Classification of genes using probabilistic models of microarray expression profiles. - Paul Pavlidis; Christopher Tang; William Stafford Noble (BIOKDD, 2001)

Promoter Region-Based Classification of Genes. - Paul Pavlidis; Terrence S. Furey; M. Liberto; David Haussler; William Noble Grundy (Pacific Symposium on Biocomputing, 2001)

Gene functional classification from heterogeneous data. - Paul Pavlidis; Jason Weston; Jinsong Cai; William Noble Grundy (RECOMB, 2001)

Exploring Gene Expression Data with Class Scores. - Paul Pavlidis; Darrin P. Lewis; William Stafford Noble (Pacific Symposium on Biocomputing, 2002)

Learning Gene Functional Classifications from Multiple Data Types. - Paul Pavlidis; Jason Weston; Jinsong Cai; William Stafford Noble (J. Comput. Biol., 2002)

The effect of replication on gene expression microarray experiments. - Paul Pavlidis; Qinghong Li; William Stafford Noble (Bioinform., 2003)

Matrix2png: a utility for visualizing matrix data. - Paul Pavlidis; William Stafford Noble (Bioinform., 2003)

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. - Hanga C. Galfalvy; Loubna Erraji-Benchekroun; Peggy Smyrniotopoulos; Paul Pavlidis; Steven P. Ellis; J. John Mann; Etienne Sibille; Victoria Arango (BMC Bioinform., 2003)

Support vector machine classification on the web. - Paul Pavlidis; Ilan Wapinski; William Stafford Noble (Bioinform., 2004)

Book Review. - Paul Pavlidis (J. Biomed. Informatics, 2004)

ErmineJ: Tool for functional analysis of gene expression data sets. - Homin K. Lee; William Braynen; Kiran Keshav; Paul Pavlidis (BMC Bioinform., 2005)

Informatics in neuroscience. - Leon French; Paul Pavlidis (Briefings Bioinform., 2007)

Sharing and Reusing Gene Expression Profiling Data in Neuroscience. - Xiang Wan; Paul Pavlidis (Neuroinformatics, 2007)

Gene Ontology term overlap as a measure of gene functional similarity. - Meeta Mistry; Paul Pavlidis (BMC Bioinform., 2008)

Application and evaluation of automated semantic annotation of gene expression experiments. - Leon French; Suzanne Lane; Tamryn Law; Lydia Xu; Paul Pavlidis (Bioinform., 2009)

A methodology for the analysis of differential coexpression across the human lifespan. - Jesse A. Gillis; Paul Pavlidis (BMC Bioinform., 2009)

Automated recognition of brain region mentions in neuroscience literature. - Leon French; Suzanne Lane; Lydia Xu; Paul Pavlidis (Frontiers Neuroinformatics, 2009)

The role of indirect connections in gene networks in predicting function. - Jesse A. Gillis; Paul Pavlidis (Bioinform., 2011)

Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. - Leon French; Powell Patrick Cheng Tan; Paul Pavlidis (Frontiers Neuroinformatics, 2011)

Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain. - Leon French; Paul Pavlidis (PLoS Comput. Biol., 2011)

Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. - Leon French; Suzanne Lane; Lydia Xu; Celia Siu; Cathy Kwok; Yiqi Chen; Claudia Krebs; Paul Pavlidis (Bioinform., 2012)

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. - Anton Zoubarev; Kelsey M. Hamer; Kiran Keshav; E. Luke McCarthy; Joseph Roy C. Santos; Thea Van Rossum; Cameron McDonald; Adam Hall; Xiang Wan; Raymond Lim; Jesse A. Gillis; Paul Pavlidis (Bioinform., 2012)

Progress and challenges in the computational prediction of gene function using networks. - Paul Pavlidis; Jesse A. Gillis (F1000Research, 2012)

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing. - Spiro P. Pantazatos; Ardesheer Talati; Paul Pavlidis; Joy Hirsch (NeuroImage, 2012)

"Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. - Jesse A. Gillis; Paul Pavlidis (PLoS Comput. Biol., 2012)

Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity. - Spiro P. Pantazatos; Ardesheer Talati; Paul Pavlidis; Joy Hirsch (PLoS Comput. Biol., 2012)

Assessing identity, redundancy and confounds in Gene Ontology annotations over time. - Jesse A. Gillis; Paul Pavlidis (Bioinform., 2013)

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). - Jesse A. Gillis; Paul Pavlidis (BMC Bioinform., 2013)

Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355-1363]. - Spiro P. Pantazatos; Ardesheer Talati; Paul Pavlidis; Joy Hirsch (NeuroImage, 2013)

Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application. - Leon French; Po Liu; Olivia Marais; Tianna Koreman; Lucia Tseng; Artemis Lai; Paul Pavlidis (Frontiers Neuroinformatics, 2015)

Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. - Nikolaus Fortelny; Sharon Yang; Paul Pavlidis; Philipp F. Lange; Christopher M. Overall (Nucleic Acids Res., 2015)

Linking Wikidata to the Rest of the Semantic Web. - Andra Waagmeester; Egon L. Willighagen; Núria Queralt Rosinach; Elvira Mitraka; Sebastian Burgstaller-Muehlbacher; Tim E. Putman; Julia Turner; Lynn M. Schriml; Paul Pavlidis; Andrew I. Su; Benjamin M. Good (SWAT4LS, 2016)

Wikidata as a semantic framework for the Gene Wiki initiative. - Sebastian Burgstaller-Muehlbacher; Andra Waagmeester; Elvira Mitraka; Julia Turner; Tim E. Putman; Justin Leong; Chinmay Naik; Paul Pavlidis; Lynn M. Schriml; Benjamin M. Good; Andrew I. Su (Database J. Biol. Databases Curation, 2016)

EGAD: ultra-fast functional analysis of gene networks. - Sara Ballouz; Melanie Weber 001; Paul Pavlidis; Jesse A. Gillis (Bioinform., 2017)

Can we predict protein from mRNA levels? - Nikolaus Fortelny; Christopher M. Overall; Paul Pavlidis; Gabriela V. Cohen Freue (Nat., 2017)

Transcriptomic correlates of neuron electrophysiological diversity. - Shreejoy J. Tripathy; Lilah Toker; Brenna Li; Cindy-Lee Crichlow; Dmitry Tebaykin; B. Ogan Mancarci; Paul Pavlidis (PLoS Comput. Biol., 2017)

Differential coexpression in human tissues and the confounding effect of mean expression levels. - Marjan Farahbod; Paul Pavlidis (Bioinform., 2019)

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes. - Claire Bomkamp; Shreejoy J. Tripathy; Carolina Bengtsson Gonzales; Jens Hjerling-Leffler; Ann Marie Craig; Paul Pavlidis (PLoS Comput. Biol., 2019)

Curation of over 10 000 transcriptomic studies to enable data reuse. - Nathaniel Lim; Stepan Tesar; Manuel Belmadani; Guillaume Poirier-Morency; Burak Ogan Mancarci; Jordan Sicherman; Matthew Jacobson; Justin Leong; Patrick Tan; Paul Pavlidis (Database J. Biol. Databases Curation, 2021)

Experiment level curation of transcriptional regulatory interactions in neurodevelopment. - Eric Ching-Pan Chu; Alexander M. Morin; Tak Hou Calvin Chang; Tue Nguyen; Yi-Cheng Tsai; Aman Sharma; Chao Chun Liu; Paul Pavlidis (PLoS Comput. Biol., 2021)

The Canadian Open Neuroscience Platform - An open science framework for the neuroscience community. - Rachel J. Harding; Patrick Bermudez; Alexander Bernier; Michael J. S. Beauvais; Pierre Bellec; Sean L. Hill; Agah Karakuzu; Bartha M. Knoppers; Paul Pavlidis; Jean-Baptiste Poline; Jane Roskams; Nikola Stikov; et al. (PLoS Comput. Biol., 2023)

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics. - Alexander M. Morin; Eric Ching-Pan Chu; Paul Pavlidis (PLoS Comput. Biol., 2025)