Education

Degree	Institution	Major
B.Sc.	University of Lisbon	Biochemistry
Ph.D.	University of Wales	Biological Sciences

Post-Graduate Training

Training	Institution	Specialty
Postdoctoral	University of Wales	Computational Biology: Project title: "Metabolic control analysis using neural networks: a means for obtaining parameters by measuring variables"
Postdoctoral	University of Wales	Computational Biology: Project title: “A user-oriented simulation and optimisation system for the rational improvement of biotechnological processes”
Postdoctoral	University of Wales	Computational Biology: Project title: “Gepasi 4 – a metabolic engineering simulator for all”

Awards

Name of Award/Honor	Awarding Organization
Elected Member	Connecticut Academy of Science and Engineering
Honorary Professor of Software Systems	The University of Manchester

Name & Description	Category	Role	Type	Scope	Start Year	End Year
22nd International Conference on Systems Biology	Professional/Scientific Organization	Conference Co-Chair	External	International	2023	2023
NIGMS R24 Review ZGM1 BBCB-G (MD)	Study Section	Member	External	National	2023	2023
PLOS Computational Biology	Editorial Board	Section Editor for Systems Biology	External	International	2023
International Conference on Systems Biology	Workshop/Conference	Scientific Committee and Session Co-Chair	External	International	2022	2022
Research Council	Advisory Committee	Member	UConn Health	University	2021
Centers for Cell Analysis and Modeling and Quantitative Medicine	Other	Director	UConn Health	University	2020
PLOS Computational Biology	Editorial Board	Associate Editor	External	International	2019
NIH BioData Management and Analysis (BDMA)	Study Section	Chair	External	National	2019	2023
21st International Conference on Systems Biology	Workshop/Conference	Chair	External	International	2019	2021
NIH ZRG1 BST-W (50) Metabolomics Analysis and Interpretation	Study Section	Ad-hoc member	External	National	2018	2018
Scientific Advisory Board for Center for Reproducible Biomedical Modeling	Advisory Committee	Member	External	National	2018
MDPI Computation	Editorial Board	Associate Editor	External	International	2017	2020
National Advisory General Medical Sciences Council (NIH)	Advisory Committee	Ad-hoc member	External	National	2016	2016
13th Conference on Computational Methods in Systems Biology	Workshop/Conference	Member	External	International	2015	2015
HARMONY 2014 Hackathon: Organising Committee	Workshop/Conference	Member	External	International	2014
12th Conference on Computational Methods in Systems Biology	Workshop/Conference	Chair	External	International	2014	2014
National Institutes of Health - Modeling and Analysis of Biological Systems	Study Section	Ad-hoc member	External	National	2014	2014
BMC Systems Biology	Editorial Board	Section Editor	External	National	2012
Biotechnology and Biological Sciences Research Council: Expert Working Group on Digital Organisms	Professional/Scientific Organization	Member	External	International	2012	2013
10th Conference on Computational Methods in Systems Biology: Scientific Committee	Workshop/Conference	Member	External	International	2012	2012
National Institutes of Health: special study section for National Centers for Systems Biology	Study Section	Ad-hoc Member	External	National	2012	2012
Gordon Research Conference on Cellular Systems Biology	Workshop/Conference	Chair	External	State	2011	2011
IET Systems Biology	Editorial Board	Associate Editor	External	National	2010
International Conference on Systems Biology: Scientific Committee and Session co-chair	Workshop/Conference	Member	External	International	2010	2010
National Institutes of Health: Special Study Section for review of National Centers for Biomedical Computing applications	Study Section	Ad-hoc Member	External	National	2010	2010
BioModels Database, European Bioinformatics Institute	Advisory Committee	Member	External	Local	2009
European Bioinformatics Institute: Review Panel for Research Activities	Study Section	Member	External	International	2009	2009
Biotechnology and Biological Sciences Research Council: Research Committee C, Technological and Methodological Development	Study Section	Member	External	National	2009	2012
National Institutes of Health: Special Study Section BST-M(58) for Reviewing ARRA Applications	Study Section	Ad-Hoc Member	External	National	2009	2009
Science Foundation Ireland: Review Panel for Principal Investigator Programme Grants	Study Section	Member	External	National	2009	2009
Human Metabolic Network Reconstruction Jamboree	Workshop/Conference	Member	External	International	2009	2009
9th International Conference on Systems Biology: Scientific Committee	Workshop/Conference	Member	External	International	2008	2008
Science Foundation Ireland: Site Visit Panel for Systems Biology Institute	Study Section	Member	External	International	2008	2008
Gordon Research Conference on Macromolecular Interactions and Enzyme Function	Workshop/Conference	Vice-Chair	External	International	2008	2008
Metabolomics Conference	Workshop/Conference	Session Chair	External	International	2007	2007
4th International Conference on Plant Metabolomics: Scientific committee	Workshop/Conference	Member	External	International	2006	2006
7th International Conference on Systems Biology: Scientific Committee and Session Chair	Workshop/Conference	Member	External	International	2006	2006
Helmholtz Foundation: Review Panel for Systems Biology Center Grants	Study Section	Member	External	International	2006	2006
National Institutes of Health: Special Study Section, NHLBI	Study Section	Ad-hoc Member	External	National	2006	2006
Transactions on Computational Systems Biology	Editorial Board	Member	External	National	2005
Metabolomics	Editorial Board	Member	External	National	2005	2010
National Insititute on Environmental Health Sciences: Working Group on Integrated and Computational Toxicology	Professional/Scientific Organization	Member	External	National	2005	2005
NIEHS Working Group on Toxicogenomics and Systems Biology	Professional/Scientific Organization	Consultant	External	National	2005	2005
1st Workshop on Metabolomics Standards: Organizing Committee	Workshop/Conference	Member	External	National	2005	2005
National Institutes of Health: Modeling and Analysis of Biological Systems	Study Section	Standing Member	External	National	2005	2009
National Academies of Sciences: Committee Report on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human Health	Professional/Scientific Organization	Unpaid Consultant	External	National	2004	2004
3rd International Conference on Plant Metabolomics: Scientific Advisory Board	Workshop/Conference	Member	External	National	2004	2004
5th International Conference on Systems Biology: Scientific Committee and Session Chair	Workshop/Conference	Member	External	International	2004	2004
National Science Foundation: Review Panel for the Plant Genome Research Program	Study Section	Ad-hoc reviewer	External	National	2004	2004
2nd European Conference on Computational Biology: Scientific Committee	Workshop/Conference	Member	External	International	2003	2003
2nd International Conference on Plant Metabolomics: Supervisory Board	Workshop/Conference	Member	External	International	2003	2003
Metabonomics: Biomarkers of Health and Disease Workshop: Organizing Committee	Workshop/Conference	Member	External	National	2003	2003
National Science Foundation: Reverse Site Visit Panel for Plant Genome Program Grant	Study Section	Member	External	National	2003	2003
National Institutes of Health: Special Study Section H	Study Section	Ad-hoc Member	External	National	2003	2003
National Science Foundation: Review Panel for the Plant Genome Research Program grants	Study Section	Member	External	National	2003	2003
SBML Hackathon, Virginia Bioinformatics Institute	Workshop/Conference	Chair	External	State	2003	2003
National Institutes of Health: Special Study Section 90S	Study Section	Member	External	National	2002	2002
National Institutes of Health: Site visit panel for National Resource of Cell Analysis & Modeling, CDF-2 Study Section	Study Section	Member	External	National	2002	2002
National Institutes of Health: Special Emphasis Panel to review the Biomedical Information Science and Technology Initiative (BISTI) pre-Centers applications	Study Section	Member	External	National	2002	2002
National Science Foundation: IGERT Full Proposals Review Panel	Study Section	Member	External	National	2002	2002
National Science Foundation	Study Section	Ad-hoc electronic reviewer	External	National	2002
Workshop on Modeling Biochemical Networks	Workshop/Conference	Chair	External	National	2002	2002
Special Interest Group on Simulation (SIGSIM) of the International Society of Computational Biology: Steering Committee	Professional/Scientific Organization	Member	External	International	2001	2003
National Science Foundation: IGERT pre-proposals review panel	Study Section	Member	External	National	2001	2001
National Institutes of Health: Special Emphasis Panel to review the Biomedical Information Science and Technology Initiative (BISTI) pre-Centers applications	Study Section	Member	External	National	2001	2001
National Institutes of Health: Genetics Study Section	Study Section	Ad-Hoc Member	External	National	2001
Comparative and Functional Genomics	Editorial Board	Member	External	National	2000	2006
1st International Conference on Systems Biology: Scientific Committee	Workshop/Conference	Member	External	International	2000	2000
The Cancer Research Campaign	Study Section	Mail Reviewer	External	International
Genome Canada	Study Section	Mail Reviewer	External	International
N.O.W. (The Netherlands)	Study Section	Mail Reviewer	External	International
National Research Foundation (South Africa)	Study Section	Mail Reviewer	External	International
The Wellcome Trust (UK)	Study Section	Mail Reviewer	External	International
Medical Research Council (UK)	Study Section	Mail Reviewer	External	International

My research is in the area of computational systems biology, which aims to better understand biological systems through the use of computer models. My active areas of research are:

- Development of modelling and simulation software: I was the author of the popular simulator Gepasi and now the leader of the new COPASI simulator (w/ U. Kummer). I have also been actively involved in the development of SBML, the systems biology markup language, and the MIRIAM proposal for model annotation.

- Construction of biochemical models: I am currently working on models of mammalian iron metabolism, eukaryotic translation, and microbial central metabolism. I am also developing methods for the construction of large-scale kinetic models of entire cells.

- Parameter estimation and systems identification: I have pioneered the application of numerical global optimization in biochemical kinetic modelling. I am interested in using formal systems identification techniques in systems biology, particularly for reverse engineering models from data.

- Reverse engineering biological networks: a long-term objective of systems biology is to be able to construct models directly from large-scale genomics, proteomics and metabolomics data sets. I have been interested in this problem for a while, having been involved in the development of a few methods for reverse engineering, as well as creating artificial networks to benchmark that type of algorithms (eg the AGN system).

- Biological data mining using machine learning: to analyse the large amounts of data produced in systems biology experiments, such as looking for common or unusual patterns in those data, or to classify (and identify the determinants) predefined behaviours.

Research in the areas listed above requires a broad interdisciplinary approach and I work with people from most areas of science, either in my own research group or as collaborators.

 

Accepting Lab Rotation Students: Summer 2022, Fall 2022, and Spring 2023

Journal Articles

Book Chapters

Conference Papers

Letters

Reviews

Title or Abstract	Type	Sponsor/Event	Date/Year	Location
Regulation of Mammalian Iron Physiology Across Scales	Lecture	International Conference on Systems Biology	2022	Berlin
Metabolic {kinetic} model development with COPASI	Plenary Lecture	Workshop on Metabolism and Mathematical Models	2022	Online
Strategies for modeling biological systems at multiple scales illustrated with iron physiology	Lecture	COMBINE 2021	2021	online (Zoom)
Bistability in ferroptosis leads to an irreversible switch	Poster	8th Congress of the International BioIron Society	2019	Heidelberg, Germany
Bistability in ferroptosis leads to an irreversible switch	Lecture	20th International Conference on Systems Biology	2019	Okinawa, Japan
Advanced modelling with COPASI	Other	20th International Conference on Systems Biology	2019	Okinawa, Japan
An Introduction to COPASI	Lecture	20th Annual Workshop Computational Cell Biology	2019	UConn Health, Farmington, CT
COPASI - Its features and applications	Plenary Lecture	Integrative pathway modeling in systems biology and systems medicine	2019	Frankfurt, Germany
Parameter estimation with COPASI	Lecture	SysBio 2018 Advanced Lecture Course on Systems Biology	2018	Innsbruck, Austria
COPASI software for systems biology and medicine - towards personalized models for iron physiology	Other	IEEE International Work Conference on Bioinspired Intelligence	2018	San Carlos, Costa Rica
An introduction to COPASI	Lecture	Virtual Cell and COPASI Workshop	2018	Farmington, CT
Modeling iron Physiology - From mice to humans	Poster	International Study Group for Systems Biology Conference 2018	2018	Tromso, Norway
Computer modeling of iron metabolism and homeostasis towards personalized models	Lecture	Departmental Seminar	2018	Faculty of Medicine, Universidad de la Republica, Montevideo, Uruguay
Advanced modelling with COPASI	Lecture	2018 International Conference on Systems Biology	2018	Lyon, France
Reproducible research using biomodels	Other	FAIRDOM Workshop - FAIR Data Management in Life-Sciences (ICSB satellite)	2018	Lyon, France
Transforming physiological models from mice to humans. The case of iron homeostasis.	Plenary Lecture	2018 International Conference on Systems Biology	2018	Lyon, France
Modeling Iron Physiology - Towards a Personalized Medicine Approach	Talk	Departmental Seminar	2017	Mount Sinai School of Medicine
COPASI Tutorial	Lecture	18th International Conference on Systems Biology	2017	Blacksburg, VA
A Mathematical Model of Iron Dynamics in a Mouse	Poster	7th Congress of the International Bioiron Society	2017	Los Angeles, CA
Modeling Iron Physiology - Towards a Personalized Medicine Approach	Talk	Departmental Seminar	2017	Stony Brook University, NY
Biochemistry by Numbers: Modeling and Simulation in Systems Biology	Plenary Lecture	Expert Scientific Meeting on Load Kinetics Measurement	2016	Lisbon, Portugal
Optimization and parameter estimation (with COPASI)	Lecture	2nd Porto Meeting on Mathematics in Biology	2016	Porto, Portugal
Computational Systems Biology for Toxicology	Plenary Lecture	EuroTox 2014 Conference	2014	Edinburgh, UK
Modelling and parameter estimation – should we do it? and how?	Lecture	Departmental Seminar	2014	University of Warwick, UK
Computational modelling of biochemical networks	Lecture	Departmental Seminar	2014	University of Liverpool, UK
ThEcoli: A Kinetic Model of Escherichia Coli Central Metabolism	Talk	International Conference on Systems Biology	2013	Copenhagen, Denmark
Kinetic Models of Whole-Cell Metabolism – Progress and Applications	Talk	Cambridge Workshop: Modeling for Industrial Biotechnology	2013	Cambridge, England
Digital Organisms, Biochemical Simulations and the Cloud	Talk	AstraZeneca 2013 Modelling and Simulation Symposium	2013	Alderley Park, UK
Systems Biology for Improving Production of Cellular Products	Talk	Symposium on Advances in Recombinant Protein Technology	2013	Alderley Park, UK
From Genomes to Large-Scale Kinetic Models of Metabolism	Talk	French Conference on Biology, Computer Science and Mathematics	2013	Toulouse, France
From Genomes to Large-Scale Kinetic Models of Metabolism	Talk	Symposium on Computational Biology Applications	2013	Farmington, Connecticut
Optimisation and Parameter Estimation in COPASI	Talk	Latvia University of Agriculture	2013	Jelgava, Latvia
A Computational Model of Human Iron Metabolism	Talk	Conference on Systems Biology of Mammalian Cells	2012	Leipzig, Germany
ManyCell: A Multiscale Simulator for Cellular Systems	Talk	Conference on Computational Methods in Systems Biology	2012	London, England
From Genomes to Large-Scale Kinetic Models of Metabolism	Talk	Japanese Biochemical Society	2012	Fukuoka, Japan
COPASI. Wellcome Trust Workshop on Open Source Software for Systems, Pathways, Interactions and Networks	Talk	European Bioinformatics Institute	2012	Hinxton, England
Modelling the Dynamics of Eukaryotic Protein Synthesis	Talk	International Workshop on Systems and Synthetic Biology	2012	Mallorca, Spain
Towards Whole-Genome Kinetic Models of Metabolism	Talk	Systems Biology Europe Symposium	2012	Madrid, Spain
Adventures in Modelling and Simulation of Biochemical Networks	Talk	Formal Approaches to Modelling Biomolecular Networks	2012	Edinburgh, Scotland
Modelling the Dynamics of Eukaryotic Protein Synthesis	Talk	University of Tokyo	2012	Tokyo, Japan
Modelling and Simulation of Biochemical Networks	Talk	University of Oxford	2012	Oxford, England
From Networks to Models – Large Scale Kinetic Models of Metabolism	Talk	University of Saarbrücken	2012	Saarbrücken, Germany
Applications of Dynamic Model Optimization Using COPASI Software	Talk	Latvia University of Agriculture	2012	Jelgava, Latvia
Chasing the Flux: Selecting Target Pathways Through Flux Analysis of Carbon Metabolism	Talk	Conference on Constraint-based Reconstruction and Analysis	2011	Reykjavik, Iceland
From Genomes to Models	Talk	2nd Workshop on Medical Systems Biology	2011	Manchester, England
Kinetic Modelling of Largescale Metabolic Networks	Talk	International Conference on Computational Methods in Systems Biology	2011	Paris, France
Distance Learning in Computational Systems Biology	Talk	FutureSysBio Education Workshop	2011	Gothenburg, Sweden
Management of Data and Models in Systems Biology	Talk	Data Management for Systems Biology and the Life Sciences	2011	Heidelberg, Germany
Kinetic Modelling of Large-Scale Metabolic Networks	Talk	Boehringer Ingelheim Titisee Conference on Genomic Regulation	2011	Titisee, Germany
Metabolism, Metabolomics and Systems Biology	Talk	Australasian Metabolomics Symposium	2010	Melbourne, Australia
Computational Whole-Genome Reconstructions and Modelling of Metabolic Networks	Talk	International Conference on Systems Biology	2010	Edinburgh, Scotland
The Pre-History of Kinetic Modelling and Simulation	Talk	International Conference on Systems Biology	2010	Edinburgh, Scotland
Harnessing the Chemistry of life – Revolutionising Toxicology. Computational Chemistry and Systems Biology	Talk	European Partnership on Alternative Approaches to Animal Testing	2010	Brussels, Belgium
Standardized Enzyme Kinetics for Systems Biology	Talk	International Symposium on Experimental Standard Conditions of Enzyme Chara	2009	Rudhsheim, Germany
Software from the Manchester Centre for Integrative Systems Biology	Talk	International Conference on Yeast Genetics & Molecular Biology	2009	Manchester, England
The Pre-History of Systems Biology	Talk	UK Inter- Doctoral Training Centres Meeting	2009	Manchester, England
Advanced Simulation and Analysis of Biochemical Models Using COPASI	Talk	International Conference on Systems Biology	2008	Gothenburg, Sweden
A New Strategy for Assessing Global Sensitivity in Biochemical Network Models	Talk	Spanish Systems Biology Network	2008	Valencia, Spain
Computational Systems Biology for Modeling Cancer	Talk	Annual Symposium on Cancer Research	2008	Houston, Texas
A New Strategy for Assessing Global Sensitivity in Biochemical Network Models	Talk	Portuguese National Congress of Biochemistry	2008	Ponta Delgada, Azores, Portugal
Modelling and Simulation of Biological Systems with COPASI	Talk	Microsoft Research	2008	Cambridge, England
Adventures in Reverse Engineering of Biochemical Networks	Talk	University of Sheffield	2008	Sheffield, United Kingdom
Optimisation and Parameter Estimation	Talk	Instituto Gulbenkian de Ciência	2008	Oeiras, Portugal
Modelling and Simulation of Biological Systems with COPASI	Talk	Biotechnology and Biological Sciences Research Council MATSYB meeting	2008	Manchester, England
Software Interoperability for Systems Biology	Talk	PhD Program in Computational Biology, Instituto Gulbenkian de Ciência	2008	Oeiras, Portugal
New Developments in COPASI	Talk	Workshop on Computational Cell Biology	2008	Hinxton, England
Adventures in Reverse Engineering of Biochemical Networks	Talk	Centre for Computational and Systems Biology	2007	Trento, Italy
Adventures in Reverse Engineering of Biochemical Networks	Talk	Max Plank Institute for Molecular Generics	2007	Berlin, Germany
Integrated Data Management for Kinetic Modelling and Experimental Results	Talk	Storage and Annotation of Reaction Kinetics Data	2007	Heidelberg, Germany
Benchmarking Parameter Estimation and Reverse Engineering Strategies	Talk	Parameter Estimation in Systems Biology	2007	Manchester, England
Adventures in Reverse Engineering of Biochemical Networks	Talk	University of Pittsburgh	2006	Pittsburgh, Pennsylvania
Software e métodos na biologia de sistemas	Talk	University of Minho	2006	Braga, Portugal
Top-Down Modeling of Biochemical Networks – A Grand Challenge of Systems Biology	Talk	Instituto Gulbenkian Ciencia	2006	Oeiras, Portugal
From Data to Models: Continuous and Discrete Top-down Modeling of Biochemical Networks	Talk	Free University of Amsterdam	2006	Amsterdam, The Netherlands
Modeling and Simulation for Metabolomics Data Analysis	Talk	Duke University Medical Center	2006	Durham, North Carolina
Systems Biology	Talk	National Institutes of Health	2006	Bethesda, Maryland
Biochemical Network Dynamics	Talk	American Mathematical Society Short Course on Modeling and Biological	2006	San Antonio, Texas
Top-Down Modeling of Biochemical Networks – A Grand Challenge of Systems Biology	Talk	Integrative Bioinformatics Workshop	2006	Rothamstead, United Kingdom
Building Dynamic Models From Functional Genomics Data – A Systems Biology Challenge	Talk	Conference on Macromolecular Organization and Cell Function	2006	South Hadley, Massachusetts
A Systems Biology Approach to the Study of Stress Responses	Talk	Genome To Systems Conference	2006	Manchester, England
Metabolomics as a Component of Systems Biology: Issues in Data Fusion	Talk	Metabolomics Society Conference	2006	Boston, Massachusetts
In Silico Models for Reverse Engineering: Complexity and Realism versus Well-Defined Metrics	Talk	DREAM DIMACS Workshop	2006	New York, New York
Biochemical Networks Modelling	Talk	University of Porto Alegre	2005	Porto Alegre, Brazil
Systems Approaches to the Study of Stress Responses	Talk	BASF Corporation	2005	Ludwigshafen, Germany
Systems Approaches to the Study of Stress Responses	Talk	MicroBiotec 2005 Conference	2005	Póvoa do Varzim, Portugal
Computational Tools for Integrative 'Omics' Approaches	Talk	National Cancer Institute	2005	Rockville, Maryland
Metabolomics and Biochemical Networks Modelling	Talk	Therapeutic Applications of Computational Biology	2005	Hinxton, England
Modeling and Simulation for Metabolomics Data Analysis	Talk	British Biochemical Society	2005	Glasgow, Scotland
Databases and Visualization for Metabolomics	Talk	Metabolomics Society Conference	2005	Tsuruoka, Japan
Systems Analyses of Medicago Truncatula Stress Responses	Talk	Model Legume Conference	2005	Monterey, California
From Data to Models: Continuous and Discrete Top-down Modeling of Biochemical Networks	Talk	Biocomplexity 7 Workshop, Indiana University	2005	Bloomington, Indiana
COPASI Software	Talk	2nd Symposium on Computational Cell Biology	2005	Lenox, Massachusetts
Simulation of Biochemical Networks for Increased Understanding of Experiments	Talk	Thomas Jefferson University	2004	Philadelphia, Pennsylvania
Biochemical Network Dynamics	Talk	Wake Forest University Health Sciences Center	2004	Wake Forest, North Carolina
Inferring Biochemical Networks from Functional Genomic Data	Talk	University of Texas Health Sciences Center	2004	Houston, Texas
Plant Functional Genomics and Systems Biology	Talk	United States Department of Agriculture	2004	Beltsville, Maryland
Plant Functional Genomics and Systems Biology	Talk	The John Innes Centre	2004	Norwich, United Kingdom
Bioinformatics for Integrative Functional Genomics	Talk	European Bioinformatics Institute	2004	Hinxton, England
Metabolomics Data Analysis: Beyond Correlation	Talk	CHI Conference on Analytical Methods for Metabolic Profiling	2004	Orlando, Florida
Software and Methods for Modeling and Simulating Biochemical Networks	Talk	5th International Conference on Systems Biology	2004	Heidelberg, Germany
Biological Systems Identification From Functional Genomic Data	Talk	2nd Conference From Genomes to Systems	2004	Manchester, England
Modeling Biochemical Networks in the Context of Systems Biology	Talk	West Virginia University Workshop on Systems Biology	2004	Roanoke, West Virginia
Bioinformatics for Integrative Functional Genomics	Talk	3rd Plant Metabolomics Conference	2004	Ames, Iowa
Yeast Systems Biology at the Virginia Bioinformatics Institute	Talk	2nd International Workshop of the Yeast Systems Biology Network	2004	Copenhagen, Denmark
A Systems Biology Approach to the Study of Stress Responses	Talk	Gordon Research Conference on Structural, Functional, and Evolutionary Geno	2004	Ventura, California
Database and Visualization for Grape Functional Genomics	Talk	12th International Plant and Animal Genome Conference	2004	San Diego, California
Plant Functional Genomics and Systems Biology	Talk	Michigan State University	2003	East Lansing, Michigan
Workshop on Analysis of Complex Pathways – The Case of the Reverse Cholesterol Transport Pathway	Talk		2003	Arolla, Switzerland
Scaling up Biochemical Models ...and Artificial Gene Networks	Talk	4th International Conference on Systems Biology	2003	St. Louis, Missouri
Numerical Optimization Methods for Enzyme Networks	Talk	International Workshop on Experimental Standard Conditions of Enzyme Charac	2003	Ruedesheim/Rhein, Germany
Simulation Meets Data Analysis: The Development of Objective Tests for Functional Genomics Data Analysis Algorithms	Talk	2nd European Conference on Computational Biology	2003	Paris, France
Bioinformatics for Metabolomics	Talk	National Research Council	2003	Seattle, Washington
Computational Support for Metabolomics: Databases, Analysis, and Visualization	Talk	North-West Metabolomics Meeting	2003	Manchester, England
Database and Visualization for Grape Functional Genomics	Talk	Grape Bioinformatics Conference	2003	Tahoe, California
Computational Support for Metabolomics: Databases, Analysis, and Visualization	Talk	NIEHS Workshop on Metabonomics: Biomarkers of Health and Disease	2003	Research Triangle Park, North Carolina
Inferring Biochemical Networks from Functional Genomic Data	Talk	NIEHS & VBI Symposium on Toxicogenomics: Through the Eyes of Informatics	2003	Washington, DC
Making Sense of the Data: Analysis, Visualization and the Need for Databases	Talk	Food Forum Symposium on Individualized Nutrition and its Impact on the Food	2003	Washington, DC
Metabolomics: A Tool to Determine the Structure and Regulation of Biochemical Networks?	Talk	2nd International Conference on Plant Metabolomics	2003	Potsdam, Germany
New Methods for Biochemical Network Modeling	Talk	Virginia Commonwealth University	2002	Richmond, Virginia
Inferring Biochemical Networks from Functional Genomic Data	Talk	George Mason University	2002	Fairfax, Virginia
New Methods for Biochemical Network Modeling	Talk	Johns Hopkins University	2002	Baltimore, Maryland
Biochemistry by Numbers: Modeling Metabolic, Signaling and Genetic Networks	Talk	15th International Symposium on Mathematical Theory of Networks and Systems	2002	South Bend, Indiana
Swimming in a Sea of Data: Forward and Inverse Modeling of Biochemical Dynamics	Talk	Dynamics Days Europe	2002	Heidelberg, Germany
Biochemical Networks Modeling and Metabolomic Data Analysis	Talk	Bioinformatics & Pharmacogenomics Symposium	2002	Richmond, Virginia
Functional Genomic Data Integration	Talk	International Conference on Legume Genomics and Genetics	2002	Minneapolis, Minnesota
Data Visualization and Analysis for Metabolomics	Talk	1St International Congress on Plant Metabolomics	2002	Wageningen, The Netherlands
Functional Genomics and the Simulation of Biochemical Networks	Talk	InfoTechPharma	2002	London, England
Bioinformatics and Computational Biology for Plant Functional Genomics	Talk	Phytochemical Society of North America	2001	Oklahoma City, Oklahoma
Simulating Large-Scale Biochemical Systems: Forward and Inverse Problems	Talk	Seminar Information and Simulation Systems for the Analysis of Gene Regulat	2001	Daghstul, Germany
Two Complementary Methods for Reverse Engineering Genetic Networks	Talk	Workshop on Computation of Biochemical Pathways and Genetic Networks	2001	Heidelberg, Germany
Simulation of Biochemical and Genetic Networks – HPC in the Post-Genome Era	Talk	Sun Microsystems High Performance Computing Consortium	2001	Heidelberg, Germany
Tools for Simulating Large Biological Systems: The Need for Optimization	Talk	In Silico Technologies in Drug Discovery	2001	Bethesda, Maryland
Gepasi	Talk	International Symposium on Computational Cell Biology	2001	Lenox, Massachusetts
Numerical Optimisation for the Analysis and Design of Metabolic Pathways with Gepasi	Talk	University of Connecticut Health Center	2001	Farmington, Connecticut
Tools for Simulating Large Biological Systems – The Need for Optimization	Talk	International Conference on Systems Biology	2000	Tokyo, Japan
PathDB: A Second Generation Metabolic Database	Talk	9th BioThermoKinetics Meeting, University of Stellenbosch	2000	South Africa
Advanced Visualization of Metabolic Pathways in PathDB	Talk	Plant and Animal Genome VIII	2000	San Diego, California
Computer Simulation of Biochemical Pathways and Gene Expression	Talk	Department of Biochemistry, Virginia Tech	2000	Blacksburg, Virginia
PathDB: A Second Generation Metabolic Database	Talk	University of Southern Cape	2000	Cape Town, South Africa
Computer Simulation of Biochemical Pathways and Gene Expression	Talk	University of New Mexico	2000	Albuquerque, New Mexico
Gepasi	Talk	Caltech	2000	Pasadena, California
Metabolic Simulation as an Aid in Understanding Gene Expression Data	Talk	Computation of Biochemical Pathways and Genetic Networks	1999	Heidelberg, Germany
Computational Approaches to the Study of Biochemical Pathways and Metabolic Control	Talk	NATO Advanced Research Workshop	1999	Visegrad, Hungary
Biochemistry by Numbers: Computer Simulation of the Behaviour of Biochemical Pathways	Talk	University of Utah	1999	Salt Lake City, Utah
Plant Metabolic Pathways Database at NCGR	Talk	DuPont Life Sciences	1999	Wilmington, Delaware
Computer Applications for Metabolic Pathways	Talk	Samuel Roberts Noble Foundation	1999	Ardmore, Oklahoma
Metabolic Databases Integration with Other Biological Data Types	Talk	Gallo Life Sciences Research, Gallo Winery	1999	Modesto, California
Using Computers to Learn Metabolism	Talk	Biochemical Society Colloquium on Modelling Metabolism	1998	Leicester, England
Integration of Gene Expression with Metabolism in Kinetic Simulations	Talk	Dagstuhl Seminar Modelling and Simulation of Gene Regulation and Metabolic	1998	Dagstuhl, Germany
Numerical Optimisation for the Analysis and Design of Metabolic Pathways	Talk	Workshop on Theoretical Biophysics	1998	Hidensee, Germany
Biochemistry by Numbers: Computer Simulation of the Behaviour of Biochemical Pathways	Talk	University of Wales	1998	Aberystwyth, Wales
Biochemistry by Numbers: Simulation and Optimisation of Biochemical Pathways	Talk	Tokyo Medical and Dental University	1998	Tokyo, Japan
Biochemistry by Numbers: Simulation and Optimisation of Biochemical Pathways	Talk	The Helix Institute	1998	Tokyo, Japan
Biochemistry by Numbers: Simulation and Optimisation of Biochemical Pathways	Talk	Yamanouchi Tsukuba Research Center	1998	Tsukuba, Japan
Computer Simulation and Optimisation of Metabolic Fluxes Using Gepasi	Talk	European Science Foundation Research Conference on Control of Metabolic Flu	1997	Giens, France
Gepasi Revisited	Talk	Aberystwyth-Swansea Microbiology Meeting	1997	Grygenog, Wales
Computer Simulation of the Kinetics of Metabolic Pathways	Talk	Society for General Microbiology Symposium on Microbial Informatics	1997	Southampton, England
Metabolic Control Analysis and Kinetic Simulation	Talk	University of Lisbon	1997	Lisbon, Portugal
Computer Simulation of the Kinetics of Biochemical Pathways	Talk	University College London	1997	London, England
Biochemistry by Numbers: Simulation and Optimisation of Biochemical Pathways	Talk	University of Washington	1997	Seattle, Washington
Computer Simulation of Biochemical Kinetics	Talk	VII BioThermoKinetics	1996	Louvain-la-Neuve, Belgium
Metabolic Control Analysis and Simulation of Organised Enzyme Systems	Talk	Gordon Research Conference on Macromolecular Organization and Cell Function	1996	Oxnard, California
Exploring Biochemical Models with Gepasi, A Kinetics Simulator	Talk	International Conference on Information Processing in Cells and Tissues	1996	Liverpool, England
Gepasi 3.0 A Simulator to Investigate Metabolism	Talk	Technical University of Delft	1996	Delft, The Netherlands
Long-Range Metabolic Signalling in Heterogeneous Catalytic Systems: Computer Simulation Study	Talk	International Conference on Information Processing in Cells and Tissues	1995	Liverpool, England
Multi-Enzyme Complexes and Multifunctional Enzymes. Similarities and Differences	Talk	Aberystwyth-Swansea Microbiology Meeting	1995	Grygenog, Wales
Computer Simulation of Metabolic Processes	Talk	University of Liverpool	1995	Liverpool, England
Gepasi	Talk	European Workshop on Perceptual Control Theory	1994	Gregynog, Wales
Control Analysis of Metabolic Channelling	Talk	BioThermoKinetics Meeting	1992	Bordeaux, France
Metabolic Control Analysis	Talk	University of Lisbon	1990	Lisbon, Portugal