Community Members

Member and site manager

Andrzej M. Kierzek

I have over 15 years of experience in computational biology. My research goal is to predict the dynamic behaviour of the living cell by computer simulation of the genome scale network models representing experimental data on interaction between molecules.

I am convinced that we can fully exploit information about full genomic sequence of human and other organisms only if we use legacy of molecular biology data to build predictive mechanistic models of genotype-phenotype relationship. Due to the number of molecular components in the cell and non-linearity of their interactions this goal can only be achieved by computer simulation. The successful computer simulation of the molecular cell biology will enable prediction of the individual genetic differences on the trajectories of major diseases providing foundation for predictive and personalized medicine of the future. Likewise, industrial biotechnology is being revolutionized by increasing ability to computer simulate the effects of genetic engineering in commercial cell lines and therefore rationally design industrial fermentation processes.

Currently I am working on development of hybrid algorithms integrating Flux Balance Analysis (FBA) of quasi-steady state metabolic reaction networks and qualitative dynamic simulations of regulatory processes that cannot be model in steady state framework. In this work I capitalize on my expertise in the fields of constraint based modeling of genome scale metabolism and stochastic simulations of detailed kinetic models.

I have performed computational part of the project leading to the first reconstruction of the Genome Scale Metabolic Reaction Network of Mycobacterium tuberculosis, causative agent of Tuberculosis disease (Genome Biology, 2007). The tools developed for this project motivated have been matured into SurreyFBA software recently published by my group (Bioinformatics, 2011). I have also been working on analysis of gene expression data in the context of genome scale metabolic networks (PLoS Computational Biology, 2011) and development of software for web based computation with FBA models (BMC Bioinformatics, 2011). Industrial biotechnology is an important application area for genome scale metabolic modeling; I worked on FBA simulations in the context of bioprocess feed development for antibiotic production in Streptomyces coelicolor (Metabolic Engineering, 2008).

I have been modeling stochastic effects in molecular interaction network dynamics for 10 years. I have constructed detailed model of prokaryotic gene expression and investigated dependence between accuracy of gene expression and transcription and translation initiation rates (J. Biol. Chem, 2001). This work has also lead to the publication of STOCKS software for stochastic simulation of molecular interaction network (Bioinformatics, 2002). Subsequently, we have developed Maximal Timestep Method, a hybrid algorithm enabling stochastic simulation of systems with reaction rates varying by many orders of magnitude. The method has been applied to investigate propagation of gene expression noise to the level of metabolic processes leading to epigenetically inherited changes in single cell physiology (Biophysical Journal 2004). More recently, I was working the influence of RNA regulators on gene expression noise (Biophysical Journal 2009) and constructed stochastic kinetic model of Two Component System Signalling (Molecular Biosystems 2010).

In have past bioinformatics experience in the field of homology modeling of protein structure (Nucl. Acids. Research 2003, Nature Immunology 2003), regulatory sequence analysis (J. Biol. Chem 2005) and annotation of genome sequences (Nature 2004). I did my PhD in the area of Biophysics and worked on the agent-based simulations of protein crystal growth (Biophysical Journal 1997). I have also performed molecular dynamics simulations and analysed light scaterring spectra (J. Phys. Chem. 1999).

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Organizer and member

Johnjoe McFadden

Johnjoe McFadden’s work has focussed on elucidating virulence mechanisms and pathways of microbial pathogenesis, particularly the agents that cause tuberculosis and meningitis. In recent years his focus has shifted to systems-based approaches to investigate infectious disease. With Andrzek Kierzek he published the first genome-scale metabolic network for Mycobacterium tuberculosis in 2007 (Beste et al., 2007) and has since published transcriptomic proteomic, and mutagenesis studies of the TB bacillus (Beste et al., 2007, 2009, Borsuk et al., 2009) and of the meningococcus (Mendum

et al., 2009, 2011). His group were the first to perform 13C-Metabolic Flux Analysis on mycobacteria in 2011 (Beste et al., 2011) and he has also developed a new tool, Differential producibility Analysis (DPA) that uses a metabolic model to extract metabolomic signals from transcriptome data (Bonde et al., 2011).  He has recently also developed an interest in bionanotechnology developing several systems that use carbon nanotubes to deliver proteins, nucleic acids and drugs to mammalian cells (Heister et al, 2010, 2011, Neves et al., 2010, Sanz-Beltran, 2011).

As well as his mainstream work, McFadden has also written popular science articles wrote the book, Quantum Evolution in 2000 (published by HarperCollins in the UK and by WW Norton in the USA.  

Workshop organizer and member

Kazuyuki Shimizu

Kazuyuki Shimizu is a professor of Institute for Advanced Biosciences, Keio University, and of Kyushu Institute of Technology
He received his B.S (1972) and M.S (1974) in Chemical Engineering from Nagoya University, and Ph. D (1981) in Chemical Engineering from Northwestern University.

Research Activities & Projects: Metabolic regulation analysis of the cell using 13C isotope

Selected publications

1. Kumar R, Shimizu K: Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures. Microbial Cell Factories 2011, 10:3.
2. Kumar R, Shimizu K: Metabolic regulation of Escherichia coli and its gdhA, glnL, gltB, D mutants under different carbon and nitrogen limitations in the continuous culture. Microbial Cell Factories 2010, 9:8.

Member, organizer and web site owner

Martin Robert

Associate Professor, Tohoku University, Sendai, Japan

Martin Robert is Associate Professor at Tohoku University in Sendai, Japan. He teaches biological sciences at the G30 International Undergraduate Program including a fundamental course in cell biology and another course that merges principles of physiology and systems biology. In addition, Martin is actively pursuing research on the metabolic function of E. coli. His interests are centered on functional enzyme genomics using metabolomics, proteomics, and bioinformatics tools, the metabolic response of E. coli during adaptive evolution, and the dynamics and systems biology of this bacterium.

Research web site:

Member and organizer

Hirotada Mori

Professor, NAIST, Nara, Japan

Ahmad A. Mannan
Postdoctoral Research Fellow

Institute for Complex Systems and Mathematical Biology 
and School of Biological Sciences
University of Aberdeen, Aberdeen, Scotland, UK



Research Gate Profile:

I am currently a postdoctoral research fellow in Systems Biology, jointly at the Institute for Complex Systems and Mathematical Biology and the Department for Plant and Soil Sciences (under the School of Biological Sciences), at the University of Aberdeen, Scotland, UK.

The main areas of focus in my work are in the construction and analyses of kinetic and metabolic genome-scale flux-balance models of cellular metabolism. I am particularly interested in understanding the emergent properties of complex metabolic networks, and the implications of the change in cellular phenotype, by applying dynamical systems analyses and various flux-balance analyses techniques, as well as designing algorithms for the integration of multi-omics data.

Previously, we have collaborated with Professor Kazuyuki Shimizu (above) on construction of a kinetic model of the central carbon metabolism of E. coli, which resulted in the publication of the following paper:
Further collaborative work on the emergence of alternative metabolic phenotypes of E. coli, with Professor Shimizu and Dr Yoshihiro Toya (now at Shimizu Lab of Osaka University) is currently submitted for publication.

Previously, the models of metabolism were based on bacteria, specifically E. coli and M. tuberculosis, but my work has shifted to plants, and currently I am working to understand metabolic shift in Oryza sativa (rice) for changes in soil chemistry.

I would be very interested in discussing work and possible collaborations with our Japanese colleagues.

For further information, you are very welcome to visit my webpages or e-mail me.