Y. Kaznessis

发表

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

Yuhua Duan, Y. Duan, Boojala V. B. Reddy, 2005, Protein science : a publication of the Protein Society.

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

Y. Kaznessis, Pin-Kuang Lai, 2017, Journal of chemical theory and computation.

Trade-offs in Engineering Sugar Utilization Pathways for Titratable Control

Chase L. Beisel, C. Beisel, Y. Kaznessis, 2014, ACS synthetic biology.

Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Chase L. Beisel, C. Beisel, Y. Kaznessis, 2014, Molecular microbiology.

Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation

Wei-Shou Hu, D. Ramkrishna, Y. Kaznessis, 2011, Proceedings of the National Academy of Sciences.

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

Y. Kaznessis, P. Smadbeck, 2015, The Journal of chemical physics.

Computational methods in synthetic biology

Y. Kaznessis, 2009, Biotechnology journal.

Convergent Transcription in the Butyrolactone Regulon in Streptomyces coelicolor Confers a Bistable Genetic Switch for Antibiotic Biosynthesis

Wei-Shou Hu, Eriko Takano, Yiannis N. Kaznessis, 2011, PloS one.

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

P. H. Constantino, Y. Kaznessis, 2017, Chemical engineering science.

Modeling stochasticity in biochemical reaction networks

P. H. Constantino, Y. Kaznessis, P. Smadbeck, 2016 .

proTeOn and proTeOff, new protein devices that inducibly activate bacterial gene expression.

Katherine Volzing, Yiannis N Kaznessis, Konstantinos Biliouris, 2011, ACS chemical biology.

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

Yiannis N Kaznessis, Y. Kaznessis, V. Vivcharuk, 2011, The journal of physical chemistry. B.

Statistical Thermodynamics and Stochastic Kinetics: An Introduction for Engineers

Yiannis N. Kaznessis, Y. Kaznessis, 2012 .

Mathematical models in biology: from molecules to life

Y. Kaznessis, 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

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

H. Khandelia, Y. Kaznessis, A. Sayyed-Ahmad, 2009, Molecular simulation.

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

H. Khandelia, Y. Kaznessis, A. Langham, 2006, Biopolymers.

Chemical master equation closure for computer-aided synthetic biology.

Y. Kaznessis, P. Smadbeck, 2015, Methods in molecular biology.

SynBioSS Designer Modeling Suite

Emma M. B. Weeding, E. Weeding, Y. Kaznessis, 2014 .

Statistical Thermodynamics and Stochastic Kinetics: Stochastic simulations of chemical reaction kinetics

Y. Kaznessis, 2011 .

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

Y. Kaznessis, D. Bolintineanu, A. Sayyed-Ahmad, 2014, Journal of chemical and engineering data.

Determining the Orientation of Protegrin-1 in DLPC Bilayers Using an Implicit Solvent-Membrane Model

Y. Kaznessis, A. Sayyed-Ahmad, 2009, PloS one.

Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

Y. Kaznessis, M. Vlysidis, Brittany Forkus, 2017, Scientific Reports.

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

Y. Kaznessis, Spyridon Vicatos, 2007, Proteins.

Statistical Thermodynamics and Stochastic Kinetics: Elements of classical thermodynamics

Y. Kaznessis, 2011 .

Molecular simulations of antimicrobial peptides.

Y. Kaznessis, A. Langham, 2010, Methods in molecular biology.

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

Y. Kaznessis, N. Ostberg, 2005, Peptides.

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

Y. Kaznessis, B. Hackel, Seth C. Ritter, 2018, Biotechnology and bioengineering.

Effects of mutations on the C-terminus of protegrin-1: a molecular dynamics simulation study

Y. Kaznessis, A. Langham, 2006 .

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

R. Larson, Sangtae Kim, Y. Kaznessis, 2002, Journal of molecular biology.

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

Y. Kaznessis, P. Kyriakou, B. Ekblad, 2016, Biochimica et biophysica acta.

Retrocyclins Kill Bacilli and Germinating Spores of Bacillus anthracis and Inactivate Anthrax Lethal Toxin*

A. Waring, Wuyuan Lu, Y. Kaznessis, 2006, Journal of Biological Chemistry.

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

H. Khandelia, Y. Kaznessis, 2006, Peptides.

Moment Closure Stability Analysis of Stochastic Reaction Networks with Oscillatory Dynamics

P. H. Constantino, Y. Kaznessis, 2019, 1902.09625.

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

Boojala V. B. Reddy, Y. Kaznessis, 2007, Journal of Biosciences.

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

Y. Kaznessis, B. Hackel, Maria K. McClintock, 2016, Biotechnology and bioengineering.

Multiscale Models of the Antimicrobial Peptide Protegrin-1 on Gram-Negative Bacteria Membranes

Y. Kaznessis, D. Bolintineanu, V. Vivcharuk, 2012, International journal of molecular sciences.

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

Y. Kaznessis, J. Borrero, Kathryn Geldart, 2015, Applied and Environmental Microbiology.

Structure‐kinetic relationship analysis of the therapeutic complement inhibitor compstatin

John D Lambris, D. Ricklin, J. Lambris, 2009, Journal of molecular recognition : JMR.

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

Yiannis N Kaznessis, Jonathan R. Tomshine, Jonathan Tomshine, 2006, Biophysical journal.

Forward engineering of synthetic bio-logical and gates

Yiannis N. Kaznessis, Kavita Iyer Ramalingam, Jonathan R. Tomshine, 2008 .

Models for synthetic biology

Yiannis N. Kaznessis, Y. Kaznessis, 2007, BMC Systems Biology.

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

H. Salis, Y. Kaznessis, Y N Kaznessis, 2006, Physical biology.

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

William M. Lee, A. Waring, Y. Kaznessis, 2003, Protein science : a publication of the Protein Society.

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

Y. Kaznessis, P. Kyriakou, B. Ekblad, 2016, Biochemistry.

Modified Lactic Acid Bacteria Detect and Inhibit Multiresistant Enterococci

Yiannis N. Kaznessis, Gary M. Dunny, Y. Kaznessis, 2014, ACS synthetic biology.

Dielectric Relaxation of Dipole-Inverted Polar Polymers As Studied by Computer Simulations

Y. Kaznessis, E. Maginn, D. Hill, 1999 .

Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

Y. Kaznessis, E. Maginn, D. Hill, 1999 .

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

Y. Kaznessis, E. Maginn, D. Hill, 1999 .

A molecular dynamics study of macromolecules in good solvents: Comparison with dielectric spectroscopy experiments

Y. Kaznessis, E. Maginn, D. Hill, 1998 .

Development of a New Pharmacophore Model That Discriminates Active Compstatin Analogs

John D Lambris, Chandrika Mulakala, J. Lambris, 2008, Chemical biology & drug design.

Inferring Gene Regulatory Relationships by Combining Target–target Pattern Recognition and Regulator-specific Motif Examination

Yiannis Kaznessis, Hairong Wei, Hairong Wei, 2022 .

Stochastic simulations of the tetracycline operon

Prodromos Daoutidis, Yiannis N. Kaznessis, Konstantinos Biliouris, 2011, BMC Systems Biology.

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

Yiannis N. Kaznessis, Mark E. Snow, C. John Blankley, 2001, J. Comput. Aided Mol. Des..

Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Vassilios Sotiropoulos, Howard M. Salis, Yiannis N. Kaznessis, 2006, BMC Bioinformatics.

Analytical Derivation of Moment Equations in Stochastic Chemical Kinetics.

Vassilios Sotiropoulos, Yiannis N Kaznessis, Y. Kaznessis, 2011, Chemical engineering science.

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

Y. Kaznessis, Brittany Forkus, Kathryn Geldart, 2016, Pharmaceuticals.

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

Katherine Volzing, Yiannis N Kaznessis, Michael J Sadowsky, 2013, ACS synthetic biology.

Computer-Aided Design of Synthetic Biological Constructs with the Synthetic Biology Software Suite

Yiannis N. Kaznessis, Patrick Smadbeck, Katherine Volzing, 2013 .

SynBioSS-aided design of synthetic biological constructs.

Yiannis N Kaznessis, Y. Kaznessis, 2011, Methods in enzymology.

Tweaking biological switches through a better understanding of bistability behavior.

Wei-Shou Hu, Anushree Chatterjee, Yiannis N Kaznessis, 2008, Current opinion in biotechnology.

Model-driven designs of an oscillating gene network.

Yiannis N Kaznessis, Howard Salis, Jonathan R. Tomshine, 2005, Biophysical journal.

Numerical simulation of stochastic gene circuits

Howard M. Salis, Yiannis N. Kaznessis, H. Salis, 2005, Comput. Chem. Eng..

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

Y. Kaznessis, N. Salzman, G. Dunny, 2018, Bioengineering & translational medicine.

Cation–π Interactions Stabilize the Structure of the Antimicrobial Peptide Indolicidin near Membranes: Molecular Dynamics Simulations

H. Khandelia, Y. Kaznessis, 2007 .

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

John D Lambris, D. Ricklin, J. Lambris, 2011, Molecular immunology.

Lung Surfactants: A Molecular Perspective from Computation

R. Larson, Y. Kaznessis, 2005 .

Stochastic simulations of a synthetic bacteria-yeast ecosystem

Claudia Schmidt-Dannert, David Babson, Yiannis N. Kaznessis, 2012, BMC Systems Biology.

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

Yiannis Kaznessis, Howard Salis, H. Salis, 2005, The Journal of chemical physics.

Molecular Dynamics Simulations of Polar Polymer Brushes

Y. Kaznessis, E. Maginn, D. Hill, 1998 .

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

Y. Kaznessis, A. Langham, Abdal Ahmad, 2008, Journal of the American Chemical Society.

Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore

Yiannis N. Kaznessis, Abdallah Sayyed-Ahmad, Dan S. Bolintineanu, 2009, PLoS Comput. Biol..

Computational studies of protegrin antimicrobial peptides: A review

Y. Kaznessis, D. Bolintineanu, 2011, Peptides.

A linearization method for probability moment equations

Michail Vlysidis, Yiannis N. Kaznessis, Y. Kaznessis, 2018, Comput. Chem. Eng..

ZI-Closure Scheme: A Method to Solve and Study Stochastic Reaction Networks

Yiannis N. Kaznessis, M. Vlysidis, P. H. Constantino, 2017 .

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

Y. Kaznessis, R. Lehrer, H. Davis, 2010, Peptides.

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

Yiannis N. Kaznessis, Y. Kaznessis, 2005 .

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

Y. Kaznessis, Pin-Kuang Lai, 2018, ACS omega.

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

H. Khandelia, Y. Kaznessis, 2005, Peptides.

Systematic Mutagenesis of Oncocin Reveals Enhanced Activity and Insights into the Mechanisms of Antimicrobial Activity.

Y. Kaznessis, Pin-Kuang Lai, B. Hackel, 2018, Molecular systems design & engineering.

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

H. Khandelia, Y. Kaznessis, 2005, The journal of physical chemistry. B.

Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

Y. Kaznessis, Kathryn Geldart, 2017, Antimicrobial Agents and Chemotherapy.

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

Yiannis N Kaznessis, Chandrika Mulakala, Y. Kaznessis, 2009, Journal of the American Chemical Society.

Simulations of zwitterionic and anionic phospholipid monolayers.

R. Larson, Sangtae Kim, Y. Kaznessis, 2002, Biophysical journal.

Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity

Bo Nilsson, Yiannis N Kaznessis, Daniel Ricklin, 2015, The Journal of Immunology.

Determinants of Complement Activity into Molecular and Pathophysiological InsightComplement Component C 3 Provides Rare Loss-of-Function Mutation in Ekdahl

John D Lambris, B. Nilsson, K. Ekdahl, 2015 .

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

Yiannis N. Kaznessis, Allison A. Langham, Himanshu Khandelia, 2008, Peptides.

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

Y. Kaznessis, H. Davis, D. Bolintineanu, 2007, Molecular simulation.

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.

Patrick Smadbeck, Yiannis N Kaznessis, Y. Kaznessis, 2014, Current opinion in chemical engineering.

Multiscale models for synthetic biology

Vassilios Sotiropoulos, Yiannis N. Kaznessis, Anthony D. Hill, 2009, 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

A closure scheme for chemical master equations

Yiannis N. Kaznessis, Patrick Smadbeck, Y. Kaznessis, 2013, Proceedings of the National Academy of Sciences.

Dimerization of Protegrin-1 in Different Environments

Y. Kaznessis, V. Vivcharuk, 2010, International journal of molecular sciences.

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.

Y. Kaznessis, V. Vivcharuk, 2010, The journal of physical chemistry. B.

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

H. Khandelia, Y. Kaznessis, 2007 .

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

H. Khandelia, Y. Kaznessis, A. Langham, 2006, Biochimica et biophysica acta.

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

H. Khandelia, Y. Kaznessis, 2007, Biochimica et biophysica acta.

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

Yiannis N. Kaznessis, Jason Houle, Emma M. B. Weeding, 2010, Briefings Bioinform..

SynBioSS: the synthetic biology modeling suite

Vassilios Sotiropoulos, Yiannis N. Kaznessis, Anthony D. Hill, 2008, Bioinform..

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

Vassilios Sotiropoulos, Yiannis N. Kaznessis, Y. Kaznessis, 2007, BMC Systems Biology.

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

Michail Vlysidis, Yiannis N. Kaznessis, Y. Kaznessis, 2018, Entropy.

Solving Stochastic Reaction Networks with Maximum Entropy Lagrange Multipliers

Michail Vlysidis, Yiannis N. Kaznessis, Y. Kaznessis, 2018, Entropy.

Efficient Moment Matrix Generation for Arbitrary Chemical Networks.

Y. Kaznessis, P. Smadbeck, P Smadbeck, 2012, Chemical engineering science.

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

Patrick Smadbeck, Yiannis Kaznessis, Y. Kaznessis, 2012, The Journal of chemical physics.

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

Y. Kaznessis, A. Langham, 2005, Journal of peptide science : an official publication of the European Peptide Society.

How to Build Kinetic Models of BioBricks

Vassilios Sotiropoulos, Yiannis N. Kaznessis, Emma Weeding, 2009 .

Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation

D. Ramkrishna, Y. Kaznessis, C. Shu, 2011, Proceedings of the National Academy of Sciences.

Multiscale Models of Antibiotic Probiotics.

Yiannis N Kaznessis, Y. Kaznessis, 2014, Current opinion in chemical engineering.

Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity

John D Lambris, B. Nilsson, K. Ekdahl, 2015, The Journal of Immunology.

A simple, yet highly accurate, QSAR model captures the complement inhibitory activity of compstatin.

John D Lambris, Y. Kaznessis, Chandrika Mulakala, 2007, Bioorganic & medicinal chemistry.

Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm

Peter Dayan, Nathaniel D. Daw, Ben Seymour, 2022 .

Phase spaces, from classical to quantum mechanics, and back

Y. Kaznessis, 2011 .

Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study

Prodromos Daoutidis, Vassilios Sotiropoulos, Marie-Nathalie Contou-Carrere, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Statistical Thermodynamics and Stochastic Kinetics: Fluctuations and other ensembles

Y. Kaznessis, 2011 .

Computational methods in synthetic biology

Y. Kaznessis, 2009, Biotechnology journal.

Residue Conservation Information for Generating near-native Structures in Protein-protein Docking

Yiannis N. Kaznessis, Boojala V. B. Reddy, Yuhua Duan, 2006, J. Bioinform. Comput. Biol..

An Efficient Docking Algorithm Using Conserved Residue Information to Study Protein-Protein Interactions

Y. Duan, Boojala V. B. Reddy, Y. Kaznessis, 2004 .

John D Lambris, K. O’Rourke, Y. Kaznessis, 2022 .

Multi-scale models for gene network engineering

Yiannis N. Kaznessis, Y. Kaznessis, 2006 .

Numerical simulation of stochastic gene circuits

H. Salis, Y. Kaznessis, 2005, Comput. Chem. Eng..

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

Yiannis N Kaznessis, Howard Salis, H. Salis, 2005, The Journal of chemical physics.

Model reduction of multi-scale chemical Langevin equations

P. Daoutidis, Y. Kaznessis, M.-N. Contou-Carrere, 2011, Syst. Control. Lett..