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1

Mathematical models in biology: from molecules to life

Yiannis N. Kaznessis

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2011

Language:

english

File:

PDF, 257 KB

english, 2011

2

[Methods in Enzymology] Synthetic Biology, Part B - Computer Aided Design and DNA Assembly Volume 498 || SynBioSS-Aided Design of Synthetic Biological Constructs

Kaznessis, Yiannis N.

Year:

2011

Language:

english

File:

PDF, 687 KB

english, 2011

3

Solution of chemical master equations for nonlinear stochastic reaction networks

Smadbeck, Patrick, Kaznessis, Yiannis N

Journal:

Current Opinion in Chemical Engineering

Year:

2014

Language:

english

File:

PDF, 690 KB

english, 2014

4

A linearization method for probability moment equations

Vlysidis, Michail, Kaznessis, Yiannis N.

Journal:

Computers & Chemical Engineering

Year:

2018

Language:

english

File:

PDF, 467 KB

english, 2018

5

Statistical Thermodynamics and Stochastic Kinetics (An Introduction for Engineers) || Elements of probability and combinatorial theory

Kaznessis, Yiannis N.

Year:

2011

Language:

english

File:

PDF, 358 KB

english, 2011

6

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

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

Journal:

Year:

2006

Language:

english

File:

PDF, 1.05 MB

english, 2006

7

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

Hairong Wei, Yiannis Kaznessis

Journal:

Biotechnology and Bioengineering

Year:

2005

Language:

english

File:

PDF, 508 KB

english, 2005

8

Structure-kinetic relationship analysis of the therapeutic complement inhibitor compstatin

Paola Magotti, Daniel Ricklin, Hongchang Qu, You-Qiang Wu, Yiannis N. Kaznessis, John D. Lambris

Journal:

Journal of Molecular Recognition

Year:

2009

Language:

english

File:

PDF, 664 KB

english, 2009

9

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

Chandrika Mulakala, John D. Lambris, Yiannis Kaznessis

Journal:

Bioorganic & Medicinal Chemistry

Year:

2007

Language:

english

File:

PDF, 311 KB

english, 2007

10

Multi-scale models for gene network engineering

Yiannis N. Kaznessis

Journal:

Chemical Engineering Science

Year:

2006

Language:

english

File:

PDF, 638 KB

english, 2006

11

Analytical derivation of moment equations in stochastic chemical kinetics

Vassilios Sotiropoulos, Yiannis N. Kaznessis

Journal:

Chemical Engineering Science

Year:

2011

Language:

english

File:

PDF, 536 KB

english, 2011

12

Numerical simulation of stochastic gene circuits

Howard Salis, Yiannis Kaznessis

Journal:

Computers & Chemical Engineering

Year:

2005

Language:

english

File:

PDF, 455 KB

english, 2005

13

Tweaking biological switches through a better understanding of bistability behavior

Anushree Chatterjee, Yiannis N. Kaznessis, Wei-Shou Hu

Journal:

Current Opinion in Biotechnology

Year:

2008

Language:

english

File:

PDF, 413 KB

english, 2008

14

Model reduction of multi-scale chemical Langevin equations

Marie-Nathalie Contou-Carrere, Vassilios Sotiropoulos, Yiannis N. Kaznessis, Prodromos Daoutidis

Journal:

Systems & Control Letters

Year:

2011

Language:

english

File:

PDF, 324 KB

english, 2011

15

Stochastic simulations of the tetracycline operon

Konstantinos Biliouris, Prodromos Daoutidis, Yiannis N Kaznessis

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 1.99 MB

english, 2011

16

Prediction of distant residue contacts with the use of evolutionary information

Spyridon Vicatos, Boojala V.B. Reddy, Yiannis Kaznessis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 278 KB

english, 2005

17

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

Spyridon Vicatos, Yiannis N. Kaznessis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 323 KB

english, 2008

18

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

Allison Langham, Dr Yiannis Kaznessis

Journal:

Journal of Peptide Science

Year:

2005

Language:

english

File:

PDF, 604 KB

english, 2005

19

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

Boojala V. B. Reddy, Yiannis N. Kaznessis

Journal:

Journal of Biosciences

Year:

2007

Language:

english

File:

PDF, 96 KB

english, 2007

20

Forward engineering of synthetic bio-logical AND gates

Kavita Iyer Ramalingam, Jonathan R. Tomshine, Jennifer A. Maynard, Yiannis N. Kaznessis

Journal:

Biochemical Engineering Journal

Year:

2009

Language:

english

File:

PDF, 1.38 MB

english, 2009

21

Development of a New Pharmacophore Model That Discriminates Active Compstatin Analogs

Ting-Lan Chiu, Chandrika Mulakala, John D. Lambris, Yiannis N. Kaznessis

Journal:

Chemical Biology & Drug Design

Year:

2008

Language:

english

File:

PDF, 473 KB

english, 2008

22

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

Yiannis N. Kaznessis, Mark E. Snow, C. John Blankley

Journal:

Journal of Computer-Aided Molecular Design

Year:

2001

Language:

english

File:

PDF, 125 KB

english, 2001

23

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

Larry M. Gordon, Patrick W. Mobley, William Lee, Sepehr Eskandari, Yiannis N. Kaznessis, Mark A. Sherman, Alan J. Waring

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 490 KB

english, 2004

24

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

Hongchang Qu, Paola Magotti, Daniel Ricklin, Emilia L. Wu, Ioannis Kourtzelis, Maria Lasaosa, You-Qiang Wu, Florea Lupu, Yiannis N. Kaznessis, John D. Lambris

Journal:

Molecular Immunology

Year:

2010

Language:

english

File:

PDF, 87 KB

english, 2010

25

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

Georgia Sfyroera, Daniel Ricklin, Hui Chen, Kristina Nilsson-Ekdahl, Bo Nilsson, Emilia L. Wu, Yiannis N. Kaznessis, John D. Lambris

Journal:

Molecular Immunology

Year:

2010

Language:

english

File:

PDF, 76 KB

english, 2010

26

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

Hongchang Qu, Paola Magotti, Daniel Ricklin, Emilia L. Wu, Ioannis Kourtzelis, You-Qiang Wu, Yiannis N. Kaznessis, John D. Lambris

Journal:

Molecular Immunology

Year:

2011

Language:

english

File:

PDF, 776 KB

english, 2011

27

Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

Howard Salis, Vassilios Sotiropoulos, Yiannis N Kaznessis

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 2.83 MB

english, 2006

28

Models for synthetic biology

Yiannis N Kaznessis

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 358 KB

english, 2007

29

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

Vassilios Sotiropoulos, Yiannis N Kaznessis

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 1.80 MB

english, 2007

30

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

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

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2006

Language:

english

File:

PDF, 867 KB

english, 2006

31

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

Himanshu Khandelia, Yiannis N. Kaznessis

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2007

Language:

english

File:

PDF, 1.83 MB

english, 2007

32

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]

Himanshu Khandelia, Yiannis N. Kaznessis

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2010

Language:

english

File:

PDF, 192 KB

english, 2010

33

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

Nathan Ostberg, Yiannis Kaznessis

Journal:

Year:

2005

Language:

english

File:

PDF, 197 KB

english, 2005

34

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

Himanshu Khandelia, Yiannis N. Kaznessis

Journal:

Year:

2005

Language:

english

File:

PDF, 1.00 MB

english, 2005

35

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

Himanshu Khandelia, Yiannis N. Kaznessis

Journal:

Year:

2006

Language:

english

File:

PDF, 722 KB

english, 2006

36

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

Allison A. Langham, Himanshu Khandelia, Benjamin Schuster, Alan J. Waring, Robert I. Lehrer, Yiannis N. Kaznessis

Journal:

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

37

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

Dan Bolintineanu, Ehsan Hazrati, H. Ted Davis, Robert I. Lehrer, Yiannis N. Kaznessis

Journal:

Year:

2010

Language:

english

File:

PDF, 890 KB

english, 2010

38

Computational studies of protegrin antimicrobial peptides: A review

Dan S. Bolintineanu, Yiannis N. Kaznessis

Journal:

Year:

2011

Language:

english

File:

PDF, 577 KB

english, 2011

39

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

Yiannis N. Kaznessis, Sangtae Kim, Ronald G. Larson

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 2.72 MB

english, 2002

40

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

Salis, Howard, Kaznessis, Yiannis

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 738 KB

english, 2005

41

Molecular Dynamics Simulations of Polar Polymer Brushes

Kaznessis, Yiannis N., Hill, Davide A., Maginn, Edward J.

Journal:

Year:

1998

Language:

english

File:

PDF, 191 KB

english, 1998

42

Computational methods in synthetic biology

Yiannis N. Kaznessis

Journal:

Biotechnology Journal

Year:

2009

Language:

english

File:

PDF, 341 KB

english, 2009

43

Simulations of Zwitterionic and Anionic Phospholipid Monolayers

Kaznessis, Yiannis N., Kim, Sangtae, Larson, Ronald G.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 715 KB

english, 2002

44

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

Bolintineanu, Dan S., Kaznessis, Yiannis N., Davis, H. Ted

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 64 KB

english, 2009

45

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

Yuhua Duan, Boojala V.B. Reddy, Yiannis N. Kaznessis

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 451 KB

english, 2005

46

Stochastic simulations of a synthetic bacteria-yeast ecosystem

Konstantinos Biliouris, David Babson, Claudia Schmidt-Dannert, Yiannis N Kaznessis

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

47

Model-Driven Designs of an Oscillating Gene Network

Tuttle, Lisa M., Salis, Howard, Tomshine, Jonathan, Kaznessis, Yiannis N.

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 320 KB

english, 2005

48

Optimization of a Stochastically Simulated Gene Network Model via Simulated Annealing

Tomshine, Jonathan, Kaznessis, Yiannis N.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 153 KB

english, 2006

49

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

Vivcharuk, Victor, Kaznessis, Yiannis

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 1.83 MB

english, 2010

50

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

Volzing, Katherine, Borrero, Juan, Sadowsky, Michael J., Kaznessis, Yiannis N.

Journal:

ACS Synthetic Biology

Year:

2013

Language:

english

File:

PDF, 396 KB

english, 2013

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