Paul Pavlidis

Summary

Publications

  1. pmc Application and evaluation of automated semantic annotation of gene expression experiments
    Leon French
    University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 25:1543-9. 2009
  2. pmc Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text
    Leon French
    Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Bioinformatics 28:2963-70. 2012
  3. pmc "Guilt by association" is the exception rather than the rule in gene networks
    Jesse Gillis
    Centre for High Throughput Biology and Department of Psychiatry, University of British Columbia, Vancouver, British Colombia, Canada
    PLoS Comput Biol 8:e1002444. 2012
  4. pmc The impact of multifunctional genes on "guilt by association" analysis
    Jesse Gillis
    Department of Psychiatry, University of British Columbia, Centre for High Throughput Biology, Vancouver, British Columbia, Canada
    PLoS ONE 6:e17258. 2011
  5. pmc Relationships between gene expression and brain wiring in the adult rodent brain
    Leon French
    Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1001049. 2011
  6. pmc Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain
    Powell Patrick Cheng Tan
    Bioinformatics Graduate Program, University of British Columbia Vancouver, BC, Canada Centre for High Throughput Biology, University of British Columbia Vancouver, BC, Canada
    Front Neurosci 7:5. 2013
  7. pmc Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration
    Leon French
    Bioinformatics Graduate Program, University of British Columbia Vancouver, BC, Canada
    Front Neuroinform 5:12. 2011
  8. pmc Meta-analysis of kindling-induced gene expression changes in the rat hippocampus
    Sanja Rogic
    Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia Vancouver, BC, Canada
    Front Neurosci 3:53. 2009
  9. pmc Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls
    Meeta Mistry
    Department of Psychiatry, University of British Columbia, Vancouver BC, Canada
    BMC Neurosci 14:105. 2013
  10. pmc Genome-wide expression profiling of schizophrenia using a large combined cohort
    M Mistry
    Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
    Mol Psychiatry 18:215-25. 2013

Research Grants

  1. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2005
  2. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2005
  3. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2007
  4. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2009
  5. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2010

Collaborators

Detail Information

Publications28

  1. pmc Application and evaluation of automated semantic annotation of gene expression experiments
    Leon French
    University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 25:1543-9. 2009
    ..This hinders searching, high-throughput analysis, organization and integration of the datasets...
  2. pmc Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text
    Leon French
    Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Bioinformatics 28:2963-70. 2012
    ..We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features...
  3. pmc "Guilt by association" is the exception rather than the rule in gene networks
    Jesse Gillis
    Centre for High Throughput Biology and Department of Psychiatry, University of British Columbia, Vancouver, British Colombia, Canada
    PLoS Comput Biol 8:e1002444. 2012
    ....
  4. pmc The impact of multifunctional genes on "guilt by association" analysis
    Jesse Gillis
    Department of Psychiatry, University of British Columbia, Centre for High Throughput Biology, Vancouver, British Columbia, Canada
    PLoS ONE 6:e17258. 2011
    ..We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies...
  5. pmc Relationships between gene expression and brain wiring in the adult rodent brain
    Leon French
    Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1001049. 2011
    ..Supplementary data are available at http://www.chibi.ubc.ca/ABAMS...
  6. pmc Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain
    Powell Patrick Cheng Tan
    Bioinformatics Graduate Program, University of British Columbia Vancouver, BC, Canada Centre for High Throughput Biology, University of British Columbia Vancouver, BC, Canada
    Front Neurosci 7:5. 2013
    ..In conclusion, our work provides insights into human brain function and evolution by probing global relationships between regional cell type marker expression patterns in the human and mouse brain...
  7. pmc Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration
    Leon French
    Bioinformatics Graduate Program, University of British Columbia Vancouver, BC, Canada
    Front Neuroinform 5:12. 2011
    ..Our results exemplify what is possible when increasingly detailed large-scale cell- and gene-level data sets are integrated with connectivity data...
  8. pmc Meta-analysis of kindling-induced gene expression changes in the rat hippocampus
    Sanja Rogic
    Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia Vancouver, BC, Canada
    Front Neurosci 3:53. 2009
    ..Supplementary Material is available at http://www.chibi.ubc.ca/faculty/pavlidis/meta-analysis-of-brain-kindling/..
  9. pmc Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls
    Meeta Mistry
    Department of Psychiatry, University of British Columbia, Vancouver BC, Canada
    BMC Neurosci 14:105. 2013
    ..Here, we have applied a novel approach to combining coexpression data across seven postmortem human brain studies of schizophrenia...
  10. pmc Genome-wide expression profiling of schizophrenia using a large combined cohort
    M Mistry
    Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
    Mol Psychiatry 18:215-25. 2013
    ..A gene network analysis predicted previously unidentified functional relationships among the signature genes. Our results provide evidence for a common underlying expression signature in this heterogeneous disorder...
  11. pmc Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)
    Jesse Gillis
    Stanley Institute for Cognitive Genomic, Cold Spring Harbor Laboratory, 196 Genome Research Center, 500 Sunnyside Boulevard Woodbury, NY 11797, USA
    BMC Bioinformatics 14:S15. 2013
    ..In particular, we suggest that using the Gene Ontology (or other similar systematizations of function) as a gold standard is unlikely to be the way forward...
  12. ncbi request reprint Gene function analysis in complex data sets using ErmineJ
    Jesse Gillis
    Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
    Nat Protoc 5:1148-59. 2010
    ..The protocol should take approximately 1 h, including (one-time) installation and setup...
  13. pmc A methodology for the analysis of differential coexpression across the human lifespan
    Jesse Gillis
    Department of Psychiatry, University of British Columbia, Vancouver, Canada
    BMC Bioinformatics 10:306. 2009
    ..Here we introduce a method for analyzing changes in coexpression across multiple ordered groups (e.g., over time) and extensively test its validity and usefulness...
  14. pmc Gene Ontology term overlap as a measure of gene functional similarity
    Meeta Mistry
    Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia, British Columbia, Canada
    BMC Bioinformatics 9:327. 2008
    ..A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO)...
  15. pmc The role of indirect connections in gene networks in predicting function
    Jesse Gillis
    Centre for High Throughput Biology and Department of Psychiatry, 177 Michael Smith Laboratories, 2185 East Mall, University of British Columbia, Vancouver, BC V6T1Z4, Canada
    Bioinformatics 27:1860-6. 2011
    ..We sought to provide a unified explanation for the performance of gene function prediction algorithms in exploiting network structure and thereby simplify future analysis...
  16. pmc Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis
    Kristina Becanovic
    Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
    Hum Mol Genet 19:1438-52. 2010
    ..Further study of these genes may unravel novel pathways contributing to HD pathogenesis. DDBJ/EMBL/GenBank accession no: GSE19677...
  17. ncbi request reprint Informatics in neuroscience
    Leon French
    UBC Bioinformatics Centre UBiC, 177, Michael Smith Laboratories, 2185 East Mall, University of British Columbia, Vancouver BC V6T1Z4, Canada
    Brief Bioinform 8:446-56. 2007
    ..The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to advance the field...
  18. pmc Automated recognition of brain region mentions in neuroscience literature
    Leon French
    Bioinformatics Graduate Program, University of British Columbia Vancouver, BC, Canada
    Front Neuroinform 3:29. 2009
    ..We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. The corpus is freely available at http://www.chibi.ubc.ca/WhiteText/...
  19. pmc Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data
    Anton Zoubarev
    Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
    Bioinformatics 28:2272-3. 2012
    ..With optional registration users can save their own data and securely share it with other users. Web services and integration with third-party resources further increase the scope of the tools, which include a Cytoscape plugin...
  20. pmc Assessing identity, redundancy and confounds in Gene Ontology annotations over time
    Jesse Gillis
    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 192B Genome Research Center, 500 Sunnyside Boulevard, Woodbury, NY 11797, USA
    Bioinformatics 29:476-82. 2013
    ..The Gene Ontology (GO) is heavily used in systems biology, but the potential for redundancy, confounds with other data sources and problems with stability over time have been little explored...
  21. pmc Neurocarta: aggregating and sharing disease-gene relations for the neurosciences
    Elodie Portales-Casamar
    Centre for High Throughput Biology and Department of Psychiatry, University of British Columbia, 2125 East Mall, Vancouver, BC V6T1Z4, Canada
    BMC Genomics 14:129. 2013
    ..Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools...
  22. pmc miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability
    Ying Qiao
    Department of Pathology and Lab Medicine, BC Child and Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
    BMC Genomics 14:544. 2013
    ..It has been recently shown that genomic copy number variations (CNVs) can cause aberrant expression of integral miRNAs and their target genes, and contribute to intellectual disability (ID)...
  23. pmc Sharing and reusing gene expression profiling data in neuroscience
    Xiang Wan
    Department of Psychiatry, UBC Bioinformatics Centre, University of British Columbia, 177 Michael Smith Laboratories 2185 East Mall, Vancouver, BC V6T1Z4, Canada
    Neuroinformatics 5:161-75. 2007
    ..Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data...
  24. pmc Using text mining to link journal articles to neuroanatomical databases
    Leon French
    Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
    J Comp Neurol 520:1772-83. 2012
    ..The training data, terminologies, normalizations, evaluations, and annotated journal abstracts are freely available at http://www.chibi.ubc.ca/WhiteText/...
  25. pmc Understanding the impact of 1q21.1 copy number variant
    Chansonette Harvard
    Child and Family Research Institute, Molecular Cytogenetics and Array Laboratory, 950 West 28th Avenue, Vancouver, BC, Canada
    Orphanet J Rare Dis 6:54. 2011
    ..Here we described the consequences of the 1q21.1 CNV on genome-wide gene expression and function of selected candidate genes within 1q21.1 using cell lines from clinically well described subjects...
  26. ncbi request reprint The NeuroDevNet Neuroinformatics Core
    Elodie Portales-Casamar
    Centre for High Throughput Biology, University of British Columbia, Vancouver, BC, Canada
    Semin Pediatr Neurol 18:17-20. 2011
    ..It is an essential component to NeuroDevNet, enabling active collaboration across the country and optimizing this unique endeavor...

Research Grants6

  1. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2005
    ..This project will enable future collaborative efforts to target specific diseases or processes for examination. ..
  2. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2005
    ..This project will enable future collaborative efforts to target specific diseases or processes for examination. ..
  3. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2007
    ..This project will enable future collaborative efforts to target specific diseases or processes for examination. ..
  4. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2009
    ..This project will enable future collaborative efforts to target specific diseases or processes for examination. ..
  5. Integrative Meta-analysis of Microarray Data
    Paul Pavlidis; Fiscal Year: 2010
    ..This project will enable future collaborative efforts to target specific diseases or processes for examination. ..