koumoutsakos
PPM – A highly efficient parallel particle–mesh library for the simulation of continuum systems
J Comput Phys, 215 566-588 (2006)
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Ivo F. Sbalzarini, Jens H. Walther, Bettina Polasek, Philippe Chatelain, M. Bergdorf, Simone E. Hieber, Evangelos M. Kotsalis, Petros Koumoutsakos
A Software Framework for Portable Parallelization of Particle-Mesh Simulations
In: Proc. EuroPar (2006)(Eds.) Wolfgang E Nagel Lecture Notes in Computer Science, New York, Springer (2006), 730-739
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Ivo F. Sbalzarini
Analysis, Modeling, and Simulation of Diffusion Processes in Cell Biology
Ph.D. Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2006)

2005

Helge Ewers, Alicia E. Smith, Ivo F. Sbalzarini, Hauke Lilie, Petros Koumoutsakos, Ari Helenius
Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes
Proc Natl Acad Sci U.S.A., 102(42) 15110-15115 (2005)
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Ivo F. Sbalzarini, Anna Mezzacasa, Ari Helenius, Petros Koumoutsakos
Effects of organelle shape on fluorescence recovery after photobleaching
Biophys J, 89(3) 1482-1492 (2005)
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Ivo F. Sbalzarini, Petros Koumoutsakos
Feature point tracking and trajectory analysis for video imaging in cell biology
J Struct Biol, 151(2) 182-195 (2005)
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Cosima Luedeke, Stéphanie Buvelot Frei, Ivo F. Sbalzarini, Heinz Schwarz, Anne Spang, Yves Barral
Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth.
J Cell Biol, 169(6) 897-908 (2005)
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Ivo F. Sbalzarini, Helge Ewers, Alicia E. Smith, Ari Helenius, Petros Koumoutsakos
Heimtückische Viren auf lebenden Zellen
ETH Bulletin, 298 48-50 (2005)

2004

Ivo F. Sbalzarini, Anna Mezzacasa, Ari Helenius, Petros Koumoutsakos
Large-Scale Simulations of Diffusion in Cell Biology
ERCIM News, 59 69-70 (2004)

2002

Ivo F. Sbalzarini
Diffusion in the Endoplasmic Reticulum
Diploma Thesis,ETH Zurich, Department of Computer Science, Zurich, Switzerland (2002)

2001

Ivo F. Sbalzarini, Sibylle D. Müller, Petros Koumoutsakos
Microchannel Optimization Using Multiobjective Evolution Strategies
(2001) Lecture Notes in Computer Science, New York, Springer (2001), 516-530
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Sibylle D. Müller, Ivo F. Sbalzarini, Jens H. Walther, Petros Koumoutsakos
Evolution Strategies for the Optimization of Microdevices
In: Proceedings of the Congress on Evolutionary Computation (CEC 2001) (2001), Piscataway, N.J., IEEE (2001), 302-309
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Ivo F. Sbalzarini, Sibylle D. Müller, Petros Koumoutsakos, Georges-Henri Cottet
Evolution Strategies for Computational and Experimental Fluid Dynamics Applications
In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2001) (2001), New York, ACM (2001), 1-8