Publications in refereed journals

In refereed journals


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))

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)


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)

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))

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)

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)

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. 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)


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)

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)

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)


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. 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)

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)

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)


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)

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)

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)

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)

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)


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)

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)

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)

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)

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

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)

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)


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.

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)

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)

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)

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)

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.


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)

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)

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)

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)

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

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


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

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

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)

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)

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. 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, 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)

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)

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)

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)


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)