The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms

Linking genes to microbial growth kinetics—An integrated biochemical systems engineering approach

(2011) Michalis Koutinas et al.   METABOLIC ENGINEERING

Develop reusable and combinable designs for transcriptional logic gates

(2011) Jian Zhan et al.   Molecular Systems Biology

Noise and Robustness in Prokaryotic Regulatory Networks

(2010) Rafael Silva-Rocha et al.   Annual Review of Microbiology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Enzyme-based logic systems for information processing

(2010) Evgeny Katz et al.   CHEMICAL SOCIETY REVIEWS

The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid

(2010) Michalis Koutinas et al.   ENVIRONMENTAL MICROBIOLOGY

Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida

(2010) Paola Milanesio et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial adaptation through distributed sensing of metabolic fluxes

(2010) Oliver Kotte et al.   Molecular Systems Biology

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Genetic flexibility of regulatory networks

(2010) A. Hunziker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Carbon Assimilation Network in Escherichia coli Is Densely Connected and Largely Sign-Determined by Directions of Metabolic Fluxes

(2010) Valentina Baldazzi et al.   PLoS Computational Biology

Computational design tools for synthetic biology

(2009) Mario A Marchisio et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Designing and encoding models for synthetic biology

(2009) L. Endler et al.   Journal of the Royal Society Interface

Comparing different ODE modelling approaches for gene regulatory networks

(2009) A. Polynikis et al.   JOURNAL OF THEORETICAL BIOLOGY

Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View

(2009) M. Carmona et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Logical modelling of cell cycle control in eukaryotes: a comparative study

(2009) Adrien Fauré et al.   Molecular BioSystems

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

(2008) Anne Goelzer et al.   BMC Systems Biology

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Systems biology approaches to bioremediation

(2008) Víctor de Lorenzo   CURRENT OPINION IN BIOTECHNOLOGY

Mining logic gates in prokaryotic transcriptional regulation networks

(2008) Rafael Silva-Rocha et al.   FEBS LETTERS

Enzyme-based logic systems and their applications for novel multi-signal-responsive materials

(2008) Marcos Pita et al.   JOURNAL OF MATERIALS SCIENCE-MATERIALS IN MEDICINE

Transcriptionalwiringof the TOL plasmid regulatory network to its host involves the submission of the σ54-promoterPuto the response regulator PprA

(2008) Elena Vitale et al.   MOLECULAR MICROBIOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology

New surveyor tools for charting microbial metabolic maps

(2007) Rainer Breitling et al.   NATURE REVIEWS MICROBIOLOGY