Pedro Mendes

Publication Activity (10 Years)

Years Active: 1988-2022
Publications (10 Years): 14

Top Topics

Systems Biology

Computational Models

Benchmark Problems

Top Venues

BMC Syst. Biol.

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David 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
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50 (W1) (2022)
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 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 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR (2022)
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
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22 (2) (2021)
Jignesh H. Parmar, Pedro Mendes
A computational model to understand mouse iron physiology and disease. PLoS Comput. Biol. 15 (1) (2019)
Abhishekh Gupta, Pedro Mendes
An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Comput. 6 (1) (2018)
Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes
Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Syst. Biol. 11 (1) (2017)
Pierre Millard, Kieran Smallbone, Pedro Mendes
Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Comput. Biol. 13 (2) (2017)
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck
ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 44 (Database-Issue) (2016)
Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. 7 (2016)
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
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63 (10) (2016)
Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes
libChEBI: an API for accessing the ChEBI database. J. Cheminformatics 8 (1) (2016)
Pierre Millard, Jean-Charles Portais, Pedro Mendes
Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Syst. Biol. 9 (2015)
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
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Syst. Biol. 9 (2015)
Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth Owen, Steve Turner, Pedro Mendes, Christoph Steinbeck
ChEBI for systems biology and metabolic modelling. ICBO (2015)
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
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology. CoRR (2014)
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
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7 (2013)
Simon Mitchell, Pedro Mendes
A Computational Model of Liver Iron Metabolism. PLoS Comput. Biol. 9 (11) (2013)
Jürgen Pahle, Joseph D. Challenger, Pedro Mendes, Alan J. McKane
Biochemical fluctuations, optimisation and the linear noise approximation. BMC Syst. Biol. 6 (2012)
Benjamin D. Heavner, Kieran Smallbone, Brandon Barker, Pedro Mendes, Larry P. Walker
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst. Biol. 6 (2012)
Joseph O. Dada, Pedro Mendes
ManyCell: A Multiscale Simulator for Cellular Systems. CMSB (2012)
Dave Lee, Kieran Smallbone, Warwick B. Dunn, Ettore Murabito, Catherine Winder, Douglas B. Kell, Pedro Mendes, Neil Swainston
Improving metabolic flux predictions using absolute gene expression data. BMC Syst. Biol. 6 (2012)
Edward Kent, Stefan Hoops, Pedro Mendes
Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol. 6 (2012)
Pedro Mendes, Natalie J. Stanford, Kieran Smallbone
Kinetic modelling of large-scale metabolic networks. CMSB (2011)
Neil Swainston, Kieran Smallbone, Pedro Mendes, Douglas B. Kell, Norman W. Paton
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J. Integr. Bioinform. 8 (2) (2011)
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
Further developments towards a genome-scale metabolic model of yeast. BMC Syst. Biol. 4 (2010)
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
Systematic integration of experimental data and models in systems biology. BMC Bioinform. 11 (2010)
Neil Swainston, Daniel Jameson, Peter Li, Irena Spasic, Pedro Mendes, Norman W. Paton
Integrative Information Management for Systems Biology. DILS (2010)
Kieran Smallbone, Evangelos Simeonidis, Neil Swainston, Pedro Mendes
Towards a genome-scale kinetic model of cellular metabolism. BMC Syst. Biol. 4 (2010)
Joseph O. Dada, Irena Spasic, Norman W. Paton, Pedro Mendes
SBRML: a markup language for associating systems biology data with models. Bioinform. 26 (7) (2010)
Joseph O. Dada, Pedro Mendes
Design and Architecture of Web Services for Simulation of Biochemical Systems. DILS (2009)
Neil Swainston, Pedro Mendes
libAnnotationSBML: a library for exploiting SBML annotations. Bioinform. 25 (17) (2009)
Dingjun Chen, Chung-Yeol Lee, Cheol Hoon Park, Pedro Mendes
Parallelizing simulated annealing algorithms based on high-performance computer. J. Glob. Optim. 39 (2) (2007)
Pedro Mendes
Metabolomics and the challenges ahead. Briefings Bioinform. 7 (2) (2006)
Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson
Challenges for modeling and simulation methods in systems biology. WSC (2006)
Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer
COPASI - a COmplex PAthway SImulator. Bioinform. 22 (24) (2006)
Sven Sahle, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes
Simulation of biochemical networks using COPASI: a complex pathway simulator. WSC (2006)
Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes
Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinform. 20 (18) (2004)
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. 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
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19 (4) (2003)
Pedro Mendes, Wei Sha, Keying Ye
Artificial gene networks for objective comparison of analysis algorithms. ECCB (2003)
Dianjing Guo, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, Pedro Mendes
A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites. CSB (2002)
Pedro Mendes
Emerging bioinformatics for the metabolome. Briefings Bioinform. 3 (2) (2002)
Pedro Mendes, Douglas B. Kell
MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinform. 17 (3) (2001)
Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinform. 17 (1) (2001)
Pedro Mendes, Douglas B. Kell
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinform. 14 (10) (1998)
Pedro Mendes
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9 (5) (1993)
Harold A. Kurstedt, Kwang Lee, Pedro Mendes, Steven Berube
The Responsive System: A New Challenge for AI. IEA/AIE (Vol. 1) (1988)