Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. - Jing Gao; V. Glenn Tarcea; Alla Karnovsky; Barbara R. Mirel; Terry E. Weymouth; Christopher W. Beecher; James D. Cavalcoli; Brian D. Athey; Gilbert S. Omenn; Charles F. Burant; H. V. Jagadish (Bioinform., 2010)

ConceptGen: a gene set enrichment and gene set relation mapping tool. - Maureen A. Sartor; Vasudeva Mahavisno; Venkateshwar G. Keshamouni; James D. Cavalcoli; Zach Wright; Alla Karnovsky; Rork Kuick; H. V. Jagadish; Barbara Mirel; Terry E. Weymouth; Brian D. Athey; Gilbert S. Omenn (Bioinform., 2010)

Development of an Informed Consent Ontology to Support Biobanking. - Alla Karnovsky; Frank J. Manion; Terry E. Weymouth; V. Glenn Tarcea; Lisa Powell; Blake Roessler; Nicholas Steneck (AMIA, 2012)

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. - Alla Karnovsky; Terry E. Weymouth; Tim Hull; V. Glenn Tarcea; Giovanni Scardoni; Carlo Laudanna; Maureen A. Sartor; Kathleen A. Stringer; H. V. Jagadish; Charles F. Burant; Brian D. Athey; Gilbert S. Omenn (Bioinform., 2012)

Metab2MeSH: annotating compounds with medical subject headings. - Maureen A. Sartor; Alexander S. Ade; Zach Wright; David J. States; Gilbert S. Omenn; Brian D. Athey; Alla Karnovsky (Bioinform., 2012)

Convergence of genetic influences in comorbidity. - Richard C. McEachin; Keerthi S. Sannareddy; James D. Cavalcoli; Alla Karnovsky; Jacqueline M. Vink; Maureen A. Sartor (BMC Bioinform., 2012)

Analysis of Content Coverage for Informed Consent Concepts. - Frank J. Manion; Elizabeth Eisenhauer; Alla Karnovsky; Yongqun He; Yu Lin; Marcelline R. Harris (AMIA, 2014)

Development of a BFO-Based Informed Consent Ontology (ICO). - Yu Lin; Marcelline R. Harris; Frank J. Manion; Elizabeth Eisenhauer; Bin Zhao; Wei Shi; Alla Karnovsky; Yongqun He (ICBO, 2014)

MetDisease - connecting metabolites to diseases via literature. - William Duren; Terry E. Weymouth; Tim Hull; Gilbert S. Omenn; Brian D. Athey; Charles F. Burant; Alla Karnovsky (Bioinform., 2014)

ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. - Raymond G. Cavalcante; Snehal Patil; Terry E. Weymouth; Kestutis G. Bendinskas; Alla Karnovsky; Maureen A. Sartor (Bioinform., 2016)

Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data. - Sumanta Basu; William Duren; Charles R. Evans; Charles F. Burant; George Michailidis; Alla Karnovsky (Bioinform., 2017)

Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease. - Jing Ma; Alla Karnovsky; Farsad Afshinnia; Janis E. Wigginton; Daniel J. Rader; Loki Natarajan; Kumar Sharma; Anna C. Porter; Mahboob Rahman; Jiang He; Lee Hamm; Tariq Shafi; et al. (Bioinform., 2019)

Deep annotation of untargeted LC-MS metabolomics data with Binner. - Maureen Kachman; Hani Habra; William Duren; Janis E. Wigginton; Peter Sajjakulnukit; George Michailidis; Charles F. Burant; Alla Karnovsky (Bioinform., 2020)

DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data. - Christopher Patsalis; Gayatri Iyer; Marci Brandenburg; Alla Karnovsky; George Michailidis (BMC Bioinform., 2024)