State of the Art in Silico Tools for the Study of Signaling Pathways in Cancer

In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of interactions within a signaling pathway, make these systems complex to study. In silico resources are tools used to aid the understanding of cellular signaling pathways. Systems approaches have provided a deeper knowledge of diverse biochemical processes, including individual metabolic pathways, signaling networks and genome-scale metabolic networks. In the future, these tools will be enormously valuable, if they continue to be developed in parallel with growing biological knowledge. In this study, an overview of the bioinformatics resources that are currently available for the analysis of biological networks is provided.

• Publication year

  2012

• Venue

  International Journal of Molecular Sciences

• Publication date

  2012-05-29

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.3390/ijms13066561PMID 22837650PMCID 3397482
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2011cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2009cited by this paper
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  2009cited by this paper
• Synthetic biology: understanding biological design from synthetic circuits

  2009cited by this paper
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  2009cited by this paper
• The elusive concept of the gene.

  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
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  2009cited by this paper
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• A new probabilistic generative model of parameter inference in biochemical networks

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  2009cited by this paper
• Computational systems biology of the cell cycle

  2009cited by this paper
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  2009cited by this paper
• Heuristic Approach to Sparse Approximation of Gene Regulatory Networks

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  2008cited by this paper
• Integrative mathematical oncology

  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
• GenBank

  2008cited by this paper
• Systems biotechnology of mammalian cell factories.

  2008cited by this paper
• The Beta Workbench: a computational tool to study the dynamics of biological systems

  2008cited by this paper
• The Pfam protein families database

  2007cited by this paper
• Subnetwork analysis reveals dynamic features of complex (bio)chemical networks

  2007cited by this paper
• Cell Cycle: Principles of Control

  2007cited by this paper
• Origin of phenotypes: genes and transcripts.

  2007cited by this paper
• SBML-PET: a Systems Biology Markup Language-based parameter estimation tool

  2006cited by this paper
• Time scale and dimension analysis of a budding yeast cell cycle model

  2006cited by this paper
• Cancer: a Systems Biology disease.

  2006cited by this paper
• Integrative biology of prostate cancer progression.

  2006cited by this paper
• Linking cell division to cell growth in a spatiotemporal model of the cell cycle.

  2006cited by this paper
• Agents in bioinformatics, computational and systems biology

  2006cited by this paper
• The meaning of systems biology.

  2005cited by this paper
• Ontological analysis of gene expression data: current tools, limitations, and open problems

  2005cited by this paper
• From the Cover : Conserved patterns of protein interaction in multiple species

  2005cited by this paper
• Globally optimised parameters for a model of mitotic control in frog egg extracts.

  2005cited by this paper
• Combinatorial microRNA target predictions

  2005cited by this paper
• A human protein-protein interaction network: a resource for annotating the proteome.

  2005cited by this paper
• VitaPad: visualization tools for the analysis of pathway data

  2005cited by this paper
• BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

  2005cited by this paper
• Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.

  2005cited by this paper
• The RCSB PDB information portal for structural genomics

  2005cited by this paper
• Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

  2004cited by this paper
• VisANT: an online visualization and analysis tool for biological interaction data

  2004cited by this paper
• Systems Biology Experimental Design - Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems

  2004cited by this paper
• Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data

  2004cited by this paper
• Reactome: a knowledgebase of biological pathways

  2004cited by this paper
• A global test for groups of genes: testing association with a clinical outcome

  2004cited by this paper
• The JigCell Model Builder and Run Manager

  2004cited by this paper
• ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics

  2004cited by this paper
• A history of the study of solid tumour growth: The contribution of mathematical modelling

  2004cited by this paper
• Mathematical models in microbial systems biology.

  2004cited by this paper
• MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

  2003cited by this paper
• Cancer Modelling and Simulation

  2003cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003cited by this paper
• Proteomics: the first decade and beyond

  2003cited by this paper
• PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis

  2003cited by this paper
• Pathway studio - the analysis and navigation of molecular networks

  2003cited by this paper
• Computational systems biology

  2002cited by this paper
• GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways

  2002cited by this paper
• Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks.

  2002cited by this paper
• Interaction with the NMDA receptor locks CaMKII in an active conformation

  2001cited by this paper
• A new mathematical model for avascular tumour growth

  2001cited by this paper
• Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks

  2001cited by this paper
• Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis

  2000cited by this paper
• KEGG: Kyoto Encyclopedia of Genes and Genomes

  1999cited by this paper
• Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

  1998cited by this paper
• A general computational framework for modeling cellular structure and function.

  1997influential reference
• Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray

  1995cited by this paper
• Universal control mechanism regulating onset of M-phase

  1990cited by this paper
• Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins.

  1989cited by this paper
• Substrate specificity of the cyclic AMP-dependent protein kinase.

  1975cited by this paper

• Semantic approaches for the meta-optimization of complex biomolecular networks (Approches sémantiques pour la méta-optimisation des réseaux biomoléculaires complexes)

  2018cites this paper
• A rule-based model of insulin signalling pathway

  2016cites this paper
• Logical and Semantic Modeling of Complex Biomolecular Networks

  2016cites this paper
• Action potentials as indicators of metabolic perturbations for temporal proteomic analysis

  2014cites this paper
• The effects of stenting on shear stress: relevance to endothelial injury and repair.

  2013cites this paper
• Modeling and simulation of insulin signaling

  2013cites this paper