Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water. - Yiannis N. Kaznessis; Mark E. Snow; C. John Blankley (J. Comput. Aided Mol. Des., 2001)

Numerical simulation of stochastic gene circuits. - Howard M. Salis; Yiannis N. Kaznessis (Comput. Chem. Eng., 2005)

A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes. - Boojala V. B. Reddy; Yiannis N. Kaznessis (J. Bioinform. Comput. Biol., 2005)

Multiscale Hy3S: Hybrid stochastic simulation for supercomputers. - Howard M. Salis; Vassilios Sotiropoulos; Yiannis N. Kaznessis (BMC Bioinform., 2006)

Residue Conservation Information for Generating near-native Structures in Protein-protein Docking. - Yuhua Duan; Boojala V. B. Reddy; Yiannis N. Kaznessis (J. Bioinform. Comput. Biol., 2006)

Models for synthetic biology. - Yiannis N. Kaznessis (BMC Syst. Biol., 2007)

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. - Vassilios Sotiropoulos; Yiannis N. Kaznessis (BMC Syst. Biol., 2007)

Multiscale Models for Synthetic Biology. - Yiannis N. Kaznessis; Vassilios Sotiropoulos; Anthony D. Hill; Jonathan R. Tomshine; Katherine Volzing; John Barrett; Emma M. B. Weeding (BIOCOMP, 2008)

SynBioSS: the synthetic biology modeling suite. - Anthony D. Hill; Jonathan R. Tomshine; Emma M. B. Weeding; Vassilios Sotiropoulos; Yiannis N. Kaznessis (Bioinform., 2008)

Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore. - Dan S. Bolintineanu; Abdallah Sayyed-Ahmad; H. Ted Davis; Yiannis N. Kaznessis (PLoS Comput. Biol., 2009)

Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study. - Vassilios Sotiropoulos; Marie-Nathalie Contou-Carrere; Prodromos Daoutidis; Yiannis N. Kaznessis (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. - Emma M. B. Weeding; Jason Houle; Yiannis N. Kaznessis (Briefings Bioinform., 2010)

Stochastic simulations of the tetracycline operon. - Konstantinos Biliouris; Prodromos Daoutidis; Yiannis N. Kaznessis (BMC Syst. Biol., 2011)

Model reduction of multi-scale chemical Langevin equations. - Marie-Nathalie Contou-Carrere; Vassilios Sotiropoulos; Yiannis N. Kaznessis; Prodromos Daoutidis (Syst. Control. Lett., 2011)

Stochastic simulations of a synthetic bacteria-yeast ecosystem. - Konstantinos Biliouris; David Babson; Claudia Schmidt-Dannert; Yiannis N. Kaznessis (BMC Syst. Biol., 2012)

A linearization method for probability moment equations. - Michail Vlysidis; Yiannis N. Kaznessis (Comput. Chem. Eng., 2018)

On Differences between Deterministic and Stochastic Models of Chemical Reactions: Schlögl Solved with ZI-Closure. - Michail Vlysidis; Yiannis N. Kaznessis (Entropy, 2018)

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers. - Michail Vlysidis; Yiannis N. Kaznessis (Entropy, 2018)