Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains. - Guillaume Lamour; Julius B. Kirkegaard; Hongbin Li; Tuomas P. J. Knowles; Jörg Gsponer (Source Code Biol. Medicine, 2014)

Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations. - Julius B. Kirkegaard (BMC Bioinform., 2022)

Fast spline detection in high density microscopy data. - Albert Alonso; Julius B. Kirkegaard (CoRR, 2023)

Learning optimal integration of spatial and temporal information in noisy chemotaxis. - Albert Alonso; Julius B. Kirkegaard (CoRR, 2023)

In Vivo Deep Learning Estimation of Diffusion Coefficients of Nanoparticles. - Julius B. Kirkegaard; Nikolay Kutuzov; Rasmus Netterstrøm; Sune Darkner; Martin Johannes Lauritzen; François Lauze (MICCAI (2), 2024)

Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients. - Albert Alonso; Julius B. Kirkegaard; Robert G. Endres (CoRR, 2024)

Receptors cluster in high-curvature membrane regions for optimal spatial gradient sensing. - Albert Alonso; Robert G. Endres; Julius B. Kirkegaard (CoRR, 2024)

Spline refinement with differentiable rendering. - Frans Zdyb; Albert Alonso; Julius B. Kirkegaard (CoRR, 2025)