• MetaCore, Breast Cancer - Network Analysis of Breast Cancer Gene Clusters
• MetaCore, Combining Agile Text Mining with Expert Manually Curated Data to Provide Enhanced Understanding of Liver Fibrosis
• MetaCore, Cystic Fibrosis - Inflammation and CFTR trafficking
• MetaCore, Diabetes - Understanding Insulin-Resistant Diabetes Through Pathway Analysis
• MetaCore, HCV - Discovering Molecular Pathways of HCV
• MetaCore, Investigating mechanisms of toxicity of the environmental pollutant PFOA using the Toxicity Analysis and Interactome tools
• MetaCore, Metabolomics - Pathway Analysis of Serological Metabolite Profiles in Rheumatoid Arthritis
• MetaCore, Pathway Analysis of Genome-Wide Association Studies (GWAS) in Parkinson’s Disease
• MetaCore, Psoriasis - Discovering Molecular Pathways of Psoriasis


• MetaDrug, Clozapine - A chemogenomic approach to understanding the side effects of the former front-line anti-psychotic drug clozapine, and comparison to the structurally similar anti-psychotic drug olanzapine
• MetaDrug, Environmental Toxicants - In silico prediction of the biological effects of propiconazole
• MetaDrug, Mebendazole - Investigation of potential antineoplastic activity of the anthelmintic drug mebendazole


• MetaLink, microRNA - Network Analysis of MicroRNA
• MetaLink, Parkin - Network Analysis of protein interactions of Parkin in the brain

  Published with GeneGo Participation

• J. M. Wright, Y. Nikolsky, T. Serebryiskaya, D. R. Wetmore. MetaMiner (CF): a disease oriented bioinformatics analysis environment. Book chapter in the book “Protein networks and pathway analysis”. Editors Y. Nikolsky and J. Bryant, Humana Press, 2009, UK. Located here


• Yuri Nikolsky, Eugene Kirillov, Roman Zuev, Eugene Rakhmatulin, Tatiana Nikolskaya. Functional analysis of OMICs data and small molecule compounds in an integrated “knowledge-based” platform. Book chapter in the book “Protein networks and pathway analysis” edited by Y. Nikolsky and J. Bryant, Humana Press, 2009, UK. Located here


• Ekins S., Nikolsky Y., Bugrim A., Kirillov E., Nikolskaya T. Pathway mapping tools for analysis of high content data. Book chapter in “High Content Screening” handbook, Series ”Methods Mol. Biol.” Humana Press, 2007, v. 356, 319-350. Located here


• Perlina A., Nikolskaya T., Nikolsky Y. Methodology of functional analysis for OMICs data normalization. Book chapter in “Methods in Microarray Normalization” Drug Discovery Series, CRC Press, Editor Phillip Stafford, UK, 2008. Located here


• Bugrim A., Dezso Z., Nikolsky Y., Nikolskaya T. Integrative pathway analysis of disease molecular data. Book chapter in “Pathway Analysis for Drug Discovery”, p. 121-148. Willey & Sons, 2008. Located here


• Ekins S, Bugrim A, Nikolsky Y and Nikolskaya T, Systems biology: applications in drug discovery. In: Gad, S, Drug Discovery Handbook, Wiley & Sons, 2005. Located here

  In Press with GeneGo participation (Coming soon!)

• R.J. Brennan and S. Bureeva. Pathway data mining of compound protein networks. Invited chapter for Methods in Molecular Biology: Chemogenomics: Methods and Applications (E. Jacoby, ed.). Humana, Totowa, NJ . In press.


• Z. Dezso, A. Bugrim, R.J. Brennan, Y. Nikolsky and T. Nikolskaya. Statistical methods for functional analysis of ‘omics experimental data, in Genomics: Fundamentals and Applications (S. Choudhuri and D.B. Carlson, eds.). Informa Healthcare, NY. In press.

  Other recommendations (our Favorites)

GeneGo recommends Amazon’s book search (www.amazon.com) under pathway analysis or systems Biology or microarray analysis. Here are some of our choices:

• The Music of Life: Biology Beyond Genes by Denis Noble


• High Content Screening (Methods in Molecular Biology) by D. Lansing Taylor (Editor)


• System Modeling in Cellular Biology: From Concepts to Nuts and Bolts by Zoltan Szallasi (Editor), Joerg Stelling (Editor), Vipul Periwal (Editor)


• Systems Biology: Properties of Reconstructed Networks (Kindle Edition)


• Genomics in Drug Discovery and Development by Dimitri Semizarov (Author), Eric Blomme (Author)


• Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory by Attila Szabo (Author), Neil S. Ostlund (Author)

Training Manuals can be found within the MetaCore software here.

Recordings of the on-line webnars can be found within the MetaCore software here.