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

FINDING ATTRACTORS IN ASYNCHRONOUS BOOLEAN DYNAMICS

(2011) THOMAS SKODAWESSELY et al.   ADVANCES IN COMPLEX SYSTEMS

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

(2011) Franziska Hinkelmann et al.   BMC BIOINFORMATICS

Elementary signaling modes predict the essentiality of signal transduction network components

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

Integration of Boolean models exemplified on hepatocyte signal transduction

(2011) R. Schlatter et al.   BRIEFINGS IN BIOINFORMATICS

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

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

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

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

Computational and Experimental Analysis Reveals a Requirement for Eosinophil-Derived IL-13 for the Development of Allergic Airway Responses in C57BL/6 Mice

(2011) E. R. Walsh et al.   JOURNAL OF IMMUNOLOGY

Reduction of Boolean network models

(2011) Alan Veliz-Cuba   JOURNAL OF THEORETICAL BIOLOGY

Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light

(2011) Miyako Kusano et al.   PLANT JOURNAL

Systems Biology--Biomedical Modeling

(2011) E. A. Sobie et al.   Science Signaling

Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia

(2011) Assieh Saadatpour et al.   PLoS Computational Biology

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

Guard Cell Signal Transduction Network: Advances in Understanding Abscisic Acid, CO2, and Ca2+Signaling

(2010) Tae-Houn Kim et al.   Annual Review of Plant Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

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

(2010) Christoph Müssel et al.   BIOINFORMATICS

Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-κB signaling-induced gene expression responses in inflammation

(2010) Shih Peng et al.   BMC BIOINFORMATICS

Boolean models of within-host immune interactions

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

Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks

(2010) Regina Samaga et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Attractor analysis of asynchronous Boolean models of signal transduction networks

(2010) Assieh Saadatpour et al.   JOURNAL OF THEORETICAL BIOLOGY

Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action

(2010) Sona Pandey et al.   Molecular Systems Biology

A network model for plant-pollinator community assembly

(2010) C. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamically consistent reduction of logical regulatory graphs

(2010) Aurélien Naldi et al.   THEORETICAL COMPUTER SCIENCE

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

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

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

(2009) J. Zheng et al.   BIOINFORMATICS

The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

(2009) Anatolij P Potapov et al.   BMC BIOINFORMATICS

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

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

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

(2009) Tomáš Helikar et al.   BMC Systems Biology

Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase

(2009) E. Oksanen et al.   Journal of the Royal Society Interface

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

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

(2009) Regina Samaga et al.   PLoS Computational Biology

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

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

ON/OFF and Beyond - A Boolean Model of Apoptosis

(2009) Rebekka Schlatter et al.   PLoS Computational Biology

Synchronous versus asynchronous modeling of gene regulatory networks

(2008) A. Garg et al.   BIOINFORMATICS

Logic models of pathway biology

(2008) Steven Watterson et al.   DRUG DISCOVERY TODAY

Boolean network models of cellular regulation: prospects and limitations

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

Structure and function of a transcriptional network activated by the MAPK Hog1

(2008) Andrew P Capaldi et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Modelling and analysis of gene regulatory networks

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

Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways

(2008) Z. Zhao et al.   PLANT CELL

Network model of survival signaling in large granular lymphocyte leukemia

(2008) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Fault Diagnosis Engineering of Digital Circuits Can Identify Vulnerable Molecules in Complex Cellular Pathways

(2008) A. Abdi et al.   Science Signaling

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

(2008) Derek Ruths et al.   PLoS Computational Biology