Multi-omic landscape of human gliomas from diagnosis to treatment and recurrence, bioRxiv 2025 (et al)

Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma, Cell 2024 (et al)

A visual query builder for knowledge graphs, Bay Area Clojure Meetup, 2020

Introduction to Inventive Minds: Marvin Minsky on Education, ed Cynthia Solomon and Xiao Xiao, 2019

Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery, PLOS One 2016 (w. Sean Ekins et al)

A systematic comparison of the MetaCyc and KEGG pathway databases, BMC Bioinformatics 2013 (w. Tomer Altman et al)

EcoCyc: fusing model organism databases with systems biology, Nucleic Acids Research 2013 (w. Ingrid Keseler et al)

Groups: Knowledge Spreadsheets for Symbolic Biocomputing, Database 2013 (w. Suzanne Paley et al)

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Research 2012 (w. Ron Caspi, Tomer Altman, et al)

Ribbonfarm, blogger-in-residence writing on agency, 2012-2013

Accurate Atom-Mapping Computation for Biochemical Reactions, Journal of Chemical Information and Modeling 2012 (w. Mario Latendresse et al)

Politics and Pragmatism in Scientific Ontology Construction, Proceedings of the First International Symposium on Inconsistency Robustness, 2011.

Cancer Commons: Biomedicine in the Internet Age, in Collaborative Computational Technologies for Biomedical Research, ed Ekins, Hupcey, and Williams, 2011. (with Jeff Shrager and Jay M. Tenenbaum)

A Melanoma Molecular Disease Model, PLoS ONE, 2011 (with S. J. Vidwans, K. T. Flaherty, D. E. Fisher, J. M. Tenenbaum, and J. Shrager)

BioBIKE: A Web-based, programmable, integrated biological knowledge base . Nucleic Acids Research, 2009 (with J. Elhai, A. Taton, J.P. Massar, J.K. Myers, J. Casey, M. Slupesky, and J. Shrager).

The (Re)Birth of the Knowledge Operating System. International Lisp Conference 2005 (with J. Shrager and J.P. Massar).

BioLingua: A programmable knowledge environment for biologists. BioInformatics 2005 (with J.P. Massar, J. Elhai, and J. Shrager)

A Brief Overview of the Narrative Intelligence Reading Group. In Narrative Intelligence, eds. Michael Mateas and Phoebe Sengers, 2003. (with Marc Davis)

Dynamic Interaction in Java (retitled What is Interactive Scripting?), Dr. Dobb's Journal , January 2000.

Recursive Interfaces for Reactive Objects, Proceedings of CHI '94, in Boston, 1994.

Programming with Characters, International Workshop on Intelligent User Interfaces, 1993 (with Marc Davis)

Emotion and the Dynamics of Representation Use, MIT Media Laboratory Music and Cognition Group Technical Report #3, 1992.

Informal Interaction in Virtual Spaces, 2nd International Conference on Cyberspace, 1991.

Two Approaches to Informal Interaction Over Computer and Video Networks. In Proceedings of CHI 1991 (with Alan Borning)

A Visual Representation for Knowledge Structures. In Proceedings of Hypertext '89, 1989.

The Electric Anthill, SIGGRAPH Art Show, 1989

Animal Construction Kits. In Artificial Life: SFI Series in the Sciences of Complexity, ed. C. Langton. Addison-Wesley, 1988.