Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem

(2014) Caroline Siegenthaler et al.   PLoS One

Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

(2014) Réka Albert et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma

(2014) Marti Bernardo-Faura et al.   PLoS Computational Biology

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

(2013) Gonzalo Guillén-Gosálbez et al.   BMC Systems Biology

Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems

(2013) Maria Rodriguez-Fernandez et al.   BMC Systems Biology

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

(2013) Regina Samaga et al.   Cell Communication and Signaling

Branch-and-Lift Algorithm for Deterministic Global Optimization in Nonlinear Optimal Control

(2013) Boris Houska et al.   JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

(2013) A. F. Villaverde et al.   Journal of the Royal Society Interface

The sensor kinase KdpD ofEscherichia colisenses external K+

(2013) Vera Laermann et al.   MOLECULAR MICROBIOLOGY

Logic modeling and the ridiculome under the rug

(2012) Michael L Blinov et al.   BMC BIOLOGY

Inference of complex biological networks: distinguishability issues and optimization-based solutions

(2012) Gábor Szederkényi et al.   BMC Systems Biology

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

(2012) Camille Terfve et al.   BMC Systems Biology

MORE: Mixed Optimization for Reverse Engineering—An Application to Modeling Biological Networks Response via Sparse Systems of Nonlinear Differential Equations

(2012) Francesco Sambo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

AMIGO, a toolbox for advanced model identification in systems biology using global optimization

(2011) E. Balsa-Canto et al.   BIOINFORMATICS

Histidine kinases and response regulators in networks

(2011) Kirsten Jung et al.   CURRENT OPINION IN MICROBIOLOGY

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

The complexity of the ‘simple’ two-component system KdpD/KdpE inEscherichia coli

(2010) Ralf Heermann et al.   FEMS MICROBIOLOGY LETTERS

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

(2010) Leonidas G. Alexopoulos et al.   MOLECULAR & CELLULAR PROTEOMICS

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

An evolutionary method for complex-process optimization

(2009) Jose A. Egea et al.   COMPUTERS & OPERATIONS RESEARCH

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

(2009) Bree B. Aldridge et al.   PLoS Computational Biology

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology

Extended ant colony optimization for non-convex mixed integer nonlinear programming

(2008) Martin Schlüter et al.   COMPUTERS & OPERATIONS RESEARCH

A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design

(2007) Oliver Exler et al.   COMPUTERS & CHEMICAL ENGINEERING