The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. - J. Christopher Bare; Paul T. Shannon; Amy K. Schmid; Nitin S. Baliga (BMC Bioinform., 2007)

Integration and visualization of systems biology data in context of the genome. - J. Christopher Bare; Tie Koide; David J. Reiss; Dan Tenenbaum; Nitin S. Baliga (BMC Bioinform., 2010)

GTC: A web server for integrating systems biology data with web tools and desktop applications. - Dan Tenenbaum; J. Christopher Bare; Nitin S. Baliga (Source Code Biol. Medicine, 2010)

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. - Christopher Plaisier; J. Christopher Bare; Nitin S. Baliga (Nucleic Acids Res., 2011)

Architecture for interoperable software in biology. - James Christopher Bare; Nitin S. Baliga (Briefings Bioinform., 2014)

Network portal: a database for storage, analysis and visualization of biological networks. - Serdar Turkarslan; Elisabeth J. Wurtmann; Wei-Ju Wu; Ning Jiang; J. Christopher Bare; Karen Foley; David J. Reiss; Pavel S. Novichkov; Nitin S. Baliga (Nucleic Acids Res., 2014)

Germline contamination and leakage in whole genome somatic single nucleotide variant detection. - Dorota H. Sendorek; Cristian Caloian; Kyle Ellrott; J. Christopher Bare; Takafumi N. Yamaguchi; Adam D. Ewing; Kathleen E. Houlahan; Thea C. Norman; Adam A. Margolin; Joshua M. Stuart; Paul C. Boutros (BMC Bioinform., 2018)

Improving Segmentation of Breast Arterial Calcifications from Digital Mammography: Good Annotation is All You Need. - Kaier Wang; Melissa L. Hill; Seymour Knowles-Barley; Aristarkh Tikhonov; Lester Litchfield; James Christopher Bare (ACCV (Workshops), 2022)