Characterizing in vitro hippocampal ripples using time-frequency analysis. - Jesse A. Gillis; W. P. Luk; Liang Zhang; Frances K. Skinner (Neurocomputing, 2005)

Deficiencies in traditional measures of in vitro hippocampal rhythms. - Jesse A. Gillis; Liang Zhang; Frances K. Skinner (Neurocomputing, 2006)

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

Spatial coherence and stationarity of local field potentials in an isolated whole hippocampal preparation in vitro. - Jesse A. Gillis; Liang Zhang; Frances K. Skinner (J. Comput. Neurosci., 2010)

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

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)

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

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. - Sara Ballouz; Wim Verleyen; Jesse A. Gillis (Bioinform., 2015)

Measuring the wisdom of the crowds in network-based gene function inference. - Wim Verleyen; Sara Ballouz; Jesse A. Gillis (Bioinform., 2015)

Positive and negative forms of replicability in gene network analysis. - Wim Verleyen; Sara Ballouz; Jesse A. Gillis (Bioinform., 2016)

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. - Sara Ballouz; Jesse A. Gillis (PLoS Comput. Biol., 2016)

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

CoCoCoNet: conserved and comparative co-expression across a diverse set of species. - John Lee; Manthan Shah; Sara Ballouz; Megan Crow; Jesse A. Gillis (Nucleic Acids Res., 2020)

Defining the extent of gene function using ROC curvature. - Stephan Fischer; Jesse A. Gillis (Bioinform., 2022)

Learning single-cell chromatin accessibility profiles using meta-analytic marker genes. - Risa Karakida Kawaguchi; Ziqi Tang; Stephan Fischer; Chandana Rajesh; Rohit Tripathy 001; Peter K. Koo; Jesse A. Gillis (Briefings Bioinform., 2023)

Improving replicability in single-cell RNA-Seq cell type discovery with Dune. - Hector Roux de Bézieux; Kelly Street; Stephan Fischer; Koen Van den Berge; Rebecca Chance; Davide Risso; Jesse A. Gillis; John Ngai; Elizabeth Purdom; Sandrine Dudoit (BMC Bioinform., 2024)