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

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Integrative platform to translate gene sets to networks

(2010) Marko Laakso et al.   BIOINFORMATICS

Lists2Networks: Integrated analysis of gene/protein lists

(2010) Alexander Lachmann et al.   BMC BIOINFORMATICS

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

(2010) Mercedes Pardo et al.   Cell Stem Cell

Simplistic pathways or complex networks?

(2010) Claus Jørgensen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Comparing Families of Dynamic Causal Models

(2010) Will D. Penny et al.   PLoS Computational Biology

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

(2010) Laurence Calzone et al.   PLoS Computational Biology

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

(2009) Özgür Sahin et al.   BMC Systems Biology

A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection

(2009) Sagi D. Shapira et al.   CELL

Fuzzy modeling of signal transduction networks

(2009) Zuyi Huang et al.   CHEMICAL ENGINEERING SCIENCE

Multisite protein phosphorylation - from molecular mechanisms to kinetic models

(2009) Carlos Salazar et al.   FEBS Journal

An analysis pipeline for the inference of protein-protein interaction networks

(2009) Ronald C. Taylor et al.   International Journal of Data Mining and Bioinformatics

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

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

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Mechanisms of regulated unconventional protein secretion

(2009) Walter Nickel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Regina Samaga et al.   PLoS Computational 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

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

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

Flexible informatics for linking experimental data to mathematical models via DataRail

(2008) Julio Saez-Rodriguez et al.   BIOINFORMATICS

Logic models of pathway biology

(2008) Steven Watterson et al.   DRUG DISCOVERY TODAY

Network integration and graph analysis in mammalian molecular systems biology

(2008) A. Ma'ayan   IET Systems Biology

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

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

Protein networking: insights into global functional organization of proteomes

(2008) Enrico Pieroni et al.   PROTEOMICS

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE