DEB :: Researcher Details

Carlos Daniel Moutinho Machado

Preferred Name:

Daniel Machado

E-Mail Address:

dmachado@deb.uminho.pt @deb.uminho.pt

Activity:

PhD UMinho

Project / Theme:

Novel modelling formalisms and simulation tools in Computational Biosystems

	Start Date:	11/12/2008
	End Date:	7/31/2012
	Faculty Supervisor:	Eugénio Ferreira
	Telephone:	Office:604422 Laboratory: 604421
	Laboratory:	Laboratório de Bioinformática (ENG2)
	Office:	Gabinete Pós Doc Bioinformática EENG2
	Birthday:	August 29th
	Website:	http://biopseg.deb.uminho.pt/DanielMachado/default.htm
	Access after working hours:	Yes
	Nationality:	Portugal
	Last Update:	10/28/2011

Selected Publications

1.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	An approach towards genome-scale kinetic modelling: application to the Escherichia coli metabolism.
	12th International Conference on Systems Biology – ICSB 2011 (), -, 2011.

2.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modeling.
	IET Systems Biology 5(3), 157-163, 2011.

3.	Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.
	A critical review on modelling formalisms and simulation tools in computational biosystems.
	IWANN 2009, Part II, (S. Omatu et al., Eds.) [3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics - IWPACBB'09] Lecture Notes in Computer Science(5518), 1063-1070, 2009.

4.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Large scale dynamic model reconstruction for the central carbon metabolism of Escherichia coli.
	IWANN 2009, Part II, (S. Omatu et al., Eds.) [3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics - IWPACBB'09] Lecture Notes in Computer Science(5518), 1079-1083, 2009.

5.	Machado, D.; Costa, R.S.; Rocha, I.; Tidor, B.; Ferreira, E.C.
	Exploring the gap between dynamic and constraint-based models of metabolism.
	Gothenburg Life Science Conference XI Industrial Systems Biology - Sustainable production of fuels and chemicals – Program and Abstract Book (P11), 44-, 2010.

6.	Costa, R.S.; Machado, D.; Ferreira, E.C.; Rocha, I.
	Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments.
	IFAC Proceedings Volumes (IFAC-PapersOnline), (Proceedings of the 11th International Symposium on Computer Applications in Biotechnology - CAB 2010) (), 114-119, 2010.

7.	Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.
	Model transformation of metabolic networks using a Petri net based framework.
	International Workshop on Biological Processes & Petri Nets (BioPPN) (), 101-115, 2010.

8.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations.
	Bio Systems 100(2), 150-157, 2010.

9.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Integration of proteomic data for predicting dynamic behaviour in an E. coli central carbon network after genetic perturbations.
	Book of Abstracts of MicroBiotec09 (), 308-, 2009.

10.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Reconstruction of dynamic metabolic networks: challenges, limitations and alternative solutions.
	Jornadas de Bioinformática JB'2009 - Challenges in Bioinformatics: proceedings 2009(), 51-55, 2009.

11.	Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.
	Dynamic modeling of E. coli central carbon metabolism combining different kinetic rate laws.
	17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB) (), -, 2009.