Integration of Boolean models exemplified on hepatocyte signal transduction

Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles

(2011) John Jack et al.   BMC Systems Biology

Elementary signaling modes predict the essentiality of signal transduction network components

(2011) Rui-Sheng Wang et al.   BMC Systems Biology

Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models

(2011) J. Saez-Rodriguez et al.   CANCER RESEARCH

Cell–cell interaction and diversity of emergent behaviours

(2011) C. Damiani et al.   IET Systems Biology

Boolean Models Can Explain Bistability in the lac Operon

(2011) Alan Veliz-Cuba et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension

(2011) Chen Li et al.   Molecular BioSystems

Constructing Biological Pathways by a Two-Step Counting Approach

(2011) Hsiuying Wang et al.   PLoS One

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

Comparing Boolean and Piecewise Affine Differential Models for Genetic Networks

(2010) Madalena Chaves et al.   ACTA BIOTHEORETICA

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

(2010) Christoph Müssel et al.   BIOINFORMATICS

Odefy -- From discrete to continuous models

(2010) Jan Krumsiek et al.   BMC BIOINFORMATICS

Boolean models of within-host immune interactions

(2010) Juilee Thakar et al.   CURRENT OPINION IN MICROBIOLOGY

Tumor necrosis factor α sensitizes primary murine hepatocytes to Fas/CD95-induced apoptosis in a Bim- and Bid-dependent manner

(2010) Kathrin Schmich et al.   HEPATOLOGY

Vascularised human tissue models: A new approach for the refinement of biomedical research

(2010) Johanna Schanz et al.   JOURNAL OF BIOTECHNOLOGY

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

(2010) Michael W Sneddon et al.   NATURE METHODS

A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development

(2010) Clare E. Giacomantonio et al.   PLoS Computational Biology

Logical modelling of regulatory networks with GINsim 2.3

(2009) A. Naldi et al.   BIOSYSTEMS

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

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

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

(2009) Nicole Philippi et al.   BMC Systems Biology

The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation

(2009) Qian Zhang et al.   MOLECULAR GENETICS AND GENOMICS

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

ON/OFF and Beyond - A Boolean Model of Apoptosis

(2009) Rebekka Schlatter et al.   PLoS Computational Biology

Dynamical modeling and multi-experiment fitting with PottersWheel

(2008) Thomas Maiwald et al.   BIOINFORMATICS

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Modelling phagosomal lipid networks that regulate actin assembly

(2008) Mark Kühnel et al.   BMC Systems Biology

Modelling metabolic networks using power-laws and S-systems

(2008) Eberhard O. Voit   Essays in Biochemistry

Switch from type II to I Fas/CD95 death signaling on in vitro culturing of primary hepatocytes

(2008) Dorothée Walter et al.   HEPATOLOGY

Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms

(2008) Enrique Balleza et al.   PLoS One

Floral Morphogenesis: Stochastic Explorations of a Gene Network Epigenetic Landscape

(2008) Elena R. Álvarez-Buylla et al.   PLoS One