Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Measurement and Modeling of Signaling at the Single-Cell Level

(2012) Sarah E. Kolitz et al.   BIOCHEMISTRY

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

(2012) Camille Terfve et al.   BMC Systems Biology

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing

(2012) Irene Papatheodorou et al.   PLoS One

ASP modulo CSP: The clingcon system

(2012) MAX OSTROWSKI et al.   THEORY AND PRACTICE OF LOGIC PROGRAMMING

Automatic network reconstruction using ASP

(2011) MARKUS DURZINSKY et al.   THEORY AND PRACTICE OF LOGIC PROGRAMMING

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

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

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

Mobyle: a new full web bioinformatics framework

(2009) B. Neron et al.   BIOINFORMATICS

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

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

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

(2009) Alexander Mitsos et al.   PLoS Computational Biology

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology