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Systems Biology and Biophysics


K. B. Hoffmann and I. F. Sbalzarini. Robustness of topological defects in discrete domains. Phys. Rev. E, 103:012602, 2021. (PDF, Journal Link (Open Access))


A. Cezanne, J. Lauer, A. Solomatina, I. F. Sbalzarini, and M. Zerial. A non-linear system patterns Rab5 GTPase on the membrane. eLife, 9:e54434, 2020. (PDF, Journal Link (Open Access))


K. B. Hoffmann and I. F. Sbalzarini. A robustness measure for singular point and index estimation in discretized orientation and vector fields. Proc. Appl. Math. Mech., 20(1):e202000261, 2020. (PDF, Publisher Download (Open Access))


I. F. Sbalzarini. Systembiologie: Wird die Informatik auch die klinische Forschung revolutionieren? Allergologie, 43(8): 338-339, 2020.


A. Mietke, V. Jemseena, V. K. Kumar, I. F. Sbalzarini, and F. Jülicher. Minimal Model of Cellular Symmetry Breaking. Phys. Rev. Lett., 123: 188101, 2019. (Journal Link)


A. Mietke, F. Jülicher, and I. F. Sbalzarini. Self-organized shape dynamics of active surfaces. Proc. Natl. Acad. Sci. USA, 116(1):29—34, 2018. (Journal Link (Open Access), PDF, Supplement PDF, Supplementary Movies)


I. F. Sbalzarini and U. F. Greber. Influenza Virus: Methods and Protocols, volume 1836 of Methods in Molecular Biology, chapter How Computational Models Enable Mechanistic Insights into Virus Infection, pages 609–631. Springer Nature, 2018. (PDF)


A. Vignoni, A. Bajur, E. Knust, and I. F. Sbalzarini. Multi-objective identification from fluorescence recovery after photobleaching experiments: Understanding morphogenetic regulation of epithelial polarity. IFAC-PapersOnLine, 51(19):8–11, 2018. (Journal Link, PDF)


Y. Boada, A. Vignoni, J. Picó. Engineered Control of Genetic Variability Reveals Interplay among Quorum Sensing, Feedback Regulation, and Biochemical Noise. ACS Synth. Biol., 6(10):1903-1912, 2017.


Y. Boada, A. Vignoni, J. Picó. Multi-objective optimization for gene expression noise reduction in a synthetic gene circuit. In IFAC-PapersOnLine, 50(1), pages 4472-4477, 2017.


K. Meyer, O. Ostrenko, G. Bourantas, H. Morales-Navarrete, N. Porat-Shliom, F. Segovia-Miranda, H. Nonaka, A. Ghaemi, J.-M. Verbavatz, L. Brusch, I. F. Sbalzarini, Y. Kalaidzidis, R. Weigert, and M. Zerial. A predictive 3D multi-scale model of biliary fluid dynamics in the liver lobule. Cell Systems, 4(3):277–290, 2017. (PDF, Cover JPG, Journal Link (Open Access))


F. Raynaud, M. E. Ambühl, C. Gabella, A. Bornert, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky. Minimal model for spontaneous cell polarization and edge activity in oscillating, rotating and migrating cells. Nature Physics, 12:367–373, 2016. (Journal Page)


Yadira Boada, Alejandro Vignoni, G. Reynoso-Meza, Jesús Picó Parameter identification in synthetic biological circuits using multi-objective optimization IFAC-PapersOnLine, 49(26) 77-82 (2016).


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).


Yadira Boada, J. L. Pitarch, Alejandro Vignoni, G. Reynoso-Meza, Jesús Picó Optimization Alternatives for Robust Model-based Design of Synthetic Biological Circuits IFAC-PapersOnLine, 49(7) 821-826 (2016).


J. Kajtez, A. Solomatina, M. Novak, B. Polak, K. Vukušić, J. Rüdiger, G. Cojoc, A. Milas, I. Šumanovac Šestak, P. Risteski, F. Tavano, A. Klemm, E. Roscioli, J. Welburn, D. Cimini, M. Glunčić, N. Pavin, I. M. Tolić Overlap microtubules link sister k-fibres and balance the forces on bi-oriented kinetochores. Nat. Commun., 7 Art. No. 10298 (2016)


A. Yakimovich, Y. Yakimovich, M. Schmid, J. Mercer, I. F. Sbalzarini, and U. F. Greber. Infectio: a generic framework for computational simulation of virus transmission between cells. mSphere, 1(1):e00078–15, 2016. (PDF, Software Download)


Y. K. Shestopaloff and I. 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):e99275, 2014. (PDF)


C. Gabella, E. Bertseva, C. Bottier, N. Piacentini, A. Bornert, S. Jeney, L. Forró, I. F. Sbalzarini, J.-J. Meister, and A. B. Verkhovsky. Contact angle at the leading edge controls cell protrusion rate. Curr. Biol., 24(10):1126–1132, 2014. (PDF)


O. M. Szklarczyk, N. Gonzalez-Segredo, P. Kukura, A. Oppenheim, D. Choquet, V. Sandoghdar, A. Helenius, I. F. Sbalzarini, and H. Ewers. Receptor concentration and diffusivity control multivalent binding of SV40 to membrane bilayers. PLoS Comput. Biol., 9(11):e1003310, 2013. (PDF)


A. Yakimovich, H. Gumpert, C. J. Burckhardt, V. A. Lütschg, A. Jurgeit, I. F. Sbalzarini, and 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. (PDF)


I. F. Sbalzarini. Active flows cluster cell surface proteins. Dev. Cell, 22(6):1121–1122, 2012. (PDF)


I. F. Sbalzarini. Image-based systems biology: Modeling and simulation in image-derived geometries. In Workshop on Image-based Systems Biology, German Conference on Bioinformatics (GCB), Jena, Germany, September 2012. (PDF)


R. Ramaswamy, N. González-Segredo, I. F. Sbalzarini, and R. Grima. Discreteness-induced concentration inversion in mesoscopic chemical systems. Nat. Commun., 3:779, 2012. (PDF)


C. L. Müller, R. Ramaswamy, and I. F. Sbalzarini. Global parameter identification of stochastic reaction networks from single trajectories. In I. I. Goryanin and A. B. Goryachev, editors, Advances in Systems Biology, volume 736 of Advances in Experimental Medicine and Biology, chapter 28, pages 477–498. Springer, 2012. (PDF from arXiv, Springer link ...)


C. L. Müller and I. F. Sbalzarini. A conjecture about an upper bound of the RMSD between linear chains. In Proc. EuroCG, 27th European Workshop on Computational Geometry, pages 31–34, Morschach, Switzerland, March 2011. (PDF)


R. Ramaswamy and I. F. Sbalzarini. Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Sci. Rep., 1:154, 2011. (PDF)


Y. Yamauchi, H. Boukari, I. Banerjee, I. F. Sbalzarini, P. Horvath, and A. Helenius. Histone deacetylase 8 is required for centrosome cohesion and influenza A virus entry. PLoS Pathog., 7(10):e1002316, 2011. (PDF)


J. A. Helmuth, S. Reboux, and I. F. Sbalzarini. Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. J. Comput. Sci., 2(4):324–334, 2011. (PDF, Software Download)


Z. Smole, N. Nikolic, F. Supek, T. Smuc, I. F. Sbalzarini, and A. Krisko. Proteome sequence features carry signatures of the environmental niche of prokaryotes. BMC Evolutionary Biology, 11:26, 2011. (PDF)


O. Demirel, B. Schrader, and I. F. Sbalzarini. A parallel particle method for solving the EEG source localization forward problem. In Proc. 6th Intl. Symp. Health Informatics and Bioinformatics (HIBIT), pages 154–158, Izmir, Turkey, May 2011. (PDF)


R. Ramaswamy, I. F. Sbalzarini, and N. 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):e16045, 2011. (PDF)


A. A. Polyansky, R. Ramaswamy, P. E. Volynsky, I. F. Sbalzarini, S. J. Marrink, and R. G. Efremov. Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane. J. Phys. Chem. Lett., 1:3108–3111, 2010. (PDF, Supplementary Material PDF)


O. Awile, A. Krisko, I. F. Sbalzarini, and B. 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):e1000854, 2010. (PDF)


C. L. Müller, I. F. Sbalzarini, W. F. van Gunsteren, B. Žagrović, and P. H. Hünenberger. In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. J. Chem. Phys., 130(21):214904, 2009. (PDF)


I. F. Sbalzarini. Analysis, Modeling & Simulation of Diffusion Processes in Cell Biology. 388 pages. VDM Publishing, 2009. (Amazon link ...)


I. F. Sbalzarini. Bioinformatics, chapter "Spatiotemporal Modeling and Simulation in Biology", pages 381–432. World Scientific, 2009. (Amazon link ...)


A. Tušek, C. L. Müller, J. Supper, A. Zell, Ž. Kurtanjek, and I. F. Sbalzarini. Systems biology markup language: Case study of T-cell signal transduction network. In Proceedings of the 29th International Conference on Information Technology Interfaces (ITI07), pages 651–656. IEEE, 2007. (PDF) Erratum at http://iti.srce.hr/html/erratum2007.html


I. F. Sbalzarini, A. Hayer, A. Helenius, and P. Koumoutsakos. Simulations of (an)isotropic diffusion on curved biological surfaces, Biophysical Journal 90(3):878-885, 2006. (PDF, Software Download, F1000)


H. Ewers, A. Smith, I. F. Sbalzarini, H. Lilie, P. Koumoutsakos, and A. Helenius. Single particle tracking of murine polyomavirus-like particles on live cells and artificial membranes, Proc. Natl. Acad. Sci. USA 102(42):15110-15115, 2005. (PDF, Supplementary Material PDF, F1000, Software Download C/Java, ImageJ plug-in Download, MATLAB Software Download)


I. F. Sbalzarini, A. Mezzacasa, A. Helenius, and P. Koumoutsakos. Effects of Organelle Shape on Fluorescence Recovery after Photobleaching, Biophysical Journal 89(3):1482-1492, 2005. (PDF, Supplementary Material PDF, Software Download)


C. Luedeke, S. Buvelot-Frei, I. F. Sbalzarini, H. Schwarz, A. Spang, and Y. Barral. Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth, Journal of Cell Biology 169(6):897-908, 2005. (PDF, Supplementary Material PDF, F1000)


A. E. Smith, H. Ewers, I. Sbalzarini, P. Koumoutsakos, A. Helenius. Alternate endocytic pathways revealed by virus entry into animal cells. Molecular Biology of the Cell 15:195A, 2004.


I. F. Sbalzarini, A. Mezzacasa, A. Helenius, P. Koumoutsakos. Organelle shape has an influence on fluorescence recovery results. Molecular Biology of the Cell 13:276A, 2002. (Software Download)


Inference, Optimization, and Machine Learning


S. Maddu, D. Sturm, B. L. Cheeseman, C. L. Müller, and I. F. Sbalzarini. STENCIL-NET: Data-driven solution-adaptive discretization of partial differential equations. ArXiV, 2101.06182, 2021. (Preprint PDF)


S. Maddu, B. L. Cheeseman, C. L. Müller, and I. F. Sbalzarini. Learning physically consistent mathematical models from data using group sparsity. ArXiV, 2012.06391, 2020. (Preprint PDF)


S. Maddu, B. L. Cheeseman, I. F. Sbalzarini, C. L. Müller. Stability selection enables robust learning of partial differential equations from limited noisy data. ArXiV, 1907.07810, 2019. (Preprint PDF)


I. F. Sbalzarini. Big-Data Analytics transformiert die Lebenswissenschaften. Informatik Spektrum, 42(6): 394-400, 2019. (PDF)


G. Hempel, A. Goens, J. Asmus, J. Castrillon, and I. 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), SCOPES ’17, pages 21–30, New York, NY, USA, 2017. ACM. (PDF)


J. Asmus, C. L. Müller, and I. F. Sbalzarini. Lp-Adaptation: Simultaneous design centering and robustness estimation of electronic and biological systems. Scientific Reports, 7(1):6660, Jul 2017. (PDF, Supplement PDF, Journal Link (Open Access), MATLAB Source Code Download)


J. Asmus, D. Borchmann, I. F. Sbalzarini, and D. Walther. Towards an FCA-based recommender system for black-box optimization. In Proc.\ 3rd Intl. Workshop "What can FCA do for Artificial Intelligence?", co-located with the European Conference on Artificial Intelligence (ECAI 2014), pages 35–42, Prague, Czech Republic, 2014. (PDF)


Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini. An adaptive distributed resampling algorithm with non-proportional allocation. In Proc. ICASSP, IEEE Intl. Conf. Acoustics, Speech, and Signal Processing, pages 1635–1639, Florence, Italy, May 2014. IEEE. (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. In Proc. 10th IET Conf. Data Fusion & Target Tracking, Liverpool, UK, April 30 2014. IET. (PDF, Software Download)


S. U. Stich and C. L. Müller. On spectral invariance of Randomized Hessian and Covariance Matrix Adaptation Schemes. In Proc. Parallel Problem Solving From Nature (PPSN), Taormina, Italy, September 2012. (PDF)


C. L. Müller and I. F. Sbalzarini. Energy landscapes of atomic clusters as black-box optimization benchmarks. Evol. Comput., 20(4):543–573, 2012. (PDF)


C. L. Müller, R. Ramaswamy, and I. F. Sbalzarini. Global parameter identification of stochastic reaction networks from single trajectories. In I. I. Goryanin and A. B. Goryachev, editors, Advances in Systems Biology, volume 736 of Advances in Experimental Medicine and Biology, chapter 28, pages 477–498. Springer, 2012. (PDF from arXiv, Springer link ...)


C. L. Müller and I. F. Sbalzarini. Gaussian Adaptation for robust design centering. In Evolutionary and deterministic methods for design, optimization and control, Proc. EuroGen, pages 736–742, Capua, Italy, September 14–16 2011. (PDF, Software Download)


G. Paul, C. L. Müller, and I. F. Sbalzarini. Sensitivity analysis from evolutionary algorithm search paths. In Proc. EVOLVE, Workshop on Probability, Set Oriented Numerics and Evolutionary Computation, Luxembourg, May 2011. (PDF)


C. L. Müller. Continuous black-box optimization in linearly constrained domains using efficient Gibbs sampling. In Proc. EVOLVE, Workshop on Probability, Set Oriented Numerics and Evolutionary Computation, Luxembourg, May 2011. (PDF)


C. L. Müller and I. F. Sbalzarini. Global characterization of the CEC 2005 fitness landscapes using fitness-distance analysis. In Proc. EvoStar, volume 6624 of Leture Notes in Computer Science, pages 294–303, Torino, Italy, April 2011. Springer. (PDF)


C. L. Müller and I. 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), pages 2594–2601, Barcelona, Spain, July 2010. (PDF, Software Download)


C. L. Müller and I. F. Sbalzarini. Gaussian adaptation revisited — an entropic view on covariance matrix adaptation. In Proc. EvoStar, volume 6024 of Lecture Notes in Computer Science, pages 432–441, Istanbul, Turkey, April 2010. Springer. (PDF, Software Download) Best paper award.


J. A. Helmuth, G. Paul, and I. F. Sbalzarini. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11:372, 2010. (PDF, Software Download, ImageJ/Fiji plugin Download)


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). In Proc. Intl. Joint Conf. Computational Intelligence (IJCCI), pages 248–253, Funchal, Madeira, Portugal, October 5–7 2009. INSTICC Press. (PDF, Software Download)


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. In Proc. ACM Genetic and Evolutionary Computation Conference (GECCO’09), Montreal, Canada, July 2009. (PDF, Software Download)


C. L. Müller, B. Baumgartner, and I. F. Sbalzarini. Particle swarm CMA evolution strategy for the optimization of multi-funnel landscapes. In Proc. IEEE Congress on Evolutionary Computation (CEC), pages 2685-2692, Trondheim, Norway, May 2009. (PDF, Software Download)


J. A. Helmuth, C. J. Burckhardt, P. Koumoutsakos, U. F. Greber, and I. F. Sbalzarini. A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells, Journal of Structural Biology, 159(3):347-358, 2007. (PDF, Supplementary Material PDF, Software Download)


I. F. Sbalzarini, S. D. Mueller, and P. Koumoutsakos. Microchannel Optimization Using Multiobjective Evolution Strategies, Lecture Notes in Computer Science, 1993:516-530, 2001. (PDF)


S. D. Mueller, I. F. Sbalzarini, J. H. Walther, and P. D. Koumoutsakos. Evolution Strategies for the Optimization of Microdevices, Proceedings of the Congress on Evolutionary Computation (CEC 2001), pp. 302-309, 2001. (PDF)


I. F. Sbalzarini, S. D. Mueller, P. Koumoutsakos, and G.-H. Cottet. Evolution Strategies for Computational and Experimental Fluid Dynamics Applications. L. Spector, E. Goodman, A. Wu, W.B. Langdon, H.-M. Voigt, M. Gen, S. Sen, M. Dorigo, S. Pezeshk, M. Garzon, and E. Burke, editors. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2001), Morgan Kaufmann Publishers, San Francisco, CA, 2001. (PDF)


Algorithms and Numerical Methods


M. Hecht, K. Gonciarz, J. Michelfeit, V. Sivkin, and I. F. Sbalzarini. Multivariate Interpolation on Unisolvent Nodes -- Lifting the Curse of Dimensionality. ArXiV, 2010.10824, 2020. (Preprint PDF)


M. Hecht and I. F. Sbalzarini. Fast interpolation and Fourier transform in high-dimensional spaces. In Intelligent Computing, Proc. 2018 IEEE Computing Conf., Vol. 2, volume 857 of Advances in Intelligent Systems and Computing, pages 53–75, London, UK, 2018. Springer Nature. (PDF (OpenAccess), Publisher Link, Highlight interview on YouTube)


M. Hecht. Exact localisations of feedback sets. Theory of Computing Systems, 62(5):1048-1084, 2018. (Journal Link (Open Access), PDF)


M. Hecht, K. B. Hoffmann, B. L. Cheeseman, and I. F. Sbalzarini. Multivariate Newton Interpolation. ArXiV, 1812.04256, 2018. (Preprint PDF)


M. Hecht, B. L. Cheeseman, K. B. Hoffmann, and I. F. Sbalzarini. A Quadratic-Time Algorithm for General Multivariate Polynomial Interpolation. ArXiV, 1710.10846, 2017. (Preprint PDF)


G. C. Bourantas, B. L. Cheeseman, R. Ramaswamy, and I. F. Sbalzarini. Using DC PSE operator discretization in Eulerian meshless collocation methods improves their robustness in complex geometries. Computers & Fluids, 136:285–300, 2016. (PDF)


C. Häcki, S. Reboux, and I. F. Sbalzarini. A self-organizing adaptive-resolution particle method with anisotropic kernels. Procedia IUTAM, 18:40–55, 2015. (PDF)


R. Ramaswamy, G. Bourantas, F. Jülicher, and I. F. Sbalzarini. A hybrid particle-mesh method for incompressible active polar viscous gels. J. Comput. Phys., 291:334–361, 2015. (PDF)


N. Fietier, O. Demirel, and I. F. Sbalzarini. A meshless particle method for Poisson and diffusion problems with discontinuous coefficients and inhomogeneous boundary conditions. SIAM J. Sci. Comput., 35(6):A2469–A2493, 2013. (PDF)


I. F. Sbalzarini, C. Häcki, and S. Reboux. Anisotropic kernels for self-organizing Lagrangian particles. In IUTAM Symposium on Particle Methods in Fluid Mechanics, Copenhagen, Denmark, 2012. (PDF)


B. Schrader, S. Reboux, and I. F. Sbalzarini. Choosing the best kernel: performance models for diffusion operators in particle methods. SIAM J. Sci. Comput., 34(3):A1607–A1634, 2012. (PDF)


Y. Gong, G. Paul, and I. F. Sbalzarini. Coupled signed-distance functions for implicit surface reconstruction. In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI), pages 1000–1003, Barcelona, Spain, May 2012. (PDF) Best paper award.


S. Reboux, B. Schrader, and I. F. Sbalzarini. A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. J. Comput. Phys., 231:3623–3646, 2012. (PDF)


O. Awile, F. Büyükkeçeci, S. Reboux, and I. F. Sbalzarini. Fast neighbor lists for adaptive-resolution particle simulations. Comput. Phys. Commun., 183:1073–1081, 2012. (PDF)


R. Ramaswamy and I. F. Sbalzarini. Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. J. Chem. Phys., 135:244103, 2011. (PDF, Software Download)
Also published in: Virtual Journal of Biological Physics Research 23(1), 2012.


J. A. Helmuth, S. Reboux, and I. F. Sbalzarini. Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. J. Comput. Sci., 2(4):324–334, 2011. (PDF, Software Download)


R. Ramaswamy and I. F. Sbalzarini. A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays. J. Chem. Phys., 134(1):014106, 2011. (PDF, Software Download)
Also published in: Virtual Journal of Biological Physics Research 21(2), 2011.


R. Ramaswamy and I. F. Sbalzarini. Fast exact stochastic simulation algorithms using partial propensities. In Proc. ICNAAM, Numerical Analysis and Applied Mathematics, International Conference, pages 1338–1341, Rhodes, Greece, September 2010. AIP. (PDF, Software Download)


M. Bergdorf, I. F. Sbalzarini, and P. Koumoutsakos. A Lagrangian particle method for reaction-diffusion systems on deforming surfaces. J. Math. Biol., 61:649–663, 2010. (PDF)


B. Schrader, S. Reboux, and I. F. Sbalzarini. Discretization-Corrected PSE Operators for Particle Methods. In Proc. 8th Euromech Fluid Mechanics Conference (EFMC8), Bad Reichenhall, Germany, September 2010. (PDF)


B. Schrader, S. Reboux, and I. F. Sbalzarini. Discretization correction of general integral PSE operators in particle methods. J. Comput. Phys., 229:4159–4182, 2010. (PDF)


R. Ramaswamy and I. F. Sbalzarini. A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks. J. Chem. Phys., 132(4):044102, 2010. (PDF, Software Download)
Also published in: Virtual Journal of Biological Physics Research 19(3), 2010.
Swiss Institute of Bioinformatics Best Graduate Paper Award


R. Ramaswamy, N. González-Segredo, and I. F. Sbalzarini. A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. J. Chem. Phys., 130(24):244104, 2009. (PDF, Software Download, Notes and Corrections)
Also published in: Virtual Journal of Biological Physics Research 18(1), 2009.
Swiss Institute of Bioinformatics Best Graduate Paper Award


Parallel and High-Performance Computing


A. Gupta, P. Incardona, A. D. Aydin, S. Gumhold, U. Günther, and I. F. Sbalzarini. An Architecture for Interactive In Situ Visualization and its Transparent Implementation in OpenFPM. In Proc. Workshop on In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization (ISAV), SC20: The International Conference on High Performance Computing, Networking, Storage, and Analysis, pages 20-26, online, ACM, 2020. (Publisher Download (Open Access), PDF)


A. Gupta, U. Günther, P. Incardona, A. D. Aydin, R. Dachselt, S. Gumhold, and I. F. Sbalzarini. A Proposed Framework for Interactive Virtual Reality In Situ Visualization of Parallel Numerical Simulations. In Proc. IEEE Symposium on Large Data Analysis and Visualization, pages 95-96, Vancouver, Canada, 2019. (Publisher Download, Preprint OpenAccess)


P. Incardona, A. Leo, Y. Zaluzhnyi, R. Ramaswamy, and I. F. Sbalzarini. OpenFPM: A scalable open framework for particle and particle-mesh codes on parallel computers. Comput. Phys. Commun., 241:155– 177, 2019. (Journal Link (Open Access), PDF, Software Download)


S. Karol, T. Nett, J. Castrillon, and I. F. Sbalzarini. A domain-specific language and editor for parallel particle methods. ACM Trans. Math. Softw., 44(3):34, 2018. (Journal Link, Preprint ArXiV (PDF), Software Download)


S. Karol, T. Nett, P. Incardona, N. Khouzami, J. Castrillon, and I. F. Sbalzarini. A language and development environment for parallel particle methods. In International Conference on Particle-based Methods – Fundamentals and Applications, paper 44, pages 1–12, Hanover, Germany, 2017. (PDF)


G. Hempel, A. Goens, J. Asmus, J. Castrillon, and I. 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), SCOPES ’17, pages 21–30, New York, NY, USA, 2017. ACM. (PDF)


O. Ostrenko, P. Incardona, R. Ramaswamy, L. Brusch, and I. F. Sbalzarini. pSSAlib: The partial-propensity stochastic chemical network simulator. PLoS Comput. Biol., 13(12):e1005865, 2017. (Journal Link (Open Access), Software Download)


Y. Afshar and I. F. Sbalzarini. A parallel distributed-memory particle method enables acquisition-rate segmentation of large fluorescence microscopy images. PLoS ONE, 11(4):e0152528, 2016. (PDF, Software Download, GitHub Link)


S. Karol, P. Incardona, Y. Afshar, I. F. Sbalzarini and J Castrillón. Towards a Next-Generation Parallel Particle-Mesh Language. In Proc. Workshop DSLDI, 29th European Conference on Object-Oriented Programming (ECOOP), Prague, Czech Republic, 2015. (paper acceptance rate: 31/136). (PDF from ArXiv)


Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini. PPF – A parallel particle filtering library. In Proc. 10th IET Conf. Data Fusion & Target Tracking, Liverpool, UK, April 30 2014. IET. (PDF, Software Download)


O. Awile and I. F. Sbalzarini. A pthreads wrapper for Fortran 2003. ACM Trans. Math. Softw., 40(3):19:1–19:15, 2014. (PDF, Software Download)


O. Awile, M. Mitrovic, S. Reboux, and I. F. Sbalzarini. A domain-specific programming language for particle simulations on distributed-memory parallel computers. In Proc. III Intl. Conf. Particle-based Methods (PARTICLES), paper p52, Stuttgart, Germany, 2013. (PDF, Abstract PDF)


F. Büyükkeçeci, O. Awile and I. F. Sbalzarini. A portable OpenCL implementation of generic particle-mesh and mesh-particle interpolation 2D and 3D. Parallel Comput., 39:94-111, 2013. (PDF, Software Download)


O. Awile, M. Mitrović, and I. F. Sbalzarini. PPM: A scalable software framework for parallel particle-mesh simulations. In Proc. PDEsoft, Workshop on PDE Software Frameworks, Münster, Germany, June 18–20 2012. (PDF)


O. Awile, O. Demirel, and I. F. Sbalzarini. Toward an object-oriented core of the PPM library. In Proc. ICNAAM, Numerical Analysis and Applied Mathematics, International Conference, pages 1313–1316, Rhodes, Greece, September 2010. AIP. (PDF, Software Download)


I. F. Sbalzarini. Abstractions and middleware for petascale computing and beyond. Intl. J. Distr. Systems & Technol., 1(2):40–56, 2010. (PDF, Software Download)


J. H. Walther and I. F. Sbalzarini. Large-scale parallel discrete element simulations of granular flow. Engineering Computations, 26(6):688–697, 2009. (PDF)


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. In Proc. ACM Genetic and Evolutionary Computation Conference (GECCO’09), Montreal, Canada, July 2009. (PDF, Software Download)


H. A. Zambrano, J. H. Walther, P. Koumoutsakos, and I. F. Sbalzarini. Thermophoretic motion of water nanodroplets confined inside carbon nanotubes. Nano Letters, 9(1):66–71, 2009. (PDF)


J. H. Walther and I. F. Sbalzarini. Large-scale parallel discrete element simulations of granular flow. In Proceedings of the International Conference on Discrete Element Modelling (DEM07), Brisbane, Australia, 2007. (PDF)


I. F. Sbalzarini, J. H. Walther, B. Polasek, P. Chatelin, M. Bergdorf, S. E. Hieber, E. M. Kotsalis, and P. Koumoutsakos. A Software Framework for Portable Parallelization of Particle-Mesh Simulations, Lecture Notes in Computer Science, 4128:730-739, 2006. (PDF, Software Download)


I. F. Sbalzarini, J. H. Walther, M. Bergdorf, S. E. Hieber, E. M. Kotsalis, and P. Koumoutsakos. PPM – A Highly Efficient Parallel Particle-Mesh Library for the Simulation of Continuum Systems, Journal of Computational Physics 215(2):566-588, 2006. (PDF, Software Download)


Bio-Image Informatics and Bio-Imaging


U. Günther, K. I. S. Harrington, R. Dachselt, and I. F. Sbalzarini. Bionic tracking: Using eye tracking to track biological cells in virtual reality. In A. Bartoli and A. Fusiello, editors, Proc. Europ. Conf. Computer Vision – ECCV 2020 Workshops, volume 12535 of Lect. Notes Comput. Sci., pages 280–297, Cham, Switzerland, 2020. Springer Nature. (Publisher Download, Preprint OpenAccess)


U. Günther, T. Pietzsch, A. Gupta, K. I. S. Harrington, P. Tomancak, S. Gumhold, and I. F. Sbalzarini. scenery: Flexible Virtual Reality Visualization on the Java VM. In Proc. IEEE Conference on Visualization, pages 166-170, Vancouver, Canada, 2019. (Publisher Download, Preprint OpenAccess)


B. L. Cheeseman, U. Günther, K. Gonciarz, M. Susik, and I. F. Sbalzarini. Adaptive particle representation of fluorescence microscopy images. Nat. Commun., 9:5160, 2018. (Journal Link (Open Access), PDF, Supplement PDF, Software Download, Supplementary Movies)


Y. Gong and I. F. Sbalzarini. Curvature filters efficiently reduce certain variational energies. IEEE Trans. Image Process., 26(4):1786–1798, 2017. (PDF, C++ Source Code Download, ImageJ/Fiji Plugin Download)


X. Xiao, V. F. Geyer, H. Bowne-Anderson, J. Howard, and I. 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. (PDF, ImageJ/Fiji Plugin Download, Test Image Sets (ZIP), MATLAB codes and test images used for the paper at the time of writing Download (RAR))


I. F. Sbalzarini. Focus on Bio-Image Informatics, chapter "Seeing Is Believing – Quantifying Is Convincing: Computational Image Analysis in Biology", pages 1–39. Advances in Anatomy, Embryology and Cell Biology. Springer, 2016. (PDF Preprint, Springer link ...)


Y. Afshar and I. F. Sbalzarini. A parallel distributed-memory particle method enables acquisition-rate segmentation of large fluorescence microscopy images. PLoS ONE, 11(4):e0152528, 2016. (PDF, Software Download, GitHub Link)


Y. Gong and I. F. Sbalzarini. A natural-scene gradient distribution prior and its application in light-microscopy image processing. IEEE Journal of Selected Topics in Signal Processing, 10(1):99–114, 2016. (PDF, Supplementary PDF, ImageJ/Fiji plugin Download, MATLAB code Download)


L. A. Royer, M. Weigert, U. Günther, N. Maghelli, F. Jug, I. F. Sbalzarini, and E. W. Myers. ClearVolume: open-source live 3D visualization for light-sheet microscopy. Nat. Methods, 12(6):480–481, 2015. (PDF, Online Supplementary Information, Software Download)


X. Xiao and I. F. Sbalzarini. Globally optimal geometric segmentation of filaments. In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI), Beijing, China, May 2014. IEEE. (PDF)


Y. Gong and I. F. Sbalzarini. Image enhancement by gradient distribution specification. In C. V. Jawahar and S. Shan, editors, Computer Vision – ACCV 2014 Workshops, Revised Selected Papers, Part II, volume 9009 of Lect. Notes Comput. Sci., pages 47–62, Singapore, November 2014. Springer. (Paper PDF, Supplementary Material ZIP, Talk Slides PDF, MATLAB Software Download, ImageJ/Fiji Software Download)


N. Chenouard, I. Smal, F. de Chaumont, M. Maska, I. F. Sbalzarini, Y. Gong, J. Cardinale, C. Carthel, S. Coraluppi, M. Winter, A. R. Cohen, W. J. Godinez, K. Rohr, Y. Kalaidzidis, L. Liang, J. Duncan, H. Shen, Y. Xu, K. E. G. Magnusson, J. Jalden, H. M. Blau, P. Paul-Gilloteaux, P. Roudot, C. Kervrann, F. Waharte, J.-Y. Tinevez, S. L. Shorte, J. Willemse, K. Celler, G. P. van Wezel, H.-W. Dan, Y.-S. Tsai, C. O. de Solorzano, J.-C. Olivo-Marin, and E. Meijering. Objective comparison of particle tracking methods. Nature Methods, 11(3):281–289, 2014. (PDF, Cover PDF, Supplementary Note PDF, Software Download, Editorial, News & Views Article)


Ö. Demirel, I. Smal, W. J. Niessen, E. Meijering, and I. F. Sbalzarini. Piecewise constant sequential importance sampling for fast particle filtering. In Proc. 10th IET Conf. Data Fusion & Target Tracking, Liverpool, UK, April 30 2014. IET. (PDF, Software Download)


I. F. Sbalzarini, S. Schneider, J. Cardinale. Particle methods enable fast and simple approximation of Sobolev gradients in image segmentation. ArXiV, 1403.0240, 2014. (Preprint PDF)


A. Rizk, G. Paul, P. Incardona, M. Bugarski, M. Mansouri, A. Niemann, U. Ziegler, P. Berger, and I. F. Sbalzarini. Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh. Nature Protocols, 9(3):586–596, 2014. (PDF, Supplementary Note PDF, ImageJ/Fiji plugin Download, Supplementary Data ZIP, Supplementary Video)


Y. Gong and I. F. Sbalzarini. Local weighted Gaussian curvature for image processing. In Proc. IEEE Intl. Conf. Image Process. (ICIP), pages 534–538, Melbourne, Australia, September 15–18 2013. IEEE. (PDF)


A. Shivanandan, A. Radenovic, and I. F. Sbalzarini. MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis. BMC Bioinformatics, 14:349, 2013. (PDF, ImageJ/Fiji plugin Download)


G. Paul, J. Cardinale, and I. F. Sbalzarini. Coupling image restoration and segmentation: A generalized linear model/Bregman perspective. Int. J. Comput. Vis., 104(1):69–93, 2013. (PDF, Supplementary Material PDF, Software Download, ImageJ/Fiji plugin Download)


I. F. Sbalzarini. Modeling and simulation of biological systems from image data. Bioessays, 35(5):482–490, 2013. (PDF, Cover Art)


I. F. Sbalzarini. Image-based systems biology: Modeling and simulation in image-derived geometries. In Workshop on Image-based Systems Biology, German Conference on Bioinformatics (GCB), Jena, Germany, September 2012. (PDF)


Y. Gong, G. Paul, and I. F. Sbalzarini. Coupled signed-distance functions for implicit surface reconstruction. In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI), pages 1000–1003, Barcelona, Spain, May 2012. (PDF) Best paper award.


J. Cardinale, G. Paul, and I. F. Sbalzarini. Discrete region competition for unknown numbers of connected regions. IEEE Trans. Image Process., 21(8):3531–3545, 2012. (PDF, Software Download ITK/C++, ImageJ/Fiji plugin Download, F1000)


M. E. Ambühl, C. Brepsant, J.-J. Meister, A. B. Verkhovsky, and I. F. Sbalzarini. High-resolution cell outline segmentation and tracking from phase-contrast microscopy images. J. Microsc., 245(2):161–170, 2012. (PDF, Supplementary Movie (MP4), Software Download)


G. Paul, J. Cardinale, and I. F. Sbalzarini. An alternating split Bregman algorithm for multi-region segmentation. In Proc. 45th IEEE Asilomar Conf. Signals, Systems, and Computers, pages 426–430, Asilomar, CA, USA, 2011. Invited. (PDF)


C. Bottier, C. Gabella, 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. Lab Chip, 11:3855–3863, Oct 2011. (PDF)


J. A. Helmuth, G. Paul, and I. F. Sbalzarini. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11:372, 2010. (PDF, Software Download, ImageJ/Fiji plugin Download)


J. A. Helmuth and I. F. Sbalzarini. Deconvolving active contours for fluorescence microscopy images. In Proc. Intl. Symp. Visual Computing (ISVC), volume 5875 of Lecture Notes in Computer Science, pages 544–553, Las Vegas, USA, November 2009. Springer. (PDF, Software Download, 3D ITK implementation, ImageJ/Fiji plugin Download)


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. In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI), pages 1091-1094, Boston, USA, June 2009. (PDF, Software Download)


J. A. Helmuth, C. J. Burckhardt, U. F. Greber, and I. F. Sbalzarini. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. Journal of Structural Biology, 167:1–10, 2009. (PDF, Supplementary Material PDF, Software Download)


I. F. Sbalzarini and P. Koumoutsakos. Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology, Journal of Structural Biology 151(2):182-195, 2005. (PDF, Software Download C/Java, ImageJ/Fiji plugin Download, MATLAB Software Download)