UCONN

HEALTH

Photo of Pedro  Mendes, Ph.D.

Pedro Mendes, Ph.D.

Professor/Basic Science
Academic Office Location:
Center for Quantitative Medicine
UConn Health
263 Farmington Avenue, MC 6029
Farmington, CT 06030-6033
Phone: 860-679-7632
Fax: 860-679-7522
Email: pmendes@uchc.edu
Website(s):

Mendes Research Group

Center for Quantitative Medicine

Department of Cell Biology

Education
DegreeInstitutionMajor
B.Sc.University of LisbonBiochemistry
Ph.D.University of WalesBiological Sciences

Post-Graduate Training
TrainingInstitutionSpecialty
PostdoctoralUniversity of WalesComputational Biology: Project title: "Metabolic control analysis using neural networks: a means for obtaining parameters by measuring variables"
PostdoctoralUniversity of WalesComputational Biology: Project title: “A user-oriented simulation and optimisation system for the rational improvement of biotechnological processes”
PostdoctoralUniversity of WalesComputational Biology: Project title: “Gepasi 4 – a metabolic engineering simulator for all”
Name & DescriptionCategoryRoleTypeScopeStart YearEnd Year
13th Conference on Computational Methods in Systems BiologyWorkshop/ConferenceMemberExternalInternational20152015
HARMONY 2014 Hackathon: Organising CommitteeWorkshop/ConferenceMemberExternalInternational2014
12th Conference on Computational Methods in Systems BiologyWorkshop/ConferenceChairExternalInternational20142014
BMC Systems BiologyEditorial BoardSection EditorExternalNational2012
Biotechnology and Biological Sciences Research Council: Expert Working Group on Digital OrganismsProfessional/Scientific OrganizationMemberExternalInternational20122013
10th Conference on Computational Methods in Systems Biology: Scientific CommitteeWorkshop/ConferenceMemberExternalInternational20122012
National Institutes of Health: special study section for National Centers for Systems BiologyStudy SectionAd-hoc MemberExternalNational20122012
Gordon Research Conference on Cellular Systems BiologyWorkshop/ConferenceChairExternalState20112011
IET Systems BiologyEditorial BoardAssociate EditorExternalNational2010
International Conference on Systems Biology: Scientific Committee and Session co-chairWorkshop/ConferenceMemberExternalInternational20102010
National Institutes of Health: Special Study Section for review of National Centers for Biomedical Computing applicationsStudy SectionAd-hoc MemberExternalNational20102010
BioModels Database, European Bioinformatics InstituteAdvisory CommitteeMemberExternalLocal2009
European Bioinformatics Institute: Review Panel for Research ActivitiesStudy SectionMemberExternalInternational20092009
Biotechnology and Biological Sciences Research Council: Research Committee C, Technological and Methodological DevelopmentStudy SectionMemberExternalNational20092012
National Institutes of Health: Special Study Section BST-M(58) for Reviewing ARRA ApplicationsStudy SectionAd-Hoc MemberExternalNational20092009
Science Foundation Ireland: Review Panel for Principal Investigator Programme GrantsStudy SectionMemberExternalNational20092009
Human Metabolic Network Reconstruction JamboreeWorkshop/ConferenceMemberExternalInternational20092009
9th International Conference on Systems Biology: Scientific CommitteeWorkshop/ConferenceMemberExternalInternational20082008
Science Foundation Ireland: Site Visit Panel for Systems Biology InstituteStudy SectionMemberExternalInternational20082008
Gordon Research Conference on Macromolecular Interactions and Enzyme FunctionWorkshop/ConferenceVice-ChairExternalInternational20082008
Metabolomics ConferenceWorkshop/ConferenceSession ChairExternalInternational20072007
4th International Conference on Plant Metabolomics: Scientific committeeWorkshop/ConferenceMemberExternalInternational20062006
7th International Conference on Systems Biology: Scientific Committee and Session ChairWorkshop/ConferenceMemberExternalInternational20062006
Helmholtz Foundation: Review Panel for Systems Biology Center GrantsStudy SectionMemberExternalInternational20062006
National Institutes of Health: Special Study Section, NHLBIStudy SectionAd-hoc MemberExternalNational20062006
Transactions on Computational Systems BiologyEditorial BoardMemberExternalNational2005
MetabolomicsEditorial BoardMemberExternalNational20052010
National Insititute on Environmental Health Sciences: Working Group on Integrated and Computational ToxicologyProfessional/Scientific OrganizationMemberExternalNational20052005
NIEHS Working Group on Toxicogenomics and Systems BiologyProfessional/Scientific OrganizationConsultantExternalNational20052005
1st Workshop on Metabolomics Standards: Organizing CommitteeWorkshop/ConferenceMemberExternalNational20052005
National Institutes of Health: Modeling and Analysis of Biological SystemsStudy SectionStanding MemberExternalNational20052009
National Academies of Sciences: Committee Report on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human HealthProfessional/Scientific OrganizationUnpaid ConsultantExternalNational20042004
3rd International Conference on Plant Metabolomics: Scientific Advisory BoardWorkshop/ConferenceMemberExternalNational20042004
5th International Conference on Systems Biology: Scientific Committee and Session ChairWorkshop/ConferenceMemberExternalInternational20042004
National Science Foundation: Review Panel for the Plant Genome Research ProgramStudy SectionAd-hoc reviewerExternalNational20042004
2nd European Conference on Computational Biology: Scientific CommitteeWorkshop/ConferenceMemberExternalInternational20032003
2nd International Conference on Plant Metabolomics: Supervisory BoardWorkshop/ConferenceMemberExternalInternational20032003
Metabonomics: Biomarkers of Health and Disease Workshop: Organizing CommitteeWorkshop/ConferenceMemberExternalNational20032003
National Science Foundation: Reverse Site Visit Panel for Plant Genome Program GrantStudy SectionMemberExternalNational20032003
National Institutes of Health: Special Study Section HStudy SectionAd-hoc MemberExternalNational20032003
National Science Foundation: Review Panel for the Plant Genome Research Program grantsStudy SectionMemberExternalNational20032003
SBML Hackathon, Virginia Bioinformatics InstituteWorkshop/ConferenceChairExternalState20032003
National Institutes of Health: Special Study Section 90SStudy SectionMemberExternalNational20022002
National Institutes of Health: Site visit panel for National Resource of Cell Analysis & Modeling, CDF-2 Study SectionStudy SectionMemberExternalNational20022002
National Institutes of Health: Special Emphasis Panel to review the Biomedical Information Science and Technology Initiative (BISTI) pre-Centers applicationsStudy SectionMemberExternalNational20022002
National Science Foundation: IGERT Full Proposals Review PanelStudy SectionMemberExternalNational20022002
National Science FoundationStudy SectionAd-hoc electronic reviewerExternalNational2002
Workshop on Modeling Biochemical NetworksWorkshop/ConferenceChairExternalNational20022002
Special Interest Group on Simulation (SIGSIM) of the International Society of Computational Biology: Steering CommitteeProfessional/Scientific OrganizationMemberExternalInternational20012003
National Science Foundation: IGERT pre-proposals review panelStudy SectionMemberExternalNational20012001
National Institutes of Health: Special Emphasis Panel to review the Biomedical Information Science and Technology Initiative (BISTI) pre-Centers applicationsStudy SectionMemberExternalNational20012001
National Institutes of Health: Genetics Study SectionStudy SectionAd-Hoc MemberExternalNational2001
Comparative and Functional GenomicsEditorial BoardMemberExternalNational20002006
1st International Conference on Systems Biology: Scientific CommitteeWorkshop/ConferenceMemberExternalInternational20002000
The Cancer Research CampaignStudy SectionMail ReviewerExternalInternational
Genome CanadaStudy SectionMail ReviewerExternalInternational
N.O.W. (The Netherlands)Study SectionMail ReviewerExternalInternational
National Research Foundation (South Africa)Study SectionMail ReviewerExternalInternational
The Wellcome Trust (UK)Study SectionMail ReviewerExternalInternational
Medical Research Council (UK)Study SectionMail ReviewerExternalInternational

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 students for Lab Rotations: Summer '17, Fall '17, Spring '18

Journal Articles

Book Chapters

  • A discrete approach to top-down modeling of biochemical networks
    R. Laubenbacher and P. Mendes Computational Systems Biology 2006 Jan;
  • A Methodology for Simulation of Metabolic Pathways and Calculation of Control Coefficients
    Mendes, P., Moniz Barreto, J., Vaz Gomes, A. & Ponces Freire, A. Control of Metabolic Processes 221-224
  • Bioinformatics and Computational Biology for Plant Functional Genomics
    Mendes, P., de la Fuente, A., & Hoops, S. Recent Advances in Phytochemistry 1-13
  • Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data
    Mehrotra, B., & Mendes, P. Plant Metabolomics 105-115
  • Biothermokinetics, Metabolic Control Analysis, Metabolic Engineering and the World-Wide Web: Rapid Dissemination Over the Internet
    Mendes, P. & Kell, D.B. BioThermoKinetics of the Living Cell 254-257
  • Computational Approaches to the Study of Biochemical Pathways and Metabolic Control
    Mendes, P. Technological and Medical Implications of Metabolic Control Analysis 149-155
  • Computational Modeling of Biochemical Networks Using COPASI
    Mendes, P., Hoops, S., Sahle, S., Gauges, R., Dada, J., Kummer, U. Systems Biology 17-59
  • Computer Simulation of Biochemical Kinetics
    Mendes, P., & Kell, D.B. BioThermoKinetics of the Living Cell 245-251
  • Control Analysis of Metabolic Channelling
    Mendes, P. & Kell, D.B. Modern Trends in Biothermokinetics 211-216
  • Databases and Visualization for Metabolomics
    Li, X.J., Brazhnik, O., Kamal, A., Guo, D., Lee, C., Hoops, S. & Mendes, P. Metabolite Profiling: Its Role in Biomarker Discovery and Gene Function Analysis 293-309
  • Framework for Comparative Assessment of Parameter Estimation and Inference Methods in Systems Biology
    Mendes, P. Learning and Inference in Computational Systems Biology 33-58
  • GEPASI – A Simulator of the dDynamical Behaviour of Biochemical Pathways
    Mendes, P. Biothermokinetics 231-233
  • Gepasi 3: a 32-bit Microsoft Windows Computer Program for Simulating Biochemical Dynamics
    Mendes, P. BioThermoKinetics of the Living Cell 258-261
  • GEPASI, A User Oriented Metabolic Simulator
    Mendes, P. Modern Trends in Biothermokinetics 436-466
  • High Performance Computing for Biochemical Network Simulations
    Hoops, S., Chen, D. & Mendes, P. High Performance Computing 16-20
  • How to Vary the Proportion of Dynamic Channelling Flux at Constant Total Flux (and Decrease the Intermediate Pool Size...)
    Mendes, P., Kell, D.B. & Westerhoff, H.V. What is Controlling Life? 50 Years after Schrödinger's What is Life? 202-204
  • Long-Range Metabolic Signalling in Heterogeneous Catalytic Systems: Computer Simulation Study
    Mendes, P., Marmillot, P., Hervagault, J-F., & Welch, G.R. Computation in Cellular and Molecular Biological Systems 137-149
  • Metabolic Channelling in Organized Enzyme Systems: Experiments and Models
    Mendes, P., Kell, D.B., & Welch, G.R. Advances in Molecular and Cellular Biology 1-19
  • Numerical Optimisation and Simulation for Rational Metabolic Engineering
    Mendes, P., & Kell, D.B. BioThermoKinetics in the Post Genomic Era 345-349
  • Plant Metabolomics by GC-MS and Differential Analysis
    Shuman, J.L., Cortes, D.F., Armenta, J.M., Pokrzywa, R.M., Mendes, P. & Shulaev, V. Plant Reverse Genetics: Methods and Protocols 229-246
  • Regulatory Strength Analysis for Inferring Gene Networks
    de la Fuente, A., Brazhnik, P. & Mendes, P. Metabolic Engineering in the Post Genomic Era 107-137
  • Simultaneous Estimates of Single-Enzyme Kinetic Parameters for Multi-Enzymatic Systems Using Artificial Neural Networks
    Mendes, P., & Kell, D.B. What is Controlling Life? 50 Years after Schrödinger's What is Life? 302-304
  • Snapshots of Systems: Metabolic Control Analysis and Biotechnology in the Post-Genomic Era
    Kell, D.B., & Mendes, P. Technological and Medical Implications of Metabolic Control Analysis 3-25

Conference Papers

  • The Role of Bioinformatics in Toxicogenomics and Proteomics.
    Sobral, B., D. Eckart, R. Laubenbacher, and P. Mendes "The Role of Bioinformatics in Toxicogenomics and Proteomics." Proceedings from NATO Advanced Workshop on Toxicogenomics and Proteomics. Prague, Czech Republic, October 16-20, 2002. 11. 2002 Jan;

Letters

Title or AbstractTypeSponsor/EventDate/YearLocation
Computational Systems Biology for ToxicologyPlenary LectureEuroTox 2014 Conference2014Edinburgh, UK
Modelling and parameter estimation – should we do it? and how?LectureDepartmental Seminar2014University of Warwick, UK
Computational modelling of biochemical networksLectureDepartmental Seminar2014University of Liverpool, UK
ThEcoli: A Kinetic Model of Escherichia Coli Central MetabolismTalkInternational Conference on Systems Biology2013Copenhagen, Denmark
Kinetic Models of Whole-Cell Metabolism – Progress and ApplicationsTalkCambridge Workshop: Modeling for Industrial Biotechnology2013Cambridge, England
Digital Organisms, Biochemical Simulations and the CloudTalkAstraZeneca 2013 Modelling and Simulation Symposium2013Alderley Park, UK
Systems Biology for Improving Production of Cellular ProductsTalkSymposium on Advances in Recombinant Protein Technology2013Alderley Park, UK
From Genomes to Large-Scale Kinetic Models of MetabolismTalkFrench Conference on Biology, Computer Science and Mathematics2013Toulouse, France
From Genomes to Large-Scale Kinetic Models of MetabolismTalkSymposium on Computational Biology Applications2013Farmington, Connecticut
Optimisation and Parameter Estimation in COPASITalkLatvia University of Agriculture2013Jelgava, Latvia
A Computational Model of Human Iron MetabolismTalkConference on Systems Biology of Mammalian Cells2012Leipzig, Germany
ManyCell: A Multiscale Simulator for Cellular SystemsTalkConference on Computational Methods in Systems Biology2012London, England
From Genomes to Large-Scale Kinetic Models of MetabolismTalkJapanese Biochemical Society2012Fukuoka, Japan
COPASI. Wellcome Trust Workshop on Open Source Software for Systems, Pathways, Interactions and NetworksTalkEuropean Bioinformatics Institute2012Hinxton, England
Modelling the Dynamics of Eukaryotic Protein SynthesisTalkInternational Workshop on Systems and Synthetic Biology2012Mallorca, Spain
Towards Whole-Genome Kinetic Models of MetabolismTalkSystems Biology Europe Symposium2012Madrid, Spain
Adventures in Modelling and Simulation of Biochemical NetworksTalkFormal Approaches to Modelling Biomolecular Networks2012Edinburgh, Scotland
Modelling the Dynamics of Eukaryotic Protein SynthesisTalkUniversity of Tokyo2012Tokyo, Japan
Modelling and Simulation of Biochemical NetworksTalkUniversity of Oxford2012Oxford, England
From Networks to Models – Large Scale Kinetic Models of MetabolismTalkUniversity of Saarbrücken2012Saarbrücken, Germany
Applications of Dynamic Model Optimization Using COPASI SoftwareTalkLatvia University of Agriculture2012Jelgava, Latvia
Chasing the Flux: Selecting Target Pathways Through Flux Analysis of Carbon MetabolismTalkConference on Constraint-based Reconstruction and Analysis2011Reykjavik, Iceland
From Genomes to ModelsTalk2nd Workshop on Medical Systems Biology2011Manchester, England
Kinetic Modelling of Largescale Metabolic NetworksTalkInternational Conference on Computational Methods in Systems Biology2011Paris, France
Distance Learning in Computational Systems BiologyTalkFutureSysBio Education Workshop2011Gothenburg, Sweden
Management of Data and Models in Systems BiologyTalkData Management for Systems Biology and the Life Sciences2011Heidelberg, Germany
Kinetic Modelling of Large-Scale Metabolic NetworksTalkBoehringer Ingelheim Titisee Conference on Genomic Regulation2011Titisee, Germany
Metabolism, Metabolomics and Systems BiologyTalkAustralasian Metabolomics Symposium2010Melbourne, Australia
Computational Whole-Genome Reconstructions and Modelling of Metabolic NetworksTalkInternational Conference on Systems Biology2010Edinburgh, Scotland
The Pre-History of Kinetic Modelling and SimulationTalkInternational Conference on Systems Biology2010Edinburgh, Scotland
Harnessing the Chemistry of life – Revolutionising Toxicology. Computational Chemistry and Systems BiologyTalkEuropean Partnership on Alternative Approaches to Animal Testing2010Brussels, Belgium
Standardized Enzyme Kinetics for Systems BiologyTalkInternational Symposium on Experimental Standard Conditions of Enzyme Chara2009Rudhsheim, Germany
Software from the Manchester Centre for Integrative Systems BiologyTalkInternational Conference on Yeast Genetics & Molecular Biology2009Manchester, England
The Pre-History of Systems BiologyTalkUK Inter- Doctoral Training Centres Meeting2009Manchester, England
Advanced Simulation and Analysis of Biochemical Models Using COPASITalkInternational Conference on Systems Biology2008Gothenburg, Sweden
A New Strategy for Assessing Global Sensitivity in Biochemical Network ModelsTalkSpanish Systems Biology Network2008Valencia, Spain
Computational Systems Biology for Modeling CancerTalkAnnual Symposium on Cancer Research2008Houston, Texas
A New Strategy for Assessing Global Sensitivity in Biochemical Network ModelsTalkPortuguese National Congress of Biochemistry2008Ponta Delgada, Azores, Portugal
Modelling and Simulation of Biological Systems with COPASITalkMicrosoft Research2008Cambridge, England
Adventures in Reverse Engineering of Biochemical NetworksTalkUniversity of Sheffield2008Sheffield, United Kingdom
Optimisation and Parameter EstimationTalkInstituto Gulbenkian de Ciência2008Oeiras, Portugal
Modelling and Simulation of Biological Systems with COPASITalkBiotechnology and Biological Sciences Research Council MATSYB meeting2008Manchester, England
Software Interoperability for Systems BiologyTalkPhD Program in Computational Biology, Instituto Gulbenkian de Ciência2008Oeiras, Portugal
New Developments in COPASITalkWorkshop on Computational Cell Biology2008Hinxton, England
Adventures in Reverse Engineering of Biochemical NetworksTalkCentre for Computational and Systems Biology2007Trento, Italy
Adventures in Reverse Engineering of Biochemical NetworksTalkMax Plank Institute for Molecular Generics2007Berlin, Germany
Integrated Data Management for Kinetic Modelling and Experimental ResultsTalkStorage and Annotation of Reaction Kinetics Data2007Heidelberg, Germany
Benchmarking Parameter Estimation and Reverse Engineering StrategiesTalkParameter Estimation in Systems Biology2007Manchester, England
Adventures in Reverse Engineering of Biochemical NetworksTalkUniversity of Pittsburgh2006Pittsburgh, Pennsylvania
Software e métodos na biologia de sistemasTalkUniversity of Minho2006Braga, Portugal
Top-Down Modeling of Biochemical Networks – A Grand Challenge of Systems BiologyTalkInstituto Gulbenkian Ciencia2006Oeiras, Portugal
From Data to Models: Continuous and Discrete Top-down Modeling of Biochemical NetworksTalkFree University of Amsterdam2006Amsterdam, The Netherlands
Modeling and Simulation for Metabolomics Data AnalysisTalkDuke University Medical Center2006Durham, North Carolina
Systems BiologyTalkNational Institutes of Health2006Bethesda, Maryland
Biochemical Network DynamicsTalkAmerican Mathematical Society Short Course on Modeling and Biological2006San Antonio, Texas
Top-Down Modeling of Biochemical Networks – A Grand Challenge of Systems BiologyTalkIntegrative Bioinformatics Workshop2006Rothamstead, United Kingdom
Building Dynamic Models From Functional Genomics Data – A Systems Biology ChallengeTalkConference on Macromolecular Organization and Cell Function2006South Hadley, Massachusetts
A Systems Biology Approach to the Study of Stress ResponsesTalkGenome To Systems Conference2006Manchester, England
Metabolomics as a Component of Systems Biology: Issues in Data FusionTalkMetabolomics Society Conference2006Boston, Massachusetts
In Silico Models for Reverse Engineering: Complexity and Realism versus Well-Defined MetricsTalkDREAM DIMACS Workshop2006New York, New York
Biochemical Networks ModellingTalkUniversity of Porto Alegre2005Porto Alegre, Brazil
Systems Approaches to the Study of Stress ResponsesTalkBASF Corporation2005Ludwigshafen, Germany
Systems Approaches to the Study of Stress ResponsesTalkMicroBiotec 2005 Conference2005Póvoa do Varzim, Portugal
Computational Tools for Integrative 'Omics' ApproachesTalkNational Cancer Institute2005Rockville, Maryland
Metabolomics and Biochemical Networks ModellingTalkTherapeutic Applications of Computational Biology2005Hinxton, England
Modeling and Simulation for Metabolomics Data AnalysisTalkBritish Biochemical Society2005Glasgow, Scotland
Databases and Visualization for MetabolomicsTalkMetabolomics Society Conference2005Tsuruoka, Japan
Systems Analyses of Medicago Truncatula Stress ResponsesTalkModel Legume Conference2005Monterey, California
From Data to Models: Continuous and Discrete Top-down Modeling of Biochemical NetworksTalkBiocomplexity 7 Workshop, Indiana University2005Bloomington, Indiana
COPASI SoftwareTalk2nd Symposium on Computational Cell Biology2005Lenox, Massachusetts
Simulation of Biochemical Networks for Increased Understanding of ExperimentsTalkThomas Jefferson University2004Philadelphia, Pennsylvania
Biochemical Network DynamicsTalkWake Forest University Health Sciences Center2004Wake Forest, North Carolina
Inferring Biochemical Networks from Functional Genomic DataTalkUniversity of Texas Health Sciences Center2004Houston, Texas
Plant Functional Genomics and Systems BiologyTalkUnited States Department of Agriculture2004Beltsville, Maryland
Plant Functional Genomics and Systems BiologyTalkThe John Innes Centre2004Norwich, United Kingdom
Bioinformatics for Integrative Functional GenomicsTalkEuropean Bioinformatics Institute2004Hinxton, England
Metabolomics Data Analysis: Beyond CorrelationTalkCHI Conference on Analytical Methods for Metabolic Profiling2004Orlando, Florida
Software and Methods for Modeling and Simulating Biochemical NetworksTalk5th International Conference on Systems Biology2004Heidelberg, Germany
Biological Systems Identification From Functional Genomic DataTalk2nd Conference From Genomes to Systems2004Manchester, England
Modeling Biochemical Networks in the Context of Systems BiologyTalkWest Virginia University Workshop on Systems Biology2004Roanoke, West Virginia
Bioinformatics for Integrative Functional GenomicsTalk3rd Plant Metabolomics Conference2004Ames, Iowa
Yeast Systems Biology at the Virginia Bioinformatics InstituteTalk2nd International Workshop of the Yeast Systems Biology Network2004Copenhagen, Denmark
A Systems Biology Approach to the Study of Stress ResponsesTalkGordon Research Conference on Structural, Functional, and Evolutionary Geno2004Ventura, California
Database and Visualization for Grape Functional GenomicsTalk12th International Plant and Animal Genome Conference2004San Diego, California
Plant Functional Genomics and Systems BiologyTalkMichigan State University2003East Lansing, Michigan
Workshop on Analysis of Complex Pathways – The Case of the Reverse Cholesterol Transport PathwayTalk2003Arolla, Switzerland
Scaling up Biochemical Models ...and Artificial Gene NetworksTalk4th International Conference on Systems Biology2003St. Louis, Missouri
Numerical Optimization Methods for Enzyme NetworksTalkInternational Workshop on Experimental Standard Conditions of Enzyme Charac2003Ruedesheim/Rhein, Germany
Simulation Meets Data Analysis: The Development of Objective Tests for Functional Genomics Data Analysis AlgorithmsTalk2nd European Conference on Computational Biology2003Paris, France
Bioinformatics for MetabolomicsTalkNational Research Council2003Seattle, Washington
Computational Support for Metabolomics: Databases, Analysis, and VisualizationTalkNorth-West Metabolomics Meeting2003Manchester, England
Database and Visualization for Grape Functional GenomicsTalkGrape Bioinformatics Conference2003Tahoe, California
Computational Support for Metabolomics: Databases, Analysis, and VisualizationTalkNIEHS Workshop on Metabonomics: Biomarkers of Health and Disease2003Research Triangle Park, North Carolina
Inferring Biochemical Networks from Functional Genomic DataTalkNIEHS & VBI Symposium on Toxicogenomics: Through the Eyes of Informatics2003Washington, DC
Making Sense of the Data: Analysis, Visualization and the Need for DatabasesTalkFood Forum Symposium on Individualized Nutrition and its Impact on the Food2003Washington, DC
Metabolomics: A Tool to Determine the Structure and Regulation of Biochemical Networks?Talk2nd International Conference on Plant Metabolomics2003Potsdam, Germany
New Methods for Biochemical Network ModelingTalkVirginia Commonwealth University2002Richmond, Virginia
Inferring Biochemical Networks from Functional Genomic DataTalkGeorge Mason University2002Fairfax, Virginia
New Methods for Biochemical Network ModelingTalkJohns Hopkins University2002Baltimore, Maryland
Biochemistry by Numbers: Modeling Metabolic, Signaling and Genetic NetworksTalk15th International Symposium on Mathematical Theory of Networks and Systems2002South Bend, Indiana
Swimming in a Sea of Data: Forward and Inverse Modeling of Biochemical DynamicsTalkDynamics Days Europe2002Heidelberg, Germany
Biochemical Networks Modeling and Metabolomic Data AnalysisTalkBioinformatics & Pharmacogenomics Symposium2002Richmond, Virginia
Functional Genomic Data IntegrationTalkInternational Conference on Legume Genomics and Genetics2002Minneapolis, Minnesota
Data Visualization and Analysis for MetabolomicsTalk1St International Congress on Plant Metabolomics2002Wageningen, The Netherlands
Functional Genomics and the Simulation of Biochemical NetworksTalkInfoTechPharma2002London, England
Bioinformatics and Computational Biology for Plant Functional GenomicsTalkPhytochemical Society of North America2001Oklahoma City, Oklahoma
Simulating Large-Scale Biochemical Systems: Forward and Inverse ProblemsTalkSeminar Information and Simulation Systems for the Analysis of Gene Regulat2001Daghstul, Germany
Two Complementary Methods for Reverse Engineering Genetic NetworksTalkWorkshop on Computation of Biochemical Pathways and Genetic Networks2001Heidelberg, Germany
Simulation of Biochemical and Genetic Networks – HPC in the Post-Genome EraTalkSun Microsystems High Performance Computing Consortium2001Heidelberg, Germany
Tools for Simulating Large Biological Systems: The Need for OptimizationTalkIn Silico Technologies in Drug Discovery2001Bethesda, Maryland
GepasiTalkInternational Symposium on Computational Cell Biology2001Lenox, Massachusetts
Numerical Optimisation for the Analysis and Design of Metabolic Pathways with GepasiTalkUniversity of Connecticut Health Center2001Farmington, Connecticut
Tools for Simulating Large Biological Systems – The Need for OptimizationTalkInternational Conference on Systems Biology2000Tokyo, Japan
PathDB: A Second Generation Metabolic DatabaseTalk9th BioThermoKinetics Meeting, University of Stellenbosch2000South Africa
Advanced Visualization of Metabolic Pathways in PathDBTalkPlant and Animal Genome VIII2000San Diego, California
Computer Simulation of Biochemical Pathways and Gene ExpressionTalkDepartment of Biochemistry, Virginia Tech2000Blacksburg, Virginia
PathDB: A Second Generation Metabolic DatabaseTalkUniversity of Southern Cape2000Cape Town, South Africa
Computer Simulation of Biochemical Pathways and Gene ExpressionTalkUniversity of New Mexico2000Albuquerque, New Mexico
GepasiTalkCaltech2000Pasadena, California
Metabolic Simulation as an Aid in Understanding Gene Expression DataTalkComputation of Biochemical Pathways and Genetic Networks1999Heidelberg, Germany
Computational Approaches to the Study of Biochemical Pathways and Metabolic ControlTalkNATO Advanced Research Workshop1999Visegrad, Hungary
Biochemistry by Numbers: Computer Simulation of the Behaviour of Biochemical PathwaysTalkUniversity of Utah1999Salt Lake City, Utah
Plant Metabolic Pathways Database at NCGRTalkDuPont Life Sciences1999Wilmington, Delaware
Computer Applications for Metabolic PathwaysTalkSamuel Roberts Noble Foundation1999Ardmore, Oklahoma
Metabolic Databases Integration with Other Biological Data TypesTalkGallo Life Sciences Research, Gallo Winery1999Modesto, California
Using Computers to Learn MetabolismTalkBiochemical Society Colloquium on Modelling Metabolism1998Leicester, England
Integration of Gene Expression with Metabolism in Kinetic SimulationsTalkDagstuhl Seminar Modelling and Simulation of Gene Regulation and Metabolic1998Dagstuhl, Germany
Numerical Optimisation for the Analysis and Design of Metabolic PathwaysTalkWorkshop on Theoretical Biophysics1998Hidensee, Germany
Biochemistry by Numbers: Computer Simulation of the Behaviour of Biochemical PathwaysTalkUniversity of Wales1998Aberystwyth, Wales
Biochemistry by Numbers: Simulation and Optimisation of Biochemical PathwaysTalkTokyo Medical and Dental University1998Tokyo, Japan
Biochemistry by Numbers: Simulation and Optimisation of Biochemical PathwaysTalkThe Helix Institute1998Tokyo, Japan
Biochemistry by Numbers: Simulation and Optimisation of Biochemical PathwaysTalkYamanouchi Tsukuba Research Center1998Tsukuba, Japan
Computer Simulation and Optimisation of Metabolic Fluxes Using GepasiTalkEuropean Science Foundation Research Conference on Control of Metabolic Flu1997Giens, France
Gepasi RevisitedTalkAberystwyth-Swansea Microbiology Meeting1997Grygenog, Wales
Computer Simulation of the Kinetics of Metabolic PathwaysTalkSociety for General Microbiology Symposium on Microbial Informatics1997Southampton, England
Metabolic Control Analysis and Kinetic SimulationTalkUniversity of Lisbon1997Lisbon, Portugal
Computer Simulation of the Kinetics of Biochemical PathwaysTalkUniversity College London1997London, England
Biochemistry by Numbers: Simulation and Optimisation of Biochemical PathwaysTalkUniversity of Washington1997Seattle, Washington
Computer Simulation of Biochemical KineticsTalkVII BioThermoKinetics1996Louvain-la-Neuve, Belgium
Metabolic Control Analysis and Simulation of Organised Enzyme SystemsTalkGordon Research Conference on Macromolecular Organization and Cell Function1996Oxnard, California
Exploring Biochemical Models with Gepasi, A Kinetics SimulatorTalkInternational Conference on Information Processing in Cells and Tissues1996Liverpool, England
Gepasi 3.0 A Simulator to Investigate MetabolismTalkTechnical University of Delft1996Delft, The Netherlands
Long-Range Metabolic Signalling in Heterogeneous Catalytic Systems: Computer Simulation StudyTalkInternational Conference on Information Processing in Cells and Tissues1995Liverpool, England
Multi-Enzyme Complexes and Multifunctional Enzymes. Similarities and DifferencesTalkAberystwyth-Swansea Microbiology Meeting1995Grygenog, Wales
Computer Simulation of Metabolic ProcessesTalkUniversity of Liverpool1995Liverpool, England
GepasiTalkEuropean Workshop on Perceptual Control Theory1994Gregynog, Wales
Control Analysis of Metabolic ChannellingTalkBioThermoKinetics Meeting1992Bordeaux, France
Metabolic Control AnalysisTalkUniversity of Lisbon1990Lisbon, Portugal