D. Machado

发表

Random sampling of elementary flux modes in large-scale metabolic networks

Eugénio C. Ferreira, Isabel Rocha, Kiran Raosaheb Patil, 2012, Bioinform..

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

D. Machado, K. Patil, Melanie Tramontano, 2018, bioRxiv.

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.

Adam M. Feist, Jonathan M. Monk, Markus J. Herrgård, 2016, Cell systems.

Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling.

D. Machado, E. Ferreira, I. Rocha, 2011, IET systems biology.

Genome‐Scale Models

Markus J. Herrgård, J. Förster, Nikolaus Sonnenschein, 2016 .

Exploring optimal objective functions and additional constraints for flux prediction in genome-scale models

Nguyen Hoang Son, D. Machado, 2014 .

Editorial: Current Challenges in Modeling Cellular Metabolism

Markus J. Herrgård, Nikolaus Sonnenschein, D. Machado, 2015, Front. Bioeng. Biotechnol..

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

Emanuel J. V. Gonçalves, J. Saez-Rodriguez, D. Machado, 2017, bioRxiv.

Polarization of microbial communities between competitive and cooperative metabolism

P. Bork, D. Machado, K. Patil, 2020, bioRxiv.

Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Markus J. Herrgård, J. Förster, D. Machado, 2019, GigaScience.

Oncogenic memory underlying minimal residual disease in breast cancer

D. Machado, K. Patil, A. Alladin, 2020, bioRxiv.

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations

Eugénio C. Ferreira, Isabel Rocha, Rafael S. Costa, 2010, Biosyst..

Exploring the gap between dynamic and constraint-based models of metabolism.

Isabel Rocha, Bruce Tidor, Daniel Machado, 2012, Metabolic engineering.

Current state and challenges for dynamic metabolic modeling.

Katharina Nöh, Isabel Rocha, Marco Oldiges, 2016, Current opinion in microbiology.

Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Isabel Rocha, Daniel Machado, Markus J. Herrgård, 2015, Front. Bioeng. Biotechnol..

Modeling formalisms in Systems Biology

Miguel Rocha, Isabel Rocha, Rafael S. Costa, 2011, AMB Express.

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

U. Sauer, J. Nielsen, G. Zeller, 2021, Nature Microbiology.

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

U. Sauer, J. Nielsen, V. Beneš, 2019, bioRxiv.

MEMOTE for standardized genome-scale metabolic model testing

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2020, Nature Biotechnology.

Metabolic memory underlying minimal residual disease in breast cancer

D. Machado, K. Patil, B. Brügger, 2021, Molecular systems biology.

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Daniel Machado, Markus J. Herrgård, D. Machado, 2014, PLoS Comput. Biol..

Current Challenges in Modeling Cellular Metabolism

Nikolaus Sonnenschein, Daniel Machado, Markus J. Herrgård, 2016 .

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Isabel Rocha, Daniel Machado, Markus J. Herrgård, 2016, PLoS Comput. Biol..

Co-evolution of strain design methods based on flux balance and elementary mode analysis

Daniel Machado, Markus J. Herrgård, D. Machado, 2015, Metabolic engineering communications.

Correction: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Daniel Machado, Markus J. Herrgård, Markus Herrgård, 2014, PLoS Comput. Biol..

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2018, bioRxiv.

A kinetic model for curcumin production in Escherichia coli

Lígia R. Rodrigues, Isabel Rocha, Daniel Machado, 2014, Biosyst..

MEMOTE for standardized genome-scale metabolic model testing

Ronan M. T. Fleming, Adam M. Feist, Zachary A. King, 2020, Nature Biotechnology.

Multi-level Dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation

Rafael S. Costa, Susana Vinga, Daniel Machado, 2012, BIOINFORMATICS.

Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments

D. Machado, E. Ferreira, I. Rocha, 2010 .

Benchmarking kinetic models of Escherichia coli metabolism

Markus J. Herrgård, Denis Shepelin, Daniel Machado, 2020, bioRxiv.

A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli

Isabel Rocha, Daniel Machado, Ana Patrícia Ferreira Lima, 2016 .

Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli

Eugénio C. Ferreira, Isabel Rocha, Rafael S. Costa, 2009, IWANN.

Model Transformation of Metabolic Networks using a Petri Net Based Framework

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2010, ACSD/Petri Nets Workshops.

NOVEL MODELING FORMALISMS AND SIMULATION TOOLS IN COMPUTATIONAL BIOSYSTEMS

C. D. Machado, B. Tidor, D. Machado, 2010 .

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems

Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha, 2009, IWANN.

Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Markus J. Herrgård, D. Machado, S. Villas-Bôas, 2019, GigaScience.

Exploring the gap between dynamic and constraint-based models of metabolism.

Rafael S. Costa, B. Tidor, D. Machado, 2012, Metabolic engineering.

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Markus J. Herrgård, D. Machado, 2014, PLoS Comput. Biol..

Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli

Markus J. Herrgård, D. Machado, I. Rocha, 2015, Front. Bioeng. Biotechnol..