My research lies at the intersection of bioinformatics and neuroscience, with a focus on genomics. Please see the lab page for more information.
In addition to running my lab, I am also the Associate Director of the UBC Graduate Program in Bioinformatics (and PI of our NSERC CREATE grant to support bioinformatics training) and the Scientific Director of the NeuroDevNet Neuroinformatics Core.
(See my Google Scholar profile for more)
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.
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.
Gillis J, Pavlidis P. (2013) "Assessing identity, redundancy and confounds in Gene Ontology annotations over time." Bioinformatics. 2013 Feb 15;29(4):476-82.
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.
Pavlidis P, Gillis J. (2012) "Progress and challenges in the computational prediction of gene function using networks." F1000Research 2012, 1:14.
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.
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.
Gillis J, Pavlidis P (2012) “'Guilt by Association' Is the Exception Rather Than the Rule in Gene Networks." PLoS Comput Biol 8(3): e1002444.
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.
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.
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.
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:
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." Front Neuroinform. 2009;3:29.
Canadian Common CV:
Joined CHiBi in January 2006.