R. Alves

发表

Methods for and results from the study of design principles in molecular systems.

Albert Sorribas, Baldiri Salvado, Ester Vilaprinyo, 2011, Mathematical Biosciences.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways

A. Sorribas, B. Hernández-Bermejo, E. Vilaprinyó, 2008, Biotechnology & genetic engineering reviews.

Metabolic constraints and quantitative design principles in gene expression during adaption of yeast to heat shock

A. Sorribas, G. Bellí, Baldiri Salvadó, 2017, bioRxiv.

Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations

A. Sorribas, B. Hernández-Bermejo, E. Vilaprinyó, 2007, Biotechnology and bioengineering.

Relative Amino Acid Composition Signatures of Organisms and Environments

M. Savageau, R. Alves, A. Moura, 2013, PloS one.

Irreversibility in unbranched pathways: preferred positions based on regulatory considerations.

M A Savageau, M. Savageau, R. Alves, 2001, Biophysical journal.

Two Component Systems: Physiological Effect of a Third Component

Albert Sorribas, Baldiri Salvado, Ester Vilaprinyo, 2012, PloS one.

Evolution based on domain combinations: the case of glutaredoxins

Enrique Herrero, Albert Sorribas, Ester Vilaprinyo, 2009, BMC Evolutionary Biology.

Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress.

A. Sorribas, G. Bellí, Baldiri Salvadó, 2018, Cell Reports.

An in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation.

A. Sorribas, P. Christou, Changfu Zhu, 2014, The Plant journal : for cell and molecular biology.

Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling.

A. Sorribas, P. Christou, G. Farré, 2016, The Plant journal : for cell and molecular biology.

Multilevel interactions between native and ectopic isoprenoid pathways affect global metabolism in rice

P. Christou, G. Farré, Changfu Zhu, 2022, Transgenic Research.

Semi-Automated Reconstruction of Biological Circuits

R. Alves, Rui Alves, 2008 .

Evolution of an Iron-Detoxifying Protein: Eukaryotic and Rickettsia Frataxins Contain a Conserved Site Which Is Not Present in Their Bacterial Homologues

R. Alves, J. Tamarit, F. Delaspre, 2022, International journal of molecular sciences.

Saccharomyces cerevisiae as a Model Organism: A Comparative Study

Albert Sorribas, Ester Vilaprinyo, Rui Alves, 2011, PloS one.

Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock

Rui Alves, Ester Vilaprinyó, Albert Sorribas, 2006, BMC Bioinformatics.

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Rui Alves, Albert Sorribas, A. Sorribas, 2007, BMC Systems Biology.

Regulation of the Na+/K+-ATPase Ena1 Expression by Calcineurin/Crz1 under High pH Stress: A Quantitative Study

L. Yenush, J. Ariño, E. Vilaprinyó, 2016, PloS one.

Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes

Rui Alves, Ester Vilaprinyó, Albert Sorribas, 2010, PLoS Comput. Biol..

Energetic constraints in adaptive gene expression responses of yeast under environmental changes

A. Sorribas, E. Vilaprinyó, R. Alves, 2004 .

Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes

Michael A Savageau, Rui Alves, M. Savageau, 2005, Molecular microbiology.

Evolution of enzymes in metabolism: a network perspective.

Michael J E Sternberg, Raphael A G Chaleil, Raphael A. G. Chaleil, 2002, Journal of molecular biology.

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

Rui Alves, Albert Sorribas, Ester Vilaprinyo, 2008 .

PROTEINS: Structure, Function, and Bioinformatics 57:481–492 (2004) Predictive Reconstruction of the Mitochondrial Iron-Sulfur Cluster Assembly Metabolism. II. Role of Glutaredoxin Grx5

Enrique Herrero, Albert Sorribas, Rui Alves, 2022 .

Comparative analysis of prototype two‐component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function

Rui Alves, M. Savageau, R. Alves, 2003, Molecular microbiology.

Distributed under Creative Commons Cc-by 4.0 a Survey of Hk, Hpt, and Rr Domains and Their Organization in Two-component Systems and Phosphorelay Proteins of Organisms with Fully Sequenced Genomes

A. Sorribas, Baldiri Salvadó, E. Vilaprinyó, 2022 .

Evolution and Cellular Function of Monothiol Glutaredoxins: Involvement in Iron-Sulphur Cluster Assembly

G. Bellí, E. Herrero, P. Sunnerhagen, 2004, Comparative and functional genomics.

Hysteretic and graded responses in bacterial two‐component signal transduction

Michael A Savageau, Oleg A Igoshin, Rui Alves, 2008, Molecular microbiology.

Maximization of information transmission influences selection of native phosphorelay architectures

R. Milo, A. Sorribas, Baldiri Salvadó, 2021, PeerJ.

What influences selection of native phosphorelay architectures?

Rui Alves, Albert Sorribas, Baldiri Salvado, 2020, bioRxiv.

Tools for kinetic modeling of biochemical networks

Rui Alves, Armindo Salvador, Fernando Antunes, 2006, Nature Biotechnology.

Targeted transcriptomic and metabolic profiling reveals temporal bottlenecks in the maize carotenoid pathway that may be addressed by multigene engineering.

A. Sorribas, P. Christou, G. Farré, 2013, The Plant journal : for cell and molecular biology.

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization

Gonzalo Guillén-Gosálbez, Albert Sorribas, Laureano Jiménez, 2013, BMC Systems Biology.

Predictive reconstruction of the mitochondrial iron–sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin–ferredoxin reductase (Yah1–Arh1)

Enrique Herrero, Albert Sorribas, Rui Alves, 2004, Proteins.

Effect of overall feedback inhibition in unbranched biosynthetic pathways.

M A Savageau, M. Savageau, R. Alves, 2000, Biophysical journal.

Multi-level Optimization Framework Applied to the Systematic Evaluation of Metabolic Objective Functions

G. Guillén‐Gosálbez, A. Sorribas, P. Vaskan, 2014 .

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Gonzalo Guillén-Gosálbez, Rui Alves, Albert Sorribas, 2011, BMC Systems Biology.

Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action models.

Gonzalo Guillén-Gosálbez, Rui Alves, Albert Sorribas, 2010, Journal of biotechnology.

Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways

Rui Alves, Michael A. Savageau, M. Savageau, 2000, Bioinform..

Changing biosynthesis of terpenoid percursors in rice through synthetic biology

A. Sorribas, P. Christou, T. Capell, 2023, Frontiers in Plant Science.

Special issue on biological design principles.

Albert Sorribas, Rui Alves, A. Sorribas, 2011, Mathematical biosciences.

Extending the method of mathematically controlled comparison to include numerical comparisons

Rui Alves, Michael A. Savageau, M. Savageau, 2000, Bioinform..