All Stories

  1. Characterization of Class IIa Bacteriocin Resistance in Enterococcus faecium

    Article • Antimicrobial Agents and Chemotherapy, January 2017, ASM Journals

    Yiannis Kaznessis

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

    Article • Pharmaceuticals, October 2016, MDPI AG

    Yiannis Kaznessis

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

    Article • Biochemistry, September 2016, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, April 2016, Elsevier

    Yiannis Kaznessis

  5. Modeling stochasticity in biochemical reaction networks

    Article • Journal of Physics D Applied Physics, February 2016, Institute of Physics Publishing

    Yiannis Kaznessis

  6. Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistantEnterococci

    Article • Biotechnology and Bioengineering, September 2015, Wiley

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, May 2015, American Institute of Physics

    Yiannis Kaznessis

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

    Article • Applied and Environmental Microbiology, April 2015, ASM Journals

    Yiannis Kaznessis

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

    Article • The Journal of Immunology, February 2015, The American Association of Immunologists

    Yiannis Kaznessis

  10. Chemical Master Equation Closure for Computer-Aided Synthetic Biology

    Article • November 2014, Springer Science + Business Media

    Yiannis Kaznessis

  11. Multiscale models of antibiotic probiotics

    Article • Current Opinion in Chemical Engineering, November 2014, Elsevier

    Yiannis Kaznessis

  12. SynBioSS Designer Modeling Suite

    Article • October 2014, Wiley

    Yiannis Kaznessis

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

    Article • Journal of Chemical & Engineering Data, October 2014, American Chemical Society (ACS)

    Yiannis Kaznessis

  14. Solution of chemical master equations for nonlinear stochastic reaction networks

    Article • Current Opinion in Chemical Engineering, August 2014, Elsevier

    Yiannis Kaznessis

  15. Bacterial sugar utilization gives rise to distinct single-cell behaviours

    Article • Molecular Microbiology, July 2014, Wiley

    Yiannis Kaznessis

  16. Modified Lactic Acid Bacteria Detect and Inhibit Multiresistant Enterococci

    Article • ACS Synthetic Biology, June 2014, American Chemical Society (ACS)

    Dr Gary M Dunny, Yiannis Kaznessis

  17. Using native sugar utilization pathways as inducible systems in microorganisms

    Article • ACS Synthetic Biology, April 2014, American Chemical Society (ACS)

    Chase Beisel, Yiannis Kaznessis

  18. Antimicrobial Peptides Targeting Gram-negative Pathogens, Produced and Delivered by Lactic Acid Bacteria

    Article • ACS Synthetic Biology, November 2013, American Chemical Society (ACS)

    Yiannis Kaznessis

  19. A closure scheme for chemical master equations

    Article • Proceedings of the National Academy of Sciences, August 2013, Proceedings of the National Academy of Sciences

    Yiannis Kaznessis

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

    Article • January 2013, Elsevier

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, December 2012, American Institute of Physics

    Yiannis Kaznessis

  22. Efficient moment matrix generation for arbitrary chemical networks

    Article • Chemical Engineering Science, December 2012, Elsevier

    Yiannis Kaznessis

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

    Article • International Journal of Molecular Sciences, September 2012, MDPI AG

    Yiannis Kaznessis

  24. Stochastic simulations of a synthetic bacteria-yeast ecosystem

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Yiannis Kaznessis

  25. Thermodynamic Analysis of Protegrin-1 Insertion and Permeation through a Lipid Bilayer

    Article • The Journal of Physical Chemistry, December 2011, American Chemical Society (ACS)

    Yiannis Kaznessis

  26. proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression

    Article • ACS Chemical Biology, October 2011, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • PLoS ONE, July 2011, PLOS

    Yiannis Kaznessis

  28. Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation

    Article • Proceedings of the National Academy of Sciences, May 2011, Proceedings of the National Academy of Sciences

    Yiannis Kaznessis

  29. Mathematical models in biology: from molecules to life

    Article • WIREs Systems Biology and Medicine, February 2011, Wiley

    Yiannis Kaznessis

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

    Article • Biophysical Journal, February 2011, Elsevier

    Yiannis Kaznessis

  31. Analytical derivation of moment equations in stochastic chemical kinetics

    Article • Chemical Engineering Science, February 2011, Elsevier

    Yiannis Kaznessis

  32. Computational studies of protegrin antimicrobial peptides: A review

    Article • Peptides, January 2011, Elsevier

    Yiannis Kaznessis

  33. SynBioSS-Aided Design of Synthetic Biological Constructs

    Article • January 2011, Elsevier

    Yiannis Kaznessis

  34. Model reduction of multi-scale chemical Langevin equations

    Article • Systems & Control Letters, January 2011, Elsevier

    Yiannis Kaznessis

  35. Stochastic simulations of the tetracycline operon

    Article • BMC Systems Biology, January 2011, Springer Science + Business Media

    Yiannis Kaznessis

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

    Article • Molecular Immunology, January 2011, Elsevier

    Yiannis Kaznessis

  37. Dimerization of Protegrin-1 in Different Environments

    Article • International Journal of Molecular Sciences, September 2010, MDPI AG

    Yiannis Kaznessis

  38. Impaired ability of complement activation via the alternative pathway C3 convertase caused by a single-point mutation in the beta chain of C3

    Article • Molecular Immunology, August 2010, Elsevier

    Yiannis Kaznessis

  39. Generation of analogues of the clinical complement inhibitor compstatin with improved potency and pharmacokinetics

    Article • Molecular Immunology, August 2010, Elsevier

    Yiannis Kaznessis

  40. 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]

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, August 2010, Elsevier

    Yiannis Kaznessis

  41. 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

    Article • The Journal of Physical Chemistry, March 2010, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • Briefings in Bioinformatics, February 2010, Oxford University Press (OUP)

    Yiannis Kaznessis

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

    Article • Peptides, January 2010, Elsevier

    Yiannis Kaznessis

  44. Molecular Simulations of Antimicrobial Peptides

    Article • December 2009, Springer Science + Business Media

    Yiannis Kaznessis

  45. Forward engineering of synthetic bio-logical AND gates

    Article • Biochemical Engineering Journal, December 2009, Elsevier

    Yiannis Kaznessis

  46. Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin

    Article • Journal of Molecular Recognition, November 2009, Wiley

    Yiannis Kaznessis

  47. Computational methods in synthetic biology

    Article • Biotechnology Journal, October 2009, Wiley

    Yiannis Kaznessis

  48. Multiscale models for synthetic biology

    Article • September 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Yiannis Kaznessis

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

    Article • Molecular Simulation, August 2009, Taylor & Francis

    Yiannis Kaznessis

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

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, July 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Yiannis Kaznessis

  51. Path-Integral Method for Predicting Relative Binding Affinities of Protein−Ligand Complexes

    Article • Journal of the American Chemical Society, April 2009, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • PLoS ONE, March 2009, PLOS

    Yiannis Kaznessis

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

    Article • Biophysical Journal, February 2009, Elsevier

    Yiannis Kaznessis

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

    Article • PLoS Computational Biology, January 2009, PLOS

    Yiannis Kaznessis

  55. Statistical Thermodynamics and Stochastic Kinetics

    Article • January 2009, Cambridge University Press

    Yiannis Kaznessis

  56. Development of a New Pharmacophore Model That Discriminates Active Compstatin Analogs

    Article • Chemical Biology & Drug Design, October 2008, Wiley

    Yiannis Kaznessis

  57. Tweaking biological switches through a better understanding of bistability behavior

    Article • Current Opinion in Biotechnology, October 2008, Elsevier

    Yiannis Kaznessis

  58. SynBioSS: the synthetic biology modeling suite

    Article • Bioinformatics, August 2008, Oxford University Press (OUP)

    Yiannis Kaznessis

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

    Article • Peptides, July 2008, Elsevier

    Yiannis Kaznessis

  60. On the Nature of Antimicrobial Activity:  A Model for Protegrin-1 Pores

    Article • Journal of the American Chemical Society, April 2008, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, January 2008, American Institute of Physics

    Yiannis Kaznessis

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

    Article • Proteins Structure Function and Bioinformatics, August 2007, Wiley

    Yiannis Kaznessis

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

    Article • Journal of Biosciences, August 2007, Springer Science + Business Media

    Yiannis Kaznessis

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

    Article • Molecular Simulation, August 2007, Taylor & Francis

    Yiannis Kaznessis

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

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, March 2007, Elsevier

    Yiannis Kaznessis

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

    Article • Bioorganic & Medicinal Chemistry, February 2007, Elsevier

    Yiannis Kaznessis

  67. Models for synthetic biology

    Article • BMC Systems Biology, January 2007, Springer Science + Business Media

    Yiannis Kaznessis

  68. Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data

    Article • BMC Biochemistry, January 2007, Springer Science + Business Media

    Yiannis Kaznessis

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

    Article • The Journal of Physical Chemistry, January 2007, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • Physical Biology, December 2006, Institute of Physics Publishing

    Yiannis Kaznessis

  71. Optimization of a Stochastically Simulated Gene Network Model via Simulated Annealing

    Article • Biophysical Journal, November 2006, Elsevier

    Yiannis Kaznessis

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

    Article • Journal of Biological Chemistry, September 2006, American Society for Biochemistry & Molecular Biology (ASBMB)

    Yiannis Kaznessis

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

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, September 2006, Elsevier

    Yiannis Kaznessis

  74. RESIDUE CONSERVATION INFORMATION FOR GENERATING NEAR-NATIVE STRUCTURES IN PROTEIN–PROTEIN DOCKING

    Article • Journal of Bioinformatics and Computational Biology, August 2006, World Scientific Pub Co Pte Lt

    Yiannis Kaznessis

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

    Article • Peptides, June 2006, Elsevier

    Yiannis Kaznessis

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

    Article • Molecular Simulation, March 2006, Taylor & Francis

    Yiannis Kaznessis

  77. Multi-scale models for gene network engineering

    Article • Chemical Engineering Science, February 2006, Elsevier

    Yiannis Kaznessis

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

    Article • Biopolymers, January 2006, Wiley

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, December 2005, American Institute of Physics

    Yiannis Kaznessis

  80. Model-Driven Designs of an Oscillating Gene Network

    Article • Biophysical Journal, December 2005, Elsevier

    Yiannis Kaznessis

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

    Article • Peptides, November 2005, Elsevier

    Yiannis Kaznessis

  82. A QUANTITATIVE ANALYSIS OF INTERFACIAL AMINO ACID CONSERVATION IN PROTEIN-PROTEIN HETERO COMPLEXES

    Article • Journal of Bioinformatics and Computational Biology, October 2005, World Scientific Pub Co Pte Lt

    Yiannis Kaznessis

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

    Article • Current Medicinal Chemistry - Central Nervous System Agents, September 2005, Bentham Science Publishers

    Yiannis Kaznessis

  84. Molecular Dynamics Simulations of the Helical Antimicrobial Peptide Ovispirin-1 in a Zwitterionic Dodecylphosphocholine Micelle:  Insights into Host-Cell Toxicity

    Article • The Journal of Physical Chemistry, July 2005, American Chemical Society (ACS)

    Yiannis Kaznessis

  85. Lung Surfactants

    Article • May 2005, Taylor & Francis

    Yiannis Kaznessis

  86. Numerical simulation of stochastic gene circuits

    Article • Computers & Chemical Engineering, February 2005, Elsevier

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, February 2005, American Institute of Physics

    Yiannis Kaznessis

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

    Article • Peptides, February 2005, Elsevier

    Yiannis Kaznessis

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

    Article • Proteins Structure Function and Bioinformatics, January 2005, Wiley

    Yiannis Kaznessis

  90. Simulation of theN-terminus of HIV-1 glycoprotein 41000 fusion peptide in micelles

    Article • Journal of Peptide Science, January 2005, Wiley

    Yiannis Kaznessis

  91. Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using13C-enhanced Fourier transform infrared spectroscopy

    Article • Protein Science, April 2004, Wiley

    Yiannis Kaznessis

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

    Article • Biotechnology and Bioengineering, January 2004, Wiley

    Yiannis Kaznessis

  93. Conformational Mapping of the N-terminal Peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier Transform Infrared Spectroscopy

    Article • May 2003, Protein Data Bank, Rutgers University

    Yiannis Kaznessis

  94. Specific Mode of Interaction Between Components of Model Pulmonary Surfactants Using Computer Simulations

    Article • Journal of Molecular Biology, September 2002, Elsevier

    Yiannis Kaznessis

  95. Simulations of Zwitterionic and Anionic Phospholipid Monolayers

    Article • Biophysical Journal, April 2002, Elsevier

    Yiannis Kaznessis

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

    Article • Macromolecules, October 1999, American Chemical Society (ACS)

    Yiannis Kaznessis

  97. Molecular dynamics simulations of dielectric relaxation of concentrated polymer solutions

    Article • The Journal of Chemical Physics, July 1999, American Institute of Physics

    Yiannis Kaznessis

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

    Article • Macromolecules, February 1999, American Chemical Society (ACS)

    Yiannis Kaznessis

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

    Article • The Journal of Chemical Physics, September 1998, American Institute of Physics

    Yiannis Kaznessis

  100. Molecular Dynamics Simulations of Polar Polymer Brushes

    Article • Macromolecules, May 1998, American Chemical Society (ACS)

    Yiannis Kaznessis