Formal Biochemical Space with Semantics in Kappa and BNGL. - T. Ded; David Safránek; Matej Troják; Matej Klement; Jakub Salagovic; Lubos Brim (SASB, 2015)

E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. - Matej Troják; David Safránek; Jakub Hrabec; Jakub Salagovic; Frantiska Romanovská; Jan Cervený (CMSB, 2016)

Executable Biochemical Space for Specification and Analysis of Biochemical Systems. - Matej Troják; David Safránek; Lubos Brim; Jakub Salagovic; Jan Cervený (SASB, 2020)

Model prediction of plant morphology, water flows and xylem water potential in a growing tomato plant under heterogeneous growing conditions. - Jakub Salagovic; Pieter Verboven; Maarten Hertog; Bram Van de Poel; Bart M. Nicolaï (Comput. Electron. Agric., 2025)