Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. - David J. Reiss; Nitin S. Baliga; Richard Bonneau (BMC Bioinform., 2006)

The Gaggle: An open-source software system for integrating bioinformatics software and data sources. - Paul T. Shannon; David J. Reiss; Richard Bonneau; Nitin S. Baliga (BMC Bioinform., 2006)

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)

Model-based deconvolution of genome-wide DNA binding. - David J. Reiss; Marc T. Facciotti; Nitin S. Baliga (Bioinform., 2008)

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)

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. - Marc T. Facciotti; Wyming Lee Pang; Fang-Yin Lo; Kenia Whitehead; Tie Koide; Ken-ichi Masumura; Min Pan; Amardeep Kaur; David J. Larsen; David J. Reiss; Linh Hoang; Ewa Kalisiak; et al. (BMC Syst. Biol., 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)

Metallochaperones Regulate Intracellular Copper Levels. - Wyming Lee Pang; Amardeep Kaur; Alexander V. Ratushny; Aleksandar Cvetkovic; Sunil Kumar; Min Pan; Adam P. Arkin; John D. Aitchison; Michael W. W. Adams; Nitin S. Baliga (PLoS Comput. Biol., 2013)

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

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. - Christopher L. Plaisier; Fang-Yin Lo; Justin Ashworth; Aaron N. Brooks; Karlyn D. Beer; Amardeep Kaur; Min Pan; David J. Reiss; Marc T. Facciotti; Nitin S. Baliga (BMC Syst. Biol., 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)

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. - Samuel A. Danziger; David J. Reiss; Alexander V. Ratushny; Jennifer J. Smith; Christopher L. Plaisier; John D. Aitchison; Nitin S. Baliga (BMC Syst. Biol., 2015)