STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. - Andrzej M. Kierzek (Bioinform., 2002)

XQTav: an XQuery processor for Taverna environment. - Jacek Sroka; Grzegorz Kaczor; Jerzy Tyszkiewicz; Andrzej M. Kierzek (Bioinform., 2006)

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks. - Albert Gevorgyan; Michael E. Bushell; Claudio Avignone-Rossa; Andrzej M. Kierzek (Bioinform., 2011)

CalcTav - integration of a spreadsheet and Taverna workbench. - Jacek Sroka; Lukasz Krupa; Andrzej M. Kierzek; Jerzy Tyszkiewicz (Bioinform., 2011)

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. - Jacek Sroka; Lukasz Bieniasz-Krzywiec; Szymon Gwozdz; Dariusz Leniowski; Jakub Lacki; Mateusz Markowski; Claudio Avignone-Rossa; Michael E. Bushell; Johnjoe McFadden; Andrzej M. Kierzek (BMC Bioinform., 2011)

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis. - Bhushan K. Bonde; Dany J. V. Beste; Emma Laing; Andrzej M. Kierzek; Johnjoe McFadden (PLoS Comput. Biol., 2011)

Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity. - Rebecca B. Hoyle; Daniele Avitabile; Andrzej M. Kierzek (PLoS Comput. Biol., 2012)

QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. - Ciarán P. Fisher; Nicholas J. Plant; J. Bernadette Moore; Andrzej M. Kierzek (Bioinform., 2013)

AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks. - Wojciech Ptak; Andrzej M. Kierzek; Jacek Sroka (Petri Nets, 2016)

Verification of Dynamic Behaviour in Qualitative Molecular Networks Describing Gene Regulation, Signalling and Whole-cell Metabolism. - Marek Grabowski; Grzegorz Bokota; Jacek Sroka; Andrzej M. Kierzek (Fundam. Informaticae, 2018)

Simulation of multicellular populations with Petri nets and genome scale intracellular networks. - Kamil Kedzia; Wojtek Ptak; Jacek Sroka; Andrzej M. Kierzek (Sci. Comput. Program., 2018)