Research articles on automatic pathway construction

Research articles on automatic pathway construction:

1. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information (2011, citation:8)
2. Biological Pathway Extension Using Microarray Gene Expression Data (2008, citation:1)
3. Microarray analysis of gene expression: considerations in data mining and statistical treatment (2006, citation: 66)
4. Genomic analysis of metabolic pathway gene expression in mice (2005, citation: 67)
5. PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis (2003, citation: 54)
6. Bayesian Consensus Pathway Construction and Expansion Using Microarray Gene Expression Data (From NCBI)
7. Biological Networks (Software from UCSD)
8. Reconstructing dynamic gene regulatory networks from sample-based transcriptional data (2012, citation:3)
9. Reconstructing regulatory networks from the dynamic plasticity of gene expression by mutual information (2013, citation:0) 
10. A Gaussian graphical model for identifying significantly responsive regulatory networks from time series gene expression data (2012, citation:1) 
11. An integrative genomics approach to the reconstruction of gene networks in segregating populations (2004, citation:135) 
12. Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice () 
13. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics' (Nature Genetics, 2005, citation:333) 
14. Inferring gene transcriptional modulatory relations: a genetical genomics approach (2005, citation:77) 
15. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function (Nature Genetics, 2005, citation:515) 
16. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease (Nature Genetics, 2005, citation:410) 
17. An integrative genomics approach to infer causal associations between gene expression and disease (Nature Genetics, 2005, citation:544)

Biological Pathway Standard Format

• Systems Biology Markup Language (SBML)
• Used mainly for representation of pathways and mathematical models. Currently (Feb 2008) best suited format for structured representation of mathematical modeling and simulations.
• Proteomics standards Initiative - Molecular Interactions (PSI_MI)
• Designed for structured representation of experimental evidence information, suct as molecular interactions data.
• Biological Pathway eXchange (BioPAX)
• Integrates PSI-MI within a pathway representation format and provides mechanism to store addition information.