Semantic thumbnails: a novel method for summarizing document collections. - Arijit Sengupta; Mehmet M. Dalkilic; James C. Costello (SIGDOC, 2004)

TREC 2004 Genomics Track Experiments at IUB. - Kazuhiro Seki; James C. Costello; Vasanth R. Singan; Javed Mostafa (TREC, 2004)

Using Compression to Identify Classes of Inauthentic Texts. - Mehmet M. Dalkilic; Wyatt T. Clark; James C. Costello; Predrag Radivojac (SDM, 2006)

Using Drosophila melanogaster Data to Discover Disease-Related Protein Interactions in Humans. - James C. Costello; Jade E. Buchanan-Carter; Mehmet M. Dalkilic; Justen Andrews (CIBCB, 2007)

Limitations of Pseudogenes in Identifying Gene Losses. - James C. Costello; Mira V. Han; Matthew W. Hahn (RECOMB-CG, 2008)

Data-Driven Ontologies. - James C. Costello; Daniel R. Schrider; Jeff Gehlhausen; Mehmet M. Dalkilic (Pacific Symposium on Biocomputing, 2009)

All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes. - Daniel R. Schrider; James C. Costello; Matthew W. Hahn (J. Comput. Biol., 2009)

DREAMTools: a Python package for scoring collaborative challenges. - Thomas Cokelaer; Mukesh Bansal; Christopher Bare; Erhan Bilal; Brian M. Bot; Elias Chaibub Neto; Federica Eduati; Mehmet Gönen; Steven M. Hill; Bruce R. Hoff; Jonathan R. Karr; Robert Küffner; et al. (F1000Research, 2015)

A Spatiotemporal Model to Simulate Chemotherapy Regimens for Heterogeneous Bladder Cancer Metastases to the Lung. - Kimberly R. Kanigel Winner; James C. Costello (PSB, 2017)

GSEA-InContext: identifying novel and common patterns in expression experiments. - Rani K. Powers; Andrew Goodspeed; Harrison Pielke-Lombardo; Aik Choon Tan; James C. Costello (Bioinform., 2018)

Simulating heterogeneous populations using Boolean models. - Brian C. Ross; Mayla Boguslav; Holly Weeks; James C. Costello (BMC Syst. Biol., 2018)

SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. - Alexandra J. Lee; Dallas L. Mould; Jake Crawford; Dongbo Hu; Rani K. Powers; Georgia Doing; James C. Costello; Deborah A. Hogan; Casey S. Greene (Genom. Proteom. Bioinform., 2022)

AI Competitions and Benchmarks: The life cycle of challenges and benchmarks. - Gustavo Stolovitzky; Julio Saez-Rodriguez; Julie Bletz; Jacob Albrecht; Gaia Andreoletti; James C. Costello; Paul C. Boutros (CoRR, 2023)