Daniel Machado
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Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
D Machado, M Herrgård
PLoS computational biology 10 (4), e1003580, 2014
Modeling formalisms in systems biology
D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor, I Rocha
AMB express 1 (1), 1-14, 2011
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
D Machado, S Andrejev, M Tramontano, KR Patil
Nucleic acids research 46 (15), 7542-7553, 2018
Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes
JM Monk, A Koza, MA Campodonico, D Machado, JM Seoane, ...
Cell Systems 3 (3), 238-251. e12, 2016
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
Co-evolution of strain design methods based on flux balance and elementary mode analysis
D Machado, MJ Herrgård
Metabolic Engineering Communications 2, 85-92, 2015
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ...
Nature communications 10 (1), 2674, 2019
Random sampling of elementary flux modes in large-scale metabolic networks
D Machado, Z Soons, KR Patil, EC Ferreira, I Rocha
Bioinformatics 28 (18), i515-i521, 2012
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations
RS Costa, D Machado, I Rocha, EC Ferreira
Biosystems 100 (2), 150-157, 2010
Exploring the gap between dynamic and constraint-based models of metabolism
D Machado, RS Costa, EC Ferreira, I Rocha, B Tidor
Metabolic engineering 14 (2), 112-119, 2012
Current state and challenges for dynamic metabolic modeling
E Vasilakou, D Machado, A Theorell, I Rocha, K Nöh, M Oldiges, SA Wahl
Current Opinion in Microbiology 33, 97-104, 2016
Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
D Machado, MJ Herrgård, I Rocha
PLoS computational biology 12 (10), e1005140, 2016
Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling
RS Costa, D Machado, I Rocha, EC Ferreira
IET systems biology 5 (3), 157-163, 2011
Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
D Machado, MJ Herrgård, I Rocha
Frontiers in bioengineering and biotechnology 3, 2015
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
M Gönen, BA Weir, GS Cowley, F Vazquez, Y Guan, A Jaiswal, ...
Cell systems 5 (5), 485-497. e3, 2017
A kinetic model for curcumin production in Escherichia coli
D Machado, LR Rodrigues, I Rocha
BioSystems 125, 16-21, 2014
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
E Gonçalves, M Sciacovelli, ASH Costa, MGB Tran, TI Johnson, ...
Metabolic engineering 45, 149-157, 2018
A critical review on modelling formalisms and simulation tools in computational biosystems
D Machado, RS Costa, M Rocha, I Rocha, B Tidor, EC Ferreira
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft …, 2009
Model transformation of metabolic networks using a Petri net based framework
CD Machado, RS Costa, M Rocha, I Rocha, B Tidor, EC Ferreira
International Workshop on Biological Processes & Petri Nets (BioPPN 2010 …, 2010
Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning
S Blasche, Y Kim, R Mars, E Kafkia, M Maansson, D Machado, B Teusink, ...
bioRxiv, 541870, 2019
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