Yale Image Finder (YIF): a new search engine for retrieving biomedical images. - Songhua Xu; Jamie P. McCusker; Michael Krauthammer (Bioinform., 2008)

Semantic web data warehousing for caGrid. - Jamie P. McCusker; Joshua A. Phillips; Alejandra N. González-Beltrán; Anthony Finkelstein; Michael Krauthammer (BMC Bioinform., 2009)

Explorations into the Provenance of High Throughput Biomedical Experiments. - Jamie P. McCusker; Deborah L. McGuinness (IPAW, 2010)

Towards Identity in Linked Data. - Jamie P. McCusker; Deborah L. McGuinness (OWLED, 2010)

When owl: sameAs Isn't the Same: An Analysis of Identity in Linked Data. - Harry Halpin; Patrick J. Hayes; Jamie P. McCusker; Deborah L. McGuinness; Henry S. Thompson (ISWC (1), 2010)

Analysis of Cancer Omics Data In A Semantic Web Framework. - Matthew Holford; Jamie P. McCusker; Kei-Hoi Cheung; Michael Krauthammer (SWAT4LS, 2010)

Towards an Ontology for Conceptual Modeling. - Jamie P. McCusker; Joanne S. Luciano; Deborah L. McGuinness (ICBO, 2011)

Where did you hear that? Information and the Sources They Come From. - Jamie P. McCusker; Timothy Lebo; Li Ding 001; Cynthia Chang; Paulo Pinheiro da Silva; Deborah L. McGuinness (LISC, 2011)

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. - Joanne S. Luciano; Bosse Andersson; Colin R. Batchelor; Olivier Bodenreider; Tim Clark; Christine K. Denney; Christopher Domarew; Thomas Gambet; Lee Harland; Anja Jentzsch; Vipul Kashyap; Peter J. Kos; et al. (J. Biomed. Semant., 2011)

Linked provenance data: A semantic Web-based approach to interoperable workflow traces. - Li Ding 001; James Michaelis; Jamie P. McCusker; Deborah L. McGuinness (Future Gener. Comput. Syst., 2011)

Towards Semantically Enabled Next Generation Community Health Information Portals: The PopSciGrid Pilot. - Deborah L. McGuinness; Timothy Lebo; Li Ding 001; Jamie P. McCusker; Abdul R. Shaikh; Richard P. Moser; Glen D. Morgan; Zaria Tatalovich; Gordon Willis; Bradford W. Hesse; Noshir S. Contractor; Paul Courtney (HICSS, 2012)

Functional Requirements for Information Resource Provenance on the Web. - Jamie P. McCusker; Timothy Lebo; Alvaro Graves; Dominic DiFranzo; Paulo Pinheiro 001; Deborah L. McGuinness (IPAW, 2012)

Public Health Surveillance Using Global Health Explorer. - Jamie P. McCusker; Jeongmin Lee 001; Chavon Thomas; Deborah L. McGuinness (SATBI+SWIM, 2012)

A semantic web framework to integrate cancer omics data with biological knowledge. - Matthew Holford; Jamie P. McCusker; Kei-Hoi Cheung; Michael Krauthammer (BMC Bioinform., 2012)

Parallel Identities for Managing Open Government Data. - Jamie P. McCusker; Timothy Lebo; Cynthia Chang; Deborah L. McGuinness; Paulo Pinheiro da Silva (IEEE Intell. Syst., 2012)

Translating standards into practice - One Semantic Web API for Gene Expression. - Helena F. Deus; Eric Prud'hommeaux; Michael Miller 001; Jun Zhao 003; James Malone; Tomasz Adamusiak; Jamie P. McCusker; Sudeshna Das 001; Philippe Rocca-Serra; Ronan Fox; M. Scott Marshall (J. Biomed. Informatics, 2012)

Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications. - Jamie P. McCusker; Timothy Lebo; Michael Krauthammer; Deborah L. McGuinness (DILS, 2013)

Towards Next Generation Health Data Exploration: A Data Cube-Based Investigation into Population Statistics for Tobacco. - Jamie P. McCusker; Deborah L. McGuinness; Jeongmin Lee 001; Chavon Thomas; Paul Courtney; Zaria Tatalovich; Noshir S. Contractor; Glen D. Morgan; Abdul R. Shaikh (HICSS, 2013)

SemantEco: a next-generation web observatory. - A. Patrice Seyed; Timothy Lebo; Evan W. Patton; Jamie P. McCusker; Deborah L. McGuinness (WWW (Companion Volume), 2013)

A Nanopublication Framework for Biological Networks using Cytoscape.js. - Jamie P. McCusker; Rui Yan 007; Kusum Solanki; John S. Erickson; Cynthia Chang; Michel Dumontier; Jonathan S. Dordick; Deborah L. McGuinness (ICBO, 2014)

Identifying First Responder Communities Using Social Network Analysis. - John S. Erickson; Katherine Chastain; Zachary Fry; Jamie P. McCusker; Rui Yan 007; Evan W. Patton; Deborah L. McGuinness (ISWC (Posters & Demos), 2014)

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. - Michel Dumontier; Christopher J. O. Baker; Joachim Baran; Alison Callahan; Leonid L. Chepelev; Jose Cruz-Toledo; Nicholas R. Del Rio; Geraint Duck; Laura Inés Furlong; Nichealla Keath; Dana Klassen; Jamie P. McCusker; et al. (J. Biomed. Semant., 2014)

Formalizing the semantics of sea ice. - Ruth E. Duerr; Jamie P. McCusker; Mark A. Parsons; Siri Jodha Singh Khalsa; Peter L. Pulsifer; Cassidy Thompson; Rui Yan 007; Deborah L. McGuinness; Peter Fox 001 (Earth Sci. Informatics, 2015)

Finding melanoma drugs through a probabilistic knowledge graph. - Jamie P. McCusker; Michel Dumontier; Rui Yan 007; Sylvia He; Jonathan S. Dordick; Deborah L. McGuinness (PeerJ Prepr., 2016)

The Semantic Data Dictionary Approach to Data Annotation & Integration. - Sabbir M. Rashid; Katherine Chastain; Jeanette A. Stingone; Deborah L. McGuinness; Jamie P. McCusker (SemSci@ISWC, 2017)

Broad, Interdisciplinary Science In Tela: An Exposure and Child Health Ontology. - Jamie P. McCusker; Sabbir M. Rashid; Zhicheng Liang; Yue Liu; Katherine Chastain; Paulo Pinheiro 001; Jeanette A. Stingone; Deborah L. McGuinness (WebSci, 2017)

An Ontology for a Polymer Nanocomposite Community Data Resource. - Vipula Rawte; Jamie P. McCusker; He Zhao; L. Catherine Brinson; Wei Chen 041; Linda Schadler; Deborah L. McGuinness (WebSci, 2017)

Annotating Diverse Scientific Data With HAScO. - Paulo Pinheiro 001; Marcello Peixoto Bax; Henrique Santos 002; Sabbir M. Rashid; Zhicheng Liang; Yue Liu; Yarden Ne'eman; Jamie P. McCusker; Deborah L. McGuinness (ONTOBRAS, 2018)

Developing Scientific Knowledge Graphs Using Whyis. - Jamie P. McCusker; Sabbir M. Rashid; Nkechinyere Agu; Kristin P. Bennett; Deborah L. McGuinness (SemSci@ISWC, 2018)

The Whyis Knowledge Graph Framework in Action. - Jamie P. McCusker; Sabbir M. Rashid; Nkechinyere Agu; Kristin P. Bennett; Deborah L. McGuinness (ISWC (P&D/Industry/BlueSky), 2018)

Knowledge Integration for Disease Characterization: A Breast Cancer Example. - Oshani Seneviratne; Sabbir M. Rashid; Shruthi Chari; Jamie P. McCusker; Kristin P. Bennett; James A. Hendler; Deborah L. McGuinness (ISWC (2), 2018)

Ontology-enabled Breast Cancer Characterization. - Oshani Seneviratne; Sabbir M. Rashid; Shruthi Chari; Jamie P. McCusker; Kristin P. Bennett; Jim Hendler; Deborah L. McGuinness (ISWC (P&D/Industry/BlueSky), 2018)

G-PROV: Provenance Management for Clinical Practice Guidelines. - Nkechinyere N. Agu; Neha Keshan; Shruthi Chari; Oshani Seneviratne; Jamie P. McCusker; Deborah L. McGuinness (SeWeBMeDa@ISWC, 2019)

Ontology-enabled Analysis of Study Populations. - Shruthi Chari; Miao Qi; Nkechinyere N. Agu; Oshani Seneviratne; Jamie P. McCusker; Kristin P. Bennett; Amar K. Das; Deborah L. McGuinness (ISWC (Satellites), 2019)

Making Study Populations Visible Through Knowledge Graphs. - Shruthi Chari; Miao Qi; Nkechinyere N. Agu; Oshani Seneviratne; Jamie P. McCusker; Kristin P. Bennett; Amar K. Das; Deborah L. McGuinness (ISWC (2), 2019)

A Linked Data Representation for Summary Statistics and Grouping Criteria. - Jamie P. McCusker; Michel Dumontier; Shruthi Chari; Joanne S. Luciano; Deborah L. McGuinness (SAWSemStats@ISWC, 2019)

Reflections on: Finding Melanoma Drugs Through a Probabilistic Knowledge Graph. - Jamie P. McCusker; Michel Dumontier; Rui Yan 007; Sylvia He; Jonathan S. Dordick; Deborah L. McGuinness (JT@ISWC, 2019)

Automating Population Health Studies Through Semantics and Statistics. - Alexander New; Miao Qi; Shruthi Chari; Sabbir M. Rashid; Oshani Seneviratne; Jamie P. McCusker; John S. Erickson; Deborah L. McGuinness; Kristin P. Bennett (SAWSemStats@ISWC, 2019)

Enabling Trust in Clinical Decision Support Recommendations through Semantics. - Oshani Seneviratne; Amar K. Das; Shruthi Chari; Nkechinyere N. Agu; Sabbir M. Rashid; Ching-Hua Chen; Jamie P. McCusker; James A. Hendler; Deborah L. McGuinness (SeWeBMeDa@ISWC, 2019)

Knowledge Extraction of Cohort Characteristics in Research Publications. - Jay D. S. Franklin; Shruthi Chari; Morgan Foreman; Oshani Seneviratne; Daniel M. Gruen; Jamie P. McCusker; Amar K. Das; Deborah L. McGuinness (AMIA, 2020)

A Demonstration of CodeBreaker: A Machine Interpretable Knowledge Graph for Code. - Ibrahim Abdelaziz; Kavitha Srinivas; Julian Dolby; Jamie P. McCusker (ISWC (Demos/Industry), 2020)

NanoMine: A Knowledge Graph for Nanocomposite Materials Science. - Jamie P. McCusker; Neha Keshan; Sabbir M. Rashid; Michael Deagen; L. Catherine Brinson; Deborah L. McGuinness (ISWC (2), 2020)

A Semantic Framework for Enabling Radio Spectrum Policy Management and Evaluation. - Henrique Santos 002; Alice Mulvehill; John S. Erickson; Jamie P. McCusker; Minor Gordon; Owen Xie; Samuel Stouffer; Gerard Capraro; Alex Pidwerbetsky; John Burgess; Allan Berlinsky; Kurt A. Turck; et al. (ISWC (2), 2020)

The Dynamic Spectrum Access Policy Framework in Action. - Henrique Santos 002; Alice Mulvehill; John S. Erickson; Jamie P. McCusker; Minor Gordon; Owen Xie; Samuel Stouffer; Gerard Capraro; Alex Pidwerbetsky; John Burgess; Allan Berlinsky; Kurt A. Turck; et al. (ISWC (Demos/Industry), 2020)

Graph4Code: A Machine Interpretable Knowledge Graph for Code. - Kavitha Srinivas; Ibrahim Abdelaziz; Julian Dolby; Jamie P. McCusker (CoRR, 2020)

A Toolkit for Generating Code Knowledge Graphs. - Ibrahim Abdelaziz; Julian Dolby; Jamie P. McCusker; Kavitha Srinivas (K-CAP, 2021)

Creating and Visualizing the Materials Science Knowledge Graph with Whyis. - Jamie P. McCusker; Michael Deagen; Tolulomo Fateye; Anya Wallace; Sabbir M. Rashid; Deborah L. McGuinness (ISWC (Posters/Demos/Industry), 2021)

Geospatial Reasoning with Shapefiles for Supporting Policy Decisions. - Henrique Santos 002; Jamie P. McCusker; Deborah L. McGuinness (CoRR, 2021)

Can Machines Read Coding Manuals Yet? - A Benchmark for Building Better Language Models for Code Understanding. - Ibrahim Abdelaziz; Julian Dolby; Jamie P. McCusker; Kavitha Srinivas (AAAI, 2022)

An Ontology for Fairness Metrics. - Jade S. Franklin; Karan Bhanot; Mohamed F. Ghalwash; Kristin P. Bennett; Jamie P. McCusker; Deborah L. McGuinness (AIES, 2022)

SciKG: Tutorial on Building Scientific Knowledge Graphs from Data, Data Dictionaries, and Codebooks. - Henrique Santos 002; Paulo Pinheiro 001; Jamie P. McCusker; Sabbir M. Rashid; Deborah L. McGuinness (ESWC Workshops, 2023)

Whyis 2: An Open Source Framework for Knowledge Graph Development and Research. - Jamie P. McCusker; Deborah L. McGuinness (ESWC, 2023)

A Concise Ontology to Support Research on Complex, Multimodal Clinical Reasoning. - Sabbir M. Rashid; Jamie P. McCusker; Daniel M. Gruen; Oshani Seneviratne; Deborah L. McGuinness (ESWC, 2023)

An Ontology for Reasoning About Fairness in Regression and Machine Learning. - Jade S. Franklin; Hannah Powers; John S. Erickson; Jamie P. McCusker; Deborah L. McGuinness; Kristin P. Bennett (KGSWC, 2023)

LOKE: Linked Open Knowledge Extraction for Automated Knowledge Graph Construction. - Jamie P. McCusker (CoRR, 2023)

Semantically enabling clinical decision support recommendations. - Oshani Seneviratne; Amar K. Das; Shruthi Chari; Nkechinyere N. Agu; Sabbir M. Rashid; Jamie P. McCusker; Jade S. Franklin; Miao Qi; Kristin P. Bennett; Ching-Hua Chen; James A. Hendler; Deborah L. McGuinness (J. Biomed. Semant., 2023)

ChatBS: An Exploratory Sandbox for Bridging Large Language Models with the Open Web. - John S. Erickson; Henrique Santos 002; Jamie P. McCusker; Sola Shirai; Deborah L. McGuinness; James A. Hendler (ISWC (Posters/Demos/Industry), 2024)

ARCLIGHT: Automated Clustering and Curriculum Learning Guided by Human Training. - Jamie P. McCusker; Henrique Santos 002; Rishi Singh; Sabbir M. Rashid; Abraham Sanders; Grace Roessling; Hongji Guo; Bashirul Azam Biswas; Deborah L. McGuinness; Tomek Strzalkowski; Qiang Ji; Jay Miller (HGAIS@ISWC, 2024)

Supporting Next-Generation Science with a Semantic Ecosystem. - Sabbir M. Rashid; John S. Erickson; Jamie P. McCusker; Henrique Santos 002; Paulo Pinheiro 001; Shruthi Chari; Matthew Johnson; Jade S. Franklin; Kelsey Rook; Deborah L. McGuinness (ISWC (Posters/Demos/Industry), 2024)

Customizable Knowledge Graph Visualization using the Whyis Knowledge Explorer. - Jamie P. McCusker (VOILA@ISWC, 2024)

LLM experimentation through knowledge graphs: Towards improved management, repeatability, and verification. - John S. Erickson; Henrique Santos 002; Vládia Pinheiro; Jamie P. McCusker; Deborah L. McGuinness (J. Web Semant., 2025)