Paul Pavlidis

Profile Details:

Position/Role: Professor
Affiliation: Department of Psychiatry; Member of the Brain Research Centre
Email Address:paul[at]

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 and Pavlidis P. (2013) “Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA).” BMC Bioinformatics 2013, 14(Suppl 3):S15. pubmed


Portales-Casamar E, Ch Ng C, Lui F, St-Georges N, Zoubarev A, Lai AY, Lee M, Kwok C, Kwok W, Tseng L, Pavlidis P. (2013) “Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.” BMC Genomics. 2013 Feb 26;14(1):129. pubmed


Gillis J, Pavlidis P. (2013) “Assessing identity, redundancy and confounds in Gene Ontology annotations over time.” Bioinformatics. 2013 Feb 15;29(4):476-82. pubmed


Tan PPC, French L, Pavlidis P. (2013) “Neuron-enriched gene expression patterns are regionally anti-correlated with oligodendrocyte-enriched patterns in the adult mouse and human brain.” Front Neurosci. 2013;7:5. pubmed


Pavlidis P, Gillis J. (2012) “Progress and challenges in the computational prediction of gene function using networks.” F1000Research 2012, 1:14. f1000


French L, Lane S, Xu L, Siu C, Kwok C, Chen Y, Krebs C, Pavlidis P. (2012) “Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text.” Bioinformatics. 2012 Nov 15;28(22):2963-70. pubmed


Zoubarev A, Hamer KM, Keshav KD, McCarthy EL, Santos JR, Van Rossum T, McDonald C, Hall A, Wan X, Lim R, Gillis J, Pavlidis P. (2012) “Gemma: A resource for the re-use, sharing and meta-analysis of expression profiling data.” Bioinformatics. 2012 Sep 1;28(17):2272-3. pubmed


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


Mistry M., Gillis J., Pavlidis P. (2012) “Genome-wide expression profiling of schizophrenia using a large combined cohort.” Mol Psychiatry. 2013 Feb;18(2):215-25. pubmed


French L, Pavlidis P. (2011) “Using text mining to link journal articles to neuroanatomical databases.” J Comp Neurol. 2012 Jun 1;520(8):1772-83. pubmed


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. 2011;5:12. pubmed


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


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


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


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). pubmed


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. pubmed


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


French L, Lane S, Xu L., Pavlidis P. (2009) “Automated recognition of brain region mentions in neuroscience literature.” Front Neuroinform. 2009;3:29. pubmed


Canadian Common CV:

History: Joined CHiBi in January 2006.