Pedro Mendes

According to our database, Pedro Mendes authored at least 46 papers between 1988 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz

Briefings Bioinform., 2021

2019

A computational model to understand mouse iron physiology and disease.

Jignesh H. Parmar, Pedro Mendes

PLoS Comput. Biol., 2019

2018

An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems.

Abhishekh Gupta, Pedro Mendes

Comput., 2018

2017

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.

Pierre Millard, Kieran Smallbone, Pedro Mendes

PLoS Comput. Biol., 2017

Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient.

Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes

BMC Syst. Biol., 2017

2016

Toward Community Standards and Software for Whole-Cell Modeling.

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

IEEE Trans. Biomed. Eng., 2016

ChEBI in 2016: Improved services and an expanding collection of metabolites.

Janna Hastings, Gareth I. Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck

Nucleic Acids Res., 2016

libChEBI: an API for accessing the ChEBI database.

Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes

J. Cheminformatics, 2016

COMODI: an ontology to characterise differences in versions of computational models in biology.

Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer

J. Biomed. Semant., 2016

2015

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga

BMC Syst. Biol., 2015

Impact of kinetic isotope effects in isotopic studies of metabolic systems.

Pierre Millard, Jean-Charles Portais, Pedro Mendes

BMC Syst. Biol., 2015

ChEBI for systems biology and metabolic modelling.

Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth I. Owen, Steve Turner, Pedro Mendes, Christoph Steinbeck

Proceedings of the International Conference on Biomedical Ontology, 2015

2014

BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology.

Alejandro Fernández Villaverde, David Henriques, Kieran Smallbone, Sophia Bongard, Joachim Schmid, Damjan Cicin-Sain, Anton Crombach, Julio Saez-Rodriguez, Klaus Mauch, Eva Balsa-Canto, Pedro Mendes, Johannes Jaeger, Julio R. Banga

CoRR, 2014

2013

A Computational Model of Liver Iron Metabolism.

Simon Mitchell, Pedro Mendes

PLoS Comput. Biol., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn P. van Iersel, Sarah M. Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B. Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, Nicolas Le Novère

BMC Syst. Biol., 2013

2012

Biochemical fluctuations, optimisation and the linear noise approximation.

Jürgen Pahle, Joseph D. Challenger, Pedro Mendes, Alan J. McKane

BMC Syst. Biol., 2012

Improving metabolic flux predictions using absolute gene expression data.

Dave Lee, Kieran Smallbone, Warwick B. Dunn, Ettore Murabito, Catherine Winder, Douglas B. Kell, Pedro Mendes, Neil Swainston

BMC Syst. Biol., 2012

Condor-COPASI: high-throughput computing for biochemical networks.

Edward Kent, Stefan Hoops, Pedro Mendes

BMC Syst. Biol., 2012

Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.

Benjamin D. Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P. Walker

BMC Syst. Biol., 2012

ManyCell: A Multiscale Simulator for Cellular Systems.

Joseph O. Dada, Pedro Mendes

Proceedings of the Computational Methods in Systems Biology, 2012

2011

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.

Neil Swainston, Kieran Smallbone, Pedro Mendes, Douglas B. Kell, Norman W. Paton

J. Integr. Bioinform., 2011

Kinetic modelling of large-scale metabolic networks.

Pedro Mendes, Natalie J. Stanford, Kieran Smallbone

Proceedings of the Computational Methods in Systems Biology, 9th International Conference, 2011

2010

Towards a genome-scale kinetic model of cellular metabolism.

Kieran Smallbone, Evangelos Simeonidis, Neil Swainston, Pedro Mendes

BMC Syst. Biol., 2010

Further developments towards a genome-scale metabolic model of yeast.

Paul D. Dobson, Kieran Smallbone, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pinar Pir, Chuan Lu, Neil Swainston, Warwick B. Dunn, Paul Fisher, Duncan Hull, Marie Brown, Olusegun Oshota, Natalie J. Stanford, Douglas B. Kell, Ross D. King, Stephen G. Oliver, Robert D. Stevens, Pedro Mendes

BMC Syst. Biol., 2010

Systematic integration of experimental data and models in systems biology.

Peter Li, Joseph O. Dada, Daniel Jameson, Irena Spasic, Neil Swainston, Kathleen Carroll, Warwick B. Dunn, Farid Khan, Naglis Malys, Hanan L. Messiha, Evangelos Simeonidis, Dieter Weichart, Catherine Winder, Jill Wishart, David S. Broomhead, Carole A. Goble, Simon J. Gaskell, Douglas B. Kell, Hans V. Westerhoff, Pedro Mendes, Norman W. Paton

BMC Bioinform., 2010

SBRML: a markup language for associating systems biology data with models.

Joseph O. Dada, Irena Spasic, Norman W. Paton, Pedro Mendes

Bioinform., 2010

Integrative Information Management for Systems Biology.

Neil Swainston, Daniel Jameson, Peter Li, Irena Spasic, Pedro Mendes, Norman W. Paton

Proceedings of the Data Integration in the Life Sciences, 7th International Conference, 2010

2009

libAnnotationSBML: a library for exploiting SBML annotations.

Neil Swainston, Pedro Mendes

Bioinform., 2009

Design and Architecture of Web Services for Simulation of Biochemical Systems.

Joseph O. Dada, Pedro Mendes

Proceedings of the Data Integration in the Life Sciences, 6th International Workshop, 2009

2007

Parallelizing simulated annealing algorithms based on high-performance computer.

Dingjun Chen, Chung-Yeol Lee, Cheol Hoon Park, Pedro Mendes

J. Glob. Optim., 2007

2006

COPASI - a COmplex PAthway SImulator.

Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer

Bioinform., 2006

Metabolomics and the challenges ahead.

Pedro Mendes

Briefings Bioinform., 2006

Challenges for modeling and simulation methods in systems biology.

Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson

Proceedings of the Winter Simulation Conference WSC 2006, 2006

Simulation of biochemical networks using COPASI: a complex pathway simulator.

Sven Sahle, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes

Proceedings of the Winter Simulation Conference WSC 2006, 2006

2004

Discovery of meaningful associations in genomic data using partial correlation coefficients.

Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes

Bioinform., 2004

2003

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang

Bioinform., 2003

Artificial gene networks for objective comparison of analysis algorithms.

Pedro Mendes, Wei Sha, Keying Ye

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002

Emerging bioinformatics for the metabolome.

Pedro Mendes

Briefings Bioinform., 2002

A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites.

Dianjing Guo, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, Pedro Mendes

Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002

2001

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.

Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral

Bioinform., 2001

MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems.

Pedro Mendes, Douglas B. Kell

Bioinform., 2001

1998

Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.

Pedro Mendes, Douglas B. Kell

Bioinform., 1998

1993

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.

Pedro Mendes

Comput. Appl. Biosci., 1993

1988

The Responsive System: A New Challenge for AI.

Harold A. Kurstedt, Kwang Lee, Pedro Mendes, Steven Berube

Proceedings of the First International Conference on Industrial & Engineering Applications of Artificial Intelligence & Expert Systems, IEA/AIE 1988, June 1-3, 1988, Tullahoma, TN, USA. ACM, 1988, 1988