| 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 | 547 | 2018 |
| 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 | 453 | 2014 |
| 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 | 451* | 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 | 310 | 2019 |
| Modeling formalisms in systems biology D Machado, RS Costa, M Rocha, EC Ferreira, B Tidor, I Rocha AMB express 1 (1), 1-14, 2011 | 249 | 2011 |
| Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community S Blasche, Y Kim, RAT Mars, D Machado, M Maansson, E Kafkia, ... Nature Microbiology 6 (2), 196-208, 2021 | 218 | 2021 |
| Polarization of microbial communities between competitive and cooperative metabolism D Machado, OM Maistrenko, S Andrejev, Y Kim, P Bork, KR Patil, KR Patil Nature ecology & evolution 5 (2), 195-203, 2021 | 191 | 2021 |
| 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 | 138 | 2016 |
| Ecological modelling approaches for predicting emergent properties in microbial communities NI van den Berg, D Machado, S Santos, I Rocha, J Chacón, W Harcombe, ... Nature Ecology & Evolution, 1-11, 2022 | 112 | 2022 |
| 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 | 85 | 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 | 77 | 2012 |
| 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 | 69 | 2016 |
| 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 | 69 | 2010 |
| 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 | 59 | 2016 |
| 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 | 49 | 2012 |
| 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 | 48 | 2015 |
| 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 | 39 | 2018 |
| 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 | 36 | 2019 |
| 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 | 27 | 2011 |
| 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 | 24 | 2017 |
Isabel RochaITQB NOVA - Universidade NOVA de LisboaBestätigte E-Mail-Adresse bei itqb.unl.pt