List of works - Ivo F Sbalzarini

A C++ expression system for partial differential equations enables generic simulations of biological hydrodynamics

scientific article published in 2021

A Lagrangian particle method for reaction-diffusion systems on deforming surfaces

scientific article published on 18 December 2009

A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images

scientific article

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

scientific article published on 18 March 2017

A method for modeling growth of organs and transplants based on the general growth law: application to the liver in dogs and humans

scientific article (publication date: 2014)

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

scientific article

A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells

scientific article published on 14 April 2007

A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays

scientific article

A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks

scientific article

Active flows cluster cell surface proteins

scientific article published on 01 June 2012

Adaptive particle representation of fluorescence microscopy images

scientific article published in Nature Communications

Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets

scientific article published on 4 April 2016

Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images

scientific article

ClearVolume: open-source live 3D visualization for light-sheet microscopy

2015 scientific article

Contact angle at the leading edge controls cell protrusion rate

scientific article published on 01 May 2014

Curvature Filters Efficiently Reduce Certain Variational Energies.

scientific article

Discrete region competition for unknown numbers of connected regions.

scientific article

Discreteness-induced concentration inversion in mesoscopic chemical systems.

scientific article published on 10 April 2012

Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique.

scientific article

Effects of organelle shape on fluorescence recovery after photobleaching

scientific article

Energy landscapes of atomic clusters as black box optimization benchmarks

scientific article published on 31 August 2012

Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods

scientific article published in December 2011

Feature point tracking and trajectory analysis for video imaging in cell biology.

scientific article

Global parameter identification of stochastic reaction networks from single trajectories

scientific article published in January 2012

High-resolution cell outline segmentation and tracking from phase-contrast microscopy images

scientific article published on 17 October 2011

Histone Deacetylase 8 Is Required for Centrosome Cohesion and Influenza A Virus Entry ⬇️

scientific article (publication date: October 2011)

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

scientific article published in June 2009

Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems.

scientific article published on 11 November 2011

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans

scientific article

Inverse Dirichlet weighting enables reliable training of physics informed neural networks

scientific article published in 2022

L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems

scientific article published on 27 July 2017

Learning physically consistent differential equation models from data using group sparsity

scientific article published in 2021

Live and Interactive 3D Photomanipulation under the Microscope using Virtual Reality

scientific article published on 11 May 2024

Model-based autotuning of discretization methods in numerical simulations of partial differential equations

scientific article published in 2022

Modeling and simulation of biological systems from image data

scientific article

MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis

scientific article

Objective comparison of particle tracking methods

scientific article

Proteome sequence features carry signatures of the environmental niche of prokaryotes.

scientific article

Proven Distributed Memory Parallelization of Particle Methods

scientific article published on 18 September 2024

Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers

scientific article published on 14 November 2013

Seeing Is Believing: Quantifying Is Convincing: Computational Image Analysis in Biology.

scientific article published on January 2016

Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

scientific article

Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth

scientific article

Shape reconstruction of subcellular structures from live cell fluorescence microscopy images.

scientific article

Simulations of (an)isotropic diffusion on curved biological surfaces.

scientific article published on 11 November 2005

Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes

scientific article

Stability selection enables robust learning of differential equations from limited noisy data

scientific article published in 2022

Thermophoretic motion of water nanodroplets confined inside carbon nanotubes

scientific article published on 01 January 2009

pSSAlib: The partial-propensity stochastic chemical network simulator.

scientific article published on 4 December 2017

List of works by Ivo F Sbalzarini

A C++ expression system for partial differential equations enables generic simulations of biological hydrodynamics

A Lagrangian particle method for reaction-diffusion systems on deforming surfaces

A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

A method for modeling growth of organs and transplants based on the general growth law: application to the liver in dogs and humans

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells

A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays

A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks

Active flows cluster cell surface proteins

Adaptive particle representation of fluorescence microscopy images

Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets

Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images

ClearVolume: open-source live 3D visualization for light-sheet microscopy

Contact angle at the leading edge controls cell protrusion rate

Curvature Filters Efficiently Reduce Certain Variational Energies.

Discrete region competition for unknown numbers of connected regions.

Discreteness-induced concentration inversion in mesoscopic chemical systems.

Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique.

Effects of organelle shape on fluorescence recovery after photobleaching

Energy landscapes of atomic clusters as black box optimization benchmarks

Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods

Feature point tracking and trajectory analysis for video imaging in cell biology.

Global parameter identification of stochastic reaction networks from single trajectories

High-resolution cell outline segmentation and tracking from phase-contrast microscopy images

Histone Deacetylase 8 Is Required for Centrosome Cohesion and Influenza A Virus Entry ⬇️

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans

Inverse Dirichlet weighting enables reliable training of physics informed neural networks

L p -Adaptation: Simultaneous Design Centering and Robustness Estimation of Electronic and Biological Systems

Learning physically consistent differential equation models from data using group sparsity

Live and Interactive 3D Photomanipulation under the Microscope using Virtual Reality

Model-based autotuning of discretization methods in numerical simulations of partial differential equations

Modeling and simulation of biological systems from image data

MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis

Objective comparison of particle tracking methods

Proteome sequence features carry signatures of the environmental niche of prokaryotes.

Proven Distributed Memory Parallelization of Particle Methods

Receptor concentration and diffusivity control multivalent binding of Sv40 to membrane bilayers

Seeing Is Believing: Quantifying Is Convincing: Computational Image Analysis in Biology.

Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.

Septin-dependent compartmentalization of the endoplasmic reticulum during yeast polarized growth

Shape reconstruction of subcellular structures from live cell fluorescence microscopy images.

Simulations of (an)isotropic diffusion on curved biological surfaces.

Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes

Stability selection enables robust learning of differential equations from limited noisy data

Thermophoretic motion of water nanodroplets confined inside carbon nanotubes

pSSAlib: The partial-propensity stochastic chemical network simulator.