Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. - Erdahl T. Teber; Jason Y. Liu; Sara Ballouz; Diane Fatkin; Merridee A. Wouters (BMC Bioinform., 2009)

Conditions for the Evolution of Gene Clusters in Bacterial Genomes. - Sara Ballouz; Andrew R. Francis; Ruiting Lan; Mark M. Tanaka (PLoS Comput. Biol., 2010)

Gentrepid V2.0: a web server for candidate disease gene prediction. - Sara Ballouz; Jason Y. Liu; Richard A. George; Naresh Bains; Arthur Liu; Martin Oti; Bruno A. Gaëta; Diane Fatkin; Merridee A. Wouters (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)