List of works - Yiannis N. Kaznessis

A Review of Methods for Computational Prediction of Blood-Brain Partitioning

scientific article

A closure scheme for chemical master equations

scientific article published on 12 August 2013

A linearization method for probability moment equations

scientific article

A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes.

scientific article published in October 2005

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions

scientific article (publication date: February 2005)

An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: chemical Langevin equation, a proof of concept.

scientific article published in January 2008

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

scientific article

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.

scientific article

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

scientific article published on 17 January 2017

Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli

scientific article

Antimicrobial peptides targeting Gram-negative pathogens, produced and delivered by lactic acid bacteria.

scientific article

Bacterial sugar utilization gives rise to distinct single-cell behaviours

scientific article

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

scientific article published on January 2007

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

scientific article published on 23 January 2017

Chloride-Inducible Expression Vector for Delivery of Antimicrobial Peptides Targeting Antibiotic-Resistant Enterococcus faecium

scientific article published on 3 April 2015

Computational methods in synthetic biology

scientific article

Computational studies of protegrin antimicrobial peptides: a review.

scientific article

Computer-aided design of modular protein devices: Boolean AND gene activation.

scientific article published in November 2006

Concentration and Size Dependence of Dielectric Strength and Dielectric Relaxation of Polymers in Solutions of a ϑ Solvent via Molecular Dynamics Simulations

scientific article

Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy

scientific article published on April 2004

Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis

scientific article

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.

scientific article published on 28 March 2008

Corrigendum to “Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation” [Biochim. Biophys. Acta 1768 (2007) 509–520]

scientific article

Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model

scientific article

Development of a new pharmacophore model that discriminates active compstatin analogs

scientific article published on October 2008

Dimerization of protegrin-1 in different environments.

scientific article

Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

scientific article

Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant in the intestinal tract

scholarly article by Kathryn G Geldart et al published September 2018 in Bioengineering & Translational Medicine

Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci

scientific article published on 20 July 2015

Forward engineering of synthetic bio-logical AND gates

scientific article

Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor.

scientific article published on 16 June 2017

Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer

scientific article published on March 2010

How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.

scientific article published in January 2006

Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination.

scientific article

Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations.

scientific article

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

scientific article published on 13 January 2016

Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.

scientific article

Mathematical models in biology: from molecules to life ⬇️

scientific article published on February 18, 2011

Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics

scientific article published on 22 May 2017

Model reduction of multiscale chemical langevin equations: a numerical case study.

scientific article published in July 2009

Model-driven designs of an oscillating gene network

scientific article

Modeling Osmotic Lysis of Cells by Antimicrobial Peptides: Transient Diffusion of Ions and Osmotically-driven Flow

scientific article

Models for synthetic biology

scientific article

Modified lactic acid bacteria detect and inhibit multiresistant enterococci.

scientific article

Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

scientific article

Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

scientific article

Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?

scientific article

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

scientific article

Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions ⬇️

scientific article published on August 1, 2007

Molecular simulations of antimicrobial peptides

scientific article published on January 2010

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

scientific article published on 24 February 2006

Multiscale Models of Antibiotic Probiotics.

scientific article

Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes

scientific article

Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli

scientific article published on 20 July 2018

Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency

scientific article

Numerical simulation of stochastic gene circuits

scientific article

On Differences between Deterministic and Stochastic Models of Chemical Reactions: Schlögl Solved with ZI-Closure

scientific article published on 06 September 2018

On a theory of stability for nonlinear stochastic chemical reaction networks.

scientific article published on May 2015

On the nature of antimicrobial activity: a model for protegrin-1 pores

scientific article

Optimization of a stochastically simulated gene network model via simulated annealing.

scientific article

Path-integral method for predicting relative binding affinities of protein-ligand complexes.

scientific article published on April 2009

Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions

scientific article published on February 2005

Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore

scientific article

Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water ⬇️

scientific article published on August 1, 2001

Prediction of distant residue contacts with the use of evolutionary information.

scientific article

Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

scientific article

Rare loss-of-function mutation in complement component C3 provides insight into molecular and pathophysiological determinants of complement activity

scientific article

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

scientific article

Residue conservation information for generating near-native structures in protein-protein docking.

scientific article published in August 2006

Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin

scientific article published on 21 June 2006

Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.

scientific article published in February 2008

Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles

scientific article published in April 2005

Simulations of zwitterionic and anionic phospholipid monolayers

scientific article

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

scientific article

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers

scientific article published on 12 September 2018

Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

scientific article published in September 2002

Statistical Thermodynamics and Stochastic Kinetics

scientific article

Stochastic model reduction using a modified Hill-type kinetic rate law.

scientific article published on December 2012

Stochastic simulations of a synthetic bacteria-yeast ecosystem

scientific article

Stochastic simulations of the tetracycline operon

scientific article

Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

scientific article published on 15 December 2006

Structure-Function Analysis of the Two-Peptide Bacteriocin Plantaricin EF

scientific article published on 18 August 2016

Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin

scientific article

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

scientific article

SynBioSS: the synthetic biology modeling suite

scientific article published on 30 August 2008

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

scientific article

Thermodynamic Analysis of Protegrin-1 insertion and Permeation through a Lipid Bilayer

scientific article

Thermodynamic analysis of protegrin-1 insertion and permeation through a lipid bilayer

scientific article

Trade-offs in engineering sugar utilization pathways for titratable control

scientific article

Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER

scientific article published on 01 August 2007

pMPES: A Modular Peptide Expression System for the Delivery of Antimicrobial Peptides to the Site of Gastrointestinal Infections Using Probiotics

scientific article published on 05 October 2016

List of works by Yiannis N. Kaznessis

A Review of Methods for Computational Prediction of Blood-Brain Partitioning

A closure scheme for chemical master equations

A linearization method for probability moment equations

A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes.

Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions

An adaptive time step scheme for a system of stochastic differential equations with multiple multiplicative noise: chemical Langevin equation, a proof of concept.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

Antimicrobial mechanism of pore-forming protegrin peptides: 100 pores to kill E. coli

Antimicrobial peptides targeting Gram-negative pathogens, produced and delivered by lactic acid bacteria.

Bacterial sugar utilization gives rise to distinct single-cell behaviours

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

Chloride-Inducible Expression Vector for Delivery of Antimicrobial Peptides Targeting Antibiotic-Resistant Enterococcus faecium

Computational methods in synthetic biology

Computational studies of protegrin antimicrobial peptides: a review.

Computer-aided design of modular protein devices: Boolean AND gene activation.

Concentration and Size Dependence of Dielectric Strength and Dielectric Relaxation of Polymers in Solutions of a ϑ Solvent via Molecular Dynamics Simulations

Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy

Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis

Correlation between simulated physicochemical properties and hemolycity of protegrin-like antimicrobial peptides: predicting experimental toxicity.

Corrigendum to “Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation” [Biochim. Biophys. Acta 1768 (2007) 509–520]

Determining the orientation of protegrin-1 in DLPC bilayers using an implicit solvent-membrane model

Development of a new pharmacophore model that discriminates active compstatin analogs

Dimerization of protegrin-1 in different environments.

Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions

Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant in the intestinal tract

Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci

Forward engineering of synthetic bio-logical AND gates

Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor.

Free energy profile of the interaction between a monomer or a dimer of protegrin-1 in a specific binding orientation and a model lipid bilayer

How can a beta-sheet peptide be both a potent antimicrobial and harmfully toxic? Molecular dynamics simulations of protegrin-1 in micelles.

Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination.

Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations.

Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations

Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.

Mathematical models in biology: from molecules to life ⬇️

Maximum Entropy Prediction of Non-Equilibrium Stationary Distributions for Stochastic Reaction Networks with Oscillatory Dynamics

Model reduction of multiscale chemical langevin equations: a numerical case study.

Model-driven designs of an oscillating gene network

Modeling Osmotic Lysis of Cells by Antimicrobial Peptides: Transient Diffusion of Ions and Osmotically-driven Flow

Models for synthetic biology

Modified lactic acid bacteria detect and inhibit multiresistant enterococci.

Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: what do point mutations achieve?

Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in a zwitterionic dodecylphosphocholine micelle: insights into host-cell toxicity

Molecular dynamics simulations of three protegrin-type antimicrobial peptides: interplay between charges at the termini, β-sheet structure and amphiphilic interactions ⬇️

Molecular simulations of antimicrobial peptides

Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Multiscale Models of Antibiotic Probiotics.

Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes

Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli

Novel analogues of the therapeutic complement inhibitor compstatin with significantly improved affinity and potency

Numerical simulation of stochastic gene circuits

On Differences between Deterministic and Stochastic Models of Chemical Reactions: Schlögl Solved with ZI-Closure

On a theory of stability for nonlinear stochastic chemical reaction networks.

On the nature of antimicrobial activity: a model for protegrin-1 pores

Optimization of a stochastically simulated gene network model via simulated annealing.

Path-integral method for predicting relative binding affinities of protein-ligand complexes.

Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions

Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore

Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water ⬇️

Prediction of distant residue contacts with the use of evolutionary information.

Protegrin structure-activity relationships: using homology models of synthetic sequences to determine structural characteristics important for activity.

Rare loss-of-function mutation in complement component C3 provides insight into molecular and pathophysiological determinants of complement activity

Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

Residue conservation information for generating near-native structures in protein-protein docking.

Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin

Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations.

Simulation of the N-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles

Simulations of zwitterionic and anionic phospholipid monolayers

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers

Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

Statistical Thermodynamics and Stochastic Kinetics

Stochastic model reduction using a modified Hill-type kinetic rate law.

Stochastic simulations of a synthetic bacteria-yeast ecosystem