| 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 | 328 | 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 | 196 | 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 | 124 | 2018 |
| 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 | 101* | 2020 |
| 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 | 87 | 2019 |
| 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 | 78 | 2016 |
| 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 | 68 | 2015 |
| 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 | 60 | 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 | 55 | 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 | 37 | 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 | 32 | 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 | 32 | 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 | 24 | 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 | 23 | 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 | 14 | 2017 |
| 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 | 11 | 2019 |
| A kinetic model for curcumin production in Escherichia coli D Machado, LR Rodrigues, I Rocha BioSystems 125, 16-21, 2014 | 10 | 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 | 9 | 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 | 9 | 2009 |
| Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations K Kang, B Bergdahl, D Machado, L Dato, TL Han, J Li, S Villas-Boas, ... GigaScience 8 (4), giz015, 2019 | 7 | 2019 |
Isabel RochaITQB NOVAVerified email at itqb.unl.pt
