The TOL network ofPseudomonas putidamt-2 processes multiple environmental inputs into a narrowresponse space

The IHF regulon of exponentially growingPseudomonas putidacells

(2012) Rafael Silva-Rocha et al.   ENVIRONMENTAL MICROBIOLOGY

Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime inPseudomonas putidamt-2 exposed tom-xylene

(2012) Rafael Silva-Rocha et al.   MOLECULAR MICROBIOLOGY

A GFP-lacZ Bicistronic Reporter System for Promoter Analysis in Environmental Gram-Negative Bacteria

(2012) Rafael Silva-Rocha et al.   PLoS One

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene

(2011) Rafael Silva-Rocha et al.   BMC Systems Biology

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

(2011) Rafael Silva-Rocha et al.   ENVIRONMENTAL MICROBIOLOGY

Functional genomics of  the initial phase of cold adaptation of Pseudomonas putida KT2440

(2011) Sarah Frank et al.   FEMS MICROBIOLOGY LETTERS

A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks

(2011) E. Dubrova et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2011) Michalis Koutinas et al.   METABOLIC ENGINEERING

A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations

(2011) Rafael Silva-Rocha et al.   Molecular BioSystems

Information Routing Driven by Background Chatter in a Signaling Network

(2011) Núria Domedel-Puig et al.   PLoS Computational Biology

High Stability and Fast Recovery of Expression of the TOL Plasmid-Carried Toluene Catabolism Genes of Pseudomonas putida mt-2 under Conditions of Oxygen Limitation and Oscillation

(2010) P. M. Martinez-Lavanchy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BoolNet—an R package for generation, reconstruction and analysis of Boolean networks

(2010) Christoph Müssel et al.   BIOINFORMATICS

SnapShot: Network Motifs

(2010) Oren Shoval et al.   CELL

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

The Crc Global Regulator Inhibits thePseudomonas putidapWW0 Toluene/Xylene Assimilation Pathway by Repressing the Translation of Regulatory and Structural Genes

(2010) Renata Moreno et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation

(2009) R. Moreno et al.   NUCLEIC ACIDS RESEARCH

ON/OFF and Beyond - A Boolean Model of Apoptosis

(2009) Rebekka Schlatter et al.   PLoS Computational Biology

Mining logic gates in prokaryotic transcriptional regulation networks

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

Boolean network models of cellular regulation: prospects and limitations

(2008) S. Bornholdt   Journal of the Royal Society Interface

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

The incoherent feed-forward loop can generate non-monotonic input functions for genes

(2008) Shai Kaplan et al.   Molecular Systems Biology

Modelling and analysis of gene regulatory networks

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

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast

(2008) Maria I. Davidich et al.   PLoS One

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA