John Wagner  John Wagner photo       

contact information

Manager and Research Staff Member
IBM Research-Australia
IBM Research - Australia
Level 5
204 Lygon Street
Carlton VIC 3053 Australia
  +61dash4dash2549dash8550

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2016

Dynamic Modelling Reveals ‘Hotspots’ on the Pathway to Enzyme-Substrate Complex Formation
Gordon, Shane E and Weber, Daniel K and Downton, Matthew T and Wagner, John and Perugini, Matthew A
PLoS Comput Biol 12(3), e1004811, Public Library of Science, 2016
Abstract


2015

Unique aspects of the structure and dynamics of elementary I$\beta$ cellulose microfibrils revealed by computational simulations
Oehme, Daniel P and Downton, Matthew T and Doblin, Monika S and Wagner, John and Gidley, Michael J and Bacic, Antony
Plant physiology 168(1), 3--17, Am Soc Plant Biol, 2015
Abstract

Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption
Oehme, Daniel P and Doblin, Monika S and Wagner, John and Bacic, Antony and Downton, Matthew T and Gidley, Michael J
Cellulose 22(6), 3501--3520, Springer, 2015
Abstract

Evolutionary dynamics of the Cellulose synthase gene superfamily in grasses
Schwerdt, Julian G and MacKenzie, Katrin and Wright, Frank and Oehme, Daniel and Wagner, John M and Harvey, Andrew J and Shirley, Neil J and Burton, Rachel A and Schreiber, Miriam and Halpin, Claire and others
Plant physiology 168(3), 968--983, Am Soc Plant Biol, 2015
Abstract

Unique aspects of the structure and dynamics of elementary I$\beta$ cellulose microfibrils revealed by computational simulations
Oehme, Daniel P and Downton, Matthew T and Doblin, Monika S and Wagner, John and Gidley, Michael J and Bacic, Antony
Plant physiology 168(1), 3--17, Am Soc Plant Biol, 2015
Abstract

High performance computing enabling exhaustive analysis of higher order single nucleotide polymorphism interaction in Genome Wide Association Studies
Goudey, Benjamin and Abedini, Mani and Hopper, John L and Inouye, Michael and Makalic, Enes and Schmidt, Daniel F and Wagner, John and Zhou, Zeyu and Zobel, Justin and Reumann, Matthias
Health Information Science and Systems 3(1), S3, BioMed Central, 2015
Abstract

Chapter Nine-Quaternary Structure Analyses of an Essential Oligomeric Enzyme
da Costa, Tatiana P Soares and Christensen, Janni B and Desbois, Sebastien and Gordon, Shane E and Gupta, Ruchi and Hogan, Campbell J and Nelson, Tao G and Downton, Matthew T and Gardhi, Chamodi K and Abbott, Belinda M and others
Methods in enzymology562, 205--223, Elsevier, 2015
Abstract

Characterization of the lipid-binding site of equinatoxin II by NMR and molecular dynamics simulation
Weber, Daniel K and Yao, Shenggen and Rojko, Nejc and Anderluh, Gregor and Lybrand, Terry P and Downton, Matthew T and Wagner, John and Separovic, Frances
Biophysical journal 108(8), 1987--1996, Elsevier, 2015
Abstract

Unique aspects of the structure and dynamics of elementary I$\beta$ cellulose microfibrils revealed by computational simulations
Oehme, Daniel P and Downton, Matthew T and Doblin, Monika S and Wagner, John and Gidley, Michael J and Bacic, Antony
Plant physiology 168(1), 3--17, Am Soc Plant Biol, 2015
Abstract


2014

A large-scale physiological model of Inferior Olive neurons reveals climbing fiber intra-burst frequency depends on Olivocerebellar axon morphology
Kozloski, James and Wagner, John and Memelli, Heraldo and Gurev, Viatcheslav
BMC Neuroscience 15(Suppl 1), P149, BioMed Central, 2014
Abstract

Modelling the Interactions of Equinatoxin II with Micelles
Weber, Daniel and Yao, Shenggen and Anderluh, Gregor and Lybrand, Terry P and Downton, Matthew T and Wagner, John and Separovic, Frances
Biophysical Journal 106(2), 89a, Elsevier, 2014
Abstract

Geometric dependence of the conductance drop in a nanopore due to a particle
Kim, Sung Cheol and Kannam, Sridhar Kumar and Harrer, Stefan and Downton, Matthew T and Moore, Stephen and Wagner, John M
Physical Review E 89(4), 042702, APS, 2014
Abstract

Sensing of protein molecules through nanopores: a molecular dynamics study
Kannam, Sridhar Kumar and Kim, Sung Cheol and Rogers, Priscilla R and Gunn, Natalie and Wagner, John and Harrer, Stefan and Downton, Matthew T
Nanotechnology 25(15), 155502, IOP Publishing, 2014
Abstract


2013

Nanosensors for next generation drug screening
Kannam, Sridhar K and Downton, Matthew T and Gunn, Natalie and Kim, Sung Cheol and Rogers, Priscilla R and Schieber, Christine and Baldauf, Julia S and Wagner, John M and Scott, Daniel and Bathgate, Ross and others
SPIE Micro+ Nano Materials, Devices, and Applications, pp. 89230I--89230I, 2013
Abstract

Dimerization of Bacterial Diaminopimelate Epimerase is Essential for Catalysis
Lilian Hor, Renwick CJ Dobson, Matthew T Downton, John Wagner, Craig A Hutton, Matthew A Perugini
Journal of Biological Chemistry, ASBMB, 2013

Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition
Sarah C Atkinson, Con Dogovski, Matthew T Downton, Peter E Czabotar, Renwick CJ Dobson, Juliet A Gerrard, John Wagner, Matthew A Perugini
Plant molecular biology 81(4-5), 431--446, Springer, 2013


2012

Crystal, solution and in silico structural studies of dihydrodipicolinate synthase from the common grapevine
Sarah C Atkinson, Con Dogovski, Matthew T Downton, F Grant Pearce, Cyril F Reboul, Ashley M Buckle, Juliet A Gerrard, Renwick CJ Dobson, John Wagner, Matthew A Perugini
PLoS One 7(6), e38318, Public Library of Science, 2012

Supercomputing enabling exhaustive statistical analysis of genome wide association study data: Preliminary results
Matthias Reumann, Enes Makalic, Benjamin W Goudey, Michael Inouye, Adrian Bickerstaffe, Minh Bui, Daniel J Park, Miroslaw K Kapuscinski, Daniel F Schmidt, Zeyu Zhou, others
2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 1258--1261

Enzymology of bacterial lysine biosynthesis
Con Dogovski, SC Atkinson, SR Dommaraju, M Downton, L Hor, S Moore, JJ Paxman, MG Pevereli, TW Qiu, M Reumann, others
Biochemistry, pp. 225--262, InTech, 2012


2011

An Ultrascalable Solution to Large-scale Neural Tissue Simulation
J. Kozloski, J. Wagner
Front Neuroinform5, 15, 2011


2009

Utilizing Parallel Processing in Computational Biology Applications
J. Wagner and K. Jordan
High performance computing for high-throughput image reconstruction and analysis. A.R. Rao and G. Cecchi, eds., Artech House, 2009


2008

Stability and Time-Delay Modeling of Negative Feedback Loops
J Wagner, G Stolovitzky
Proceedings of the IEEE 96(8), 1398--1410, Institute of Electrical and Electronics Engineers, 2008

Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
Avi Ma'ayan, Guillermo A. Cecchi, John Wagner, A. Ravi Rao, Ravi Iyengar, and Gustavo Stolovitzky
Proc Natl Acad Sci U S A 105(49), 19235-19240, National Acad Sciences, 2008


2007

A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells
W Hu, Z Feng, L Ma, J Wagner, J J Rice, G Stolovitzky, A J Levine
Cancer research 67(6), 2757, AACR, 2007


2005

p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback
J. Wagner, L. Ma, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Syst Biol (Stevenage) 152(3), 109--118, 2005

A plausible model for the digital response of p53 to DNA damage
L. Ma, J. Wagner, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Proc. Natl. Acad. Sci. U.S.A. 102(40), 14266--14271, 2005


2004

Cortically restricted production of IP3 leads to propagation of the fertilization Ca2+ wave along the cell surface in a model of the Xenopus egg
C P Fall, J M Wagner, L M Loew, R Nuccitelli
Journal of theoretical biology 231(4), 487--496, Elsevier, 2004

A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support
J Wagner, C P Fall, F Hong, C E Sims, N L Allbritton, R A Fontanilla, I I Moraru, L M Loew, R Nuccitelli
Cell calcium 35(5), 433--447, Elsevier, 2004


2003

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
M Hucka, A Finney, H M Sauro, H Bolouri, J C Doyle, H Kitano, others
Bioinformatics 19(4), 524, Oxford Univ Press, 2003


2002

Computational cell biology
C P Fall
2002 - books.google.com, Springer Verlag


2001

Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell
J C Schaff, B M Slepchenko, Y S Choi, J Wagner, D Resasco, L M Loew
Chaos: An Interdisciplinary Journal of Nonlinear Science11, 115, 2001


1998

Simulation of the fertilization Ca2+ wave in Xenopus laevis eggs
J Wagner, Y X Li, J Pearson, J Keizer
Biophysical journal 75(4), 2088--2097, Elsevier, 1998


1996

Validity of the rapid buffering approximation near a point source of calcium ions
GD Smith, J Wagner, J Keizer
Biophysical Journal 70(6), 2527-2539, Elsevier, 1996


1994

Effects of rapid buffers on Ca2+ diffusion and Ca2+ oscillations
J Wagner, J Keizer
Biophysical Journal 67(1), 447--456, Elsevier, 1994


1993

On the amplification of molecular fluctuations for nonstationary systems: hydrodynamic fluctuations for the Lorenz model
J Keizer, R Fox and J Wagner
Physics Letters A 175(1), 17 22, Elsevier, 1993