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Pedro Mendes 0001

Pedro Pedrosa Mendes

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affiliation: University of Connecticut School of Medicine, Farmington, CT, USA
affiliation: University of Manchester, Institute of Biotechnology / School of Computer Science, UK
affiliation (former): Virginia Tech, Virginia Bioinformatics Institute, Blacksburg, VA, USA
affiliation (former): Universityof Wales Aberystwyth, UK
affiliation (PhD 1986): University of Maryland, MD, USA

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2020 – today

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2022
[j34]
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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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022)
[i2]
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  - journals/corr/abs-2203-06732
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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:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022)
2021
[j33]
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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): 642-663 (2021)

2010 – 2019

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2019
[j32]
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  - journals/ploscb/ParmarM19
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Jignesh H. Parmar, Pedro Mendes:
A computational model to understand mouse iron physiology and disease. PLoS Comput. Biol. 15(1) (2019)
2018
[j31]
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Abhishekh Gupta, Pedro Mendes:
An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Comput. 6(1): 9 (2018)
2017
[j30]
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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): 57:1-57:13 (2017)
[j29]
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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)
2016
[j28]
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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: 46 (2016)
[j27]
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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): 11:1-11:6 (2016)
[j26]
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Janna Hastings, Gareth I. 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): 1214-1219 (2016)
[j25]
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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): 2007-2014 (2016)
2015
[j24]
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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: 8 (2015)
[j23]
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Pierre Millard, Jean-Charles Portais, Pedro Mendes:
Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Syst. Biol. 9: 64 (2015)
[c10]
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Janna Hastings, Neil Swainston, Venkatesh Muthukrishnan, Namrata Kale, Adriano Dekker, Gareth I. Owen, Steve Turner, Pedro Mendes, Christoph Steinbeck:
ChEBI for systems biology and metabolic modelling. ICBO 2015
2014
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Pedro Mendes, Joseph O. Dada, Kieran Smallbone:
Computational Methods in Systems Biology - 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings. Lecture Notes in Computer Science 8859, Springer 2014, ISBN 978-3-319-12981-5 [contents]
[i1]
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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 abs/1407.5856 (2014)
2013
[j22]
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  - journals/bmcsb/BuchelRSWCKMSGGIKRWHHK0MZCSSLDN13
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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: 116 (2013)
[j21]
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Simon Mitchell, Pedro Mendes:
A Computational Model of Liver Iron Metabolism. PLoS Comput. Biol. 9(11) (2013)
2012
[j20]
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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: 55 (2012)
[j19]
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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: 73 (2012)
[j18]
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Jürgen Pahle, Joseph D. Challenger, Pedro Mendes, Alan J. McKane:
Biochemical fluctuations, optimisation and the linear noise approximation. BMC Syst. Biol. 6: 86 (2012)
[j17]
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Edward Kent, Stefan Hoops, Pedro Mendes:
Condor-COPASI: high-throughput computing for biochemical networks. BMC Syst. Biol. 6: 91 (2012)
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Joseph O. Dada, Pedro Mendes:
ManyCell: A Multiscale Simulator for Cellular Systems. CMSB 2012: 366-369
2011
[j16]
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  - journals/jib/SwainstonSMKP11
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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)
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Pedro Mendes, Natalie J. Stanford, Kieran Smallbone:
Kinetic modelling of large-scale metabolic networks. CMSB 2011: 5-6
2010
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  - journals/bioinformatics/DadaSPM10
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Joseph O. Dada, Irena Spasic, Norman W. Paton, Pedro Mendes:
SBRML: a markup language for associating systems biology data with models. Bioinform. 26(7): 932-938 (2010)
[j14]
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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: 582 (2010)
[j13]
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  - journals/bmcsb/SmallboneSSM10
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Kieran Smallbone, Evangelos Simeonidis, Neil Swainston, Pedro Mendes:
Towards a genome-scale kinetic model of cellular metabolism. BMC Syst. Biol. 4: 6 (2010)
[j12]
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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: 145 (2010)
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Neil Swainston, Daniel Jameson, Peter Li, Irena Spasic, Pedro Mendes, Norman W. Paton:
Integrative Information Management for Systems Biology. DILS 2010: 164-178

2000 – 2009

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2009
[j11]
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Neil Swainston, Pedro Mendes:
libAnnotationSBML: a library for exploiting SBML annotations. Bioinform. 25(17): 2292-2293 (2009)
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Joseph O. Dada, Pedro Mendes:
Design and Architecture of Web Services for Simulation of Biochemical Systems. DILS 2009: 182-195
2007
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Dingjun Chen, Chung-Yeol Lee, Cheol Hoon Park, Pedro Mendes:
Parallelizing simulated annealing algorithms based on high-performance computer. J. Glob. Optim. 39(2): 261-289 (2007)
2006
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Pedro Mendes:
Metabolomics and the challenges ahead. Briefings Bioinform. 7(2): 127 (2006)
[j8]
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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): 3067-3074 (2006)
[c5]
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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: 1698-1706
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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: 1720-1730
2004
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Alberto de la Fuente, Nan Bing, Ina Hoeschele, Pedro Mendes:
Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinform. 20(18): 3565-3574 (2004)
2003
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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:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19(4): 524-531 (2003)
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Pedro Mendes, Wei Sha, Keying Ye:
Artificial gene networks for objective comparison of analysis algorithms. ECCB 2003: 122-129
2002
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Pedro Mendes:
Emerging bioinformatics for the metabolome. Briefings Bioinform. 3(2): 134-145 (2002)
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Dianjing Guo, Xingjing Li, Aejaaz Kamal, Olga Brazhnik, Pedro Mendes:
A Reference Database for Medicago Truncatula Genes, Protiens, and Metabolites. CSB 2002: 343
2001
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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): 83-94 (2001)
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Pedro Mendes, Douglas B. Kell:
MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinform. 17(3): 288-289 (2001)

1990 – 1999

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1998
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Pedro Mendes, Douglas B. Kell:
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinform. 14(10): 869-883 (1998)
1993
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Pedro Mendes:
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9(5): 563-571 (1993)

1980 – 1989

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1988
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Harold A. Kurstedt, Kwang Lee, Pedro Mendes, Steven Berube:
The Responsive System: A New Challenge for AI. IEA/AIE (Vol. 1) 1988: 177-184

Coauthor Index

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