Profile Details:

Position/Role: Associate Professor
Affiliation: Department of Psychiatry; Member of the Brain Research Centre
Website: http://www.chibi.ubc.ca/faculty/pavlidis/lab/
Email Address:paul[at]chibi.ubc.ca
Phone:604-827-4157

Research Interests:
My research lies at the intersection of bioinformatics and neuroscience. I have a particular interest in neuropsychiatric disorders such as schizophrenia and autism, and how they affect the function of chemical synapses. A current focus of work in my lab involves the large-scale or meta-analysis of functional genomics data (e.g. microarrays). We use these approaches to study gene networks and their involvement in human neuropsychiatric diseases. To this end we collaborate closely with many laboratory-based neuroscience researchers from UBC and elsewhere. A newer area of interest is in the analysis of neuroanatomical data. Using text mining as well as existing data sources, we are engaged in the analysis of brain structure as it relates to gene expression and the brain “connectome”.

As computational biologists, we also generate methods, databases and tools. One of the tools we developed, “Gemma” is a system that permits researchers to compare and combine gene expression data sets they have generated with other data sets they select from hundreds of other data sets. Gemma will also facilitate the use of other types of data including and proteomics and genetics, and neuroscience-domain-specific data such as neuroanatomy and neuropharmacology. For more information on other resources please see the lab resources page.

In addition to running my lab, I am also the Associate Director of the UBC Graduate Program in Bioinformatics and the Scientific Director of the NeuroDevNet Neuroinformatics Core.

Selected Publications:

Gillis J, Pavlidis P (2012) “’Guilt by Association’ Is the Exception Rather Than the Rule in Gene Networks.” PLoS Comput Biol 8(3): e1002444. doi:10.1371/journal.pcbi.1002444 

Mistry M., Gillis J., Pavlidis P. (2012) “Genome-wide expression profiling of schizophrenia using a large combined cohort.” Molecular Psychiatry doi: 10.1038/mp.2011.172. 

French L, Pavlidis P. (2011) “Using text mining to link journal articles to neuroanatomical databases.” Journal of Comparative Neurology doi: 10.1002/cne.23012. 

French L, Tan PP, Pavlidis P. (2011) “Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration.” Front Neuroinform.;5:12. Epub 2011 Jul 29. 

Gillis J., Pavlidis P. (2011) “The role of indirect connections in gene networks in predicting function.” Bioinformatics 27(13):1860-6. 

Gillis J., Pavlidis P. (2011) “The impact of multifunctional genes on “guilt by association” analysis.” PLoS ONE 6(2):e17258.    Rated “Must read” by Faculty of 1000 (http://f1000.com/12745958).

French L, Pavlidis P. (2010) “Relationships between gene expression and brain wiring in the adult rodent brain.” PLoS Computational Biology 7(1):e1001049. 

Gillis J, Mistry M, Pavlidis P. (2010) “Gene function analysis in complex data sets using ErmineJ.” Nature Protocols 5:1148-1159 (peer-reviewed methods paper). 

Mistry, M., Pavlidis P. (2010) “A cross-laboratory comparison of expression profiling data from normal human postmortem brain.” Neuroscience May 5;167(2):384-95. 

Gillis J, Pavlidis P. (2009) “A methodology for the analysis of differential coexpression across the human lifespan.” BMC Bioinformatics 10:306. 

French L, Lane S, Xu L., Pavlidis P. (2009) “Automated recognition of brain region mentions in neuroscience literature.” Frontiers in Neuroinformatics doi:10.3389/neuro.11.029.2009. 

Lee HK, Braynen W, Keshav K, Pavlidis P. (2005) “ErmineJ: Tool for functional analysis of gene expression data sets.” BMC Bioinformatics 6(1):269. 

Paterlini M, Zakharenko SS, Lai WS, Qin J, Zhang H, Mukai J, Westphal KG, Olivier B, Sulzer D, Pavlidis P, Siegelbaum SA, Karayiorgou M, Gogos JA. (2005) “Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice.” Nat Neurosci 8(11):1586-94. 

Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. (2005) “Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms.” Nucleic Acids Res33(18):5914-23. 

Erraji-Benchekroun L, Underwood MD, Arango V, Galfalvy H, Pavlidis P, Smyrniotopoulos P, Mann JJ, Sibille E. (2005) “Molecular aging in human prefrontal cortex is selective and continuous throughout adult life.” Biol Psychiatry 57(5):549-58. 

History: Member for 4 years 23 weeks