Pedro Pedrosa Mendes

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Professor Pedro Mendes
Born Pedro Pedrosa Mendes
Nationality Portuguese
Fields Systems biology
Machine learning
Bioinformatics
Institutions University of Manchester
Virginia Tech (VT)
National Center for Genome Resources
Aberystwyth University
Alma mater University of Lisbon
Aberystwyth University
Thesis Computer simulation of the dynamics of biochemical pathways (1994)
Doctoral advisor Douglas Kell
Doctoral students

Diogo Camacho [1]
Stephen Checkley [2]
Hui Cheng (VT)
Alberto de la Fuente[3]

Olusegun Oshota [4]
Revonda Pokryzwa[5]
Wei Sha [6]
Ben Small [7]

Natalie Stanford [8]
Known for GEPASI
COPASI
Systems Biology Markup Language (SBML)
MIRIAM
Website
manchester.ac.uk/research/pedro.mendes/
www.comp-sys-bio.org
twitter.com/gepasi
Pedro Pedrosa Mendes is a Professor of Computational Systems Biology in the School of Computer Science at the University of Manchester. He is a member of the Manchester Centre for Integrative Systems Biology (MCISB), the Machine Learning and Optimization (MLO) group and the Virginia Bioinformatics Institute (VBI).

Education

Mendes did his undergraduate degree in Biochemistry at the University of Lisbon. He then moved to the UK and was awarded a Doctor of Philosophy from Aberystwyth University in 1994 for work on computer simulation of metabolic pathways.[9] He then moved to the National Center for Genome Resources for a year then on to the Virginia Bioinformatics Institute (VBI) of Virginia Polytechnic Institute and State University (Virginia Tech or VT) in 2000. He moved to the University of Manchester as Professor in 2007, while still keeping a 20% appointment in the VBI until the end of 2013.[10]

Research

Mendes research[11][12] is concerned with computational systems biology, which aims to better understand biological systems through the use of computer models. He is the author of the biochemical simulator GEPASI (General Pathway Simulator)[13] and leader of the new COPASI (COmplex PAthway SImulator) simulator.[14][15] He has also been actively involved in the development of the Systems Biology Markup Language (SBML),[16] and MIRIAM (Minimum Information Required in the Annotation of Models).[17] His research group work on problems in the following areas:

Construction of biochemical models Mendes is currently working on models of the yeast pentose phosphate pathway, oxidative stress response in yeast[2][8][18][19] and breast cancer cells.[20]

Parameter estimation Mendes has applied numerical global optimization in biochemical kinetic modelling and parameter estimation. He is interested in using formal systems identification techniques in systems biology, particularly for reverse engineering models from data.[21]

Reverse engineering biological networks Mendes has been involved in systems biology through the construction of metabolic models directly from large-scale genomics, proteomics and metabolomics data sets. Mendes group has created artificial networks to benchmark these problems. for example the Artificial Gene Network system.[22]

Data integration and Data fusion systems biology and metabolic engineering produces large amounts of data that originated in a diversity of techniques.[16] The Mendes group works on integrating biochemical data and also works on data fusion, numerical issues of data integration.

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) of predefined behaviours.[citation needed]

Mendes research has been funded by the Biotechnology and Biological Sciences Research Council (UK),[23] National Science Foundation (USA), National Institutes of Health (USA) and the European Commission.

References

  1. ↑ Camacho, Diogo Mayo (2007). In silico cell biology and biochemistry: a systems biology approach (PhD thesis). Virginia Polytechnic Institute and State University. 
  2. ↑ 2.0 2.1 Checkley, Stephen (2011). Engineering tuneable gene circuits in yeast (PhD thesis). University of Manchester. 
  3. ↑ De La Fuente, A.; Brazhnik, P.; Mendes, P. (2002). "Linking the genes: Inferring quantitative gene networks from microarray data". Trends in Genetics 18 (8): 395–398. doi:10.1016/S0168-9525(02)02692-6. PMID 12142007. 
  4. ↑ Oshota, Olusegun James (2012). Thesis, restricted until 21/02/2017 (PhD thesis). University of Manchester. 
  5. ↑ Pokryzwa, Revonda Maria (2009). Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information (PhD thesis). Virginia Polytechnic Institute and State University. 
  6. ↑ Sha, Wei (2006). Microarray data analysis methods and their applications to gene expression data analysis for Saccharomyces cerevisiae under oxidative stress (PhD thesis). Virginia Polytechnic Institute and State University. 
  7. ↑ Small, Benjamin Gavin (2012). The chemical and computational biology of inflammation (PhD thesis). University of Manchester. 
  8. ↑ 8.0 8.1 Stanford, Natalie Jane (2011). Towards a full genome-scale model of yeast metabolism (PhD thesis). University of Manchester. 
  9. ↑ Mendes, Pedro Pedrosa (1994). Computer simulation of the dynamics of biochemical pathways (PhD thesis). University of Aberystwyth. 
  10. ↑ "Pedro Mendes faculty page at the Virginia Bioinformatics Institute". Retrieved 2012-08-07. 
  11. ↑ List of publications from Google Scholar
  12. ↑ List of publications from the DBLP Bibliography Server
  13. ↑ Mendes, P. (1993). "GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems". Bioinformatics 9 (5): 563–571. doi:10.1093/bioinformatics/9.5.563. PMID 8293329. 
  14. ↑ Hoops, S.; Sahle, S.; Gauges, R.; Lee, C.; Pahle, J.; Simus, N.; Singhal, M.; Xu, L.; Mendes, P.; Kummer, U. (2006). "COPASI--a COmplex PAthway SImulator". Bioinformatics 22 (24): 3067–3074. doi:10.1093/bioinformatics/btl485. PMID 17032683. 
  15. ↑ Kent, E.; Hoops, S.; Mendes, P. (2012). "Condor-COPASI: High-throughput computing for biochemical networks". BMC Systems Biology 6: 91. doi:10.1186/1752-0509-6-91. PMC 3527284. PMID 22834945. 
  16. ↑ 16.0 16.1 Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, A. P.; Bray, B. J.; Cornish-Bowden, D.; Cuellar, A.; Dronov, A. A.; Gilles, S.; Ginkel, E. D.; Gor, M.; Goryanin, V.; Hedley, I. I.; Hodgman, W. J.; Hofmeyr, T. C.; Hunter, J. -H.; Juty, P. J.; Kasberger, N. S.; Kremling, J. L.; Kummer, A.; Le Novère, U.; Loew, N.; Lucio, L. M.; Mendes, D.; Minch, P.; Mjolsness, E. (2003). "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models". Bioinformatics 19 (4): 524–531. doi:10.1093/bioinformatics/btg015. PMID 12611808. 
  17. ↑ Novère, N. L.; Finney, A.; Hucka, M.; Bhalla, U. S.; Campagne, F.; Collado-Vides, J.; Crampin, E. J.; Halstead, M.; Klipp, E.; Mendes, P.; Nielsen, P.; Sauro, H.; Shapiro, B.; Snoep, J. L.; Spence, H. D.; Wanner, B. L. (2005). "Minimum information requested in the annotation of biochemical models (MIRIAM)". Nature Biotechnology 23 (12): 1509–1515. doi:10.1038/nbt1156. PMID 16333295. 
  18. ↑ Heavner, B. D.; Smallbone, K.; Barker, B.; Mendes, P.; Walker, L. P. (2012). "Yeast 5 - an expanded reconstruction of the Saccharomyces Cerevisiae metabolic network". BMC Systems Biology 6: 55. doi:10.1186/1752-0509-6-55. PMC 3413506. PMID 22663945. 
  19. ↑ Dobson, P. D.; Smallbone, K.; Jameson, D.; Simeonidis, E.; Lanthaler, K.; Pir, P.; Lu, C.; Swainston, N.; Dunn, W. B.; Fisher, P.; Hull, D.; Brown, M.; Oshota, O.; Stanford, N. J.; Kell, D. B.; King, R. D.; Oliver, S. G.; Stevens, R. D.; Mendes, P. (2010). "Further developments towards a genome-scale metabolic model of yeast". BMC Systems Biology 4: 145. doi:10.1186/1752-0509-4-145. PMC 2988745. PMID 21029416. 
  20. ↑ Chifman, J.; Kniss, A.; Neupane, P.; Williams, I.; Leung, B.; Deng, Z.; Mendes, P.; Hower, V.; Torti, F. M.; Akman, S. A.; Torti, S. V.; Laubenbacher, R. (2012). "The core control system of intracellular iron homeostasis: A mathematical model". Journal of Theoretical Biology 300: 91–99. doi:10.1016/j.jtbi.2012.01.024. PMC 3307864. PMID 22286016. 
  21. ↑ Mendes, P.; Kell, D. (1998). "Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation". Bioinformatics 14 (10): 869–883. doi:10.1093/bioinformatics/14.10.869. PMID 9927716. 
  22. ↑ Mendes, P.; Sha, W.; Ye, K. (2003). "Artificial gene networks for objective comparison of analysis algorithms". Bioinformatics (Oxford, England). 19 Suppl 2: ii122–ii129. PMID 14534181. 
  23. ↑ "Grants awarded to Pedro Mendes by the BBSRC". Retrieved 2012-08-06. 
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