Jonathan A. Rees

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Degrees

• PhD 1995, MIT, Electrical Engineering and Computer Science. Advisor: Gerald Jay Sussman. Committee: Hal Abelson and Tom Knight. Dissertation title: A Security Kernel Based on the Lambda-calculus. Graduate minor: Entomology (with coursework at Harvard and Cornell).
• SM 1989, MIT, Electrical Engineering and Computer Science.
• BS 1981, Yale College, Computer Science.

Positions held

• Research scholar, Ronin Institute, 2020–present.
• Biodiversity informatics consultant, February 2018–present.
• Software Engineer, Probabilistic Computing Project, Department of Brain and Cognitive Sciences, MIT, June 2017–January 2019.
• Software Architect, Open Tree of Life project and NESCent, Duke University, November 2012–May 2017.
• Research Affiliate, Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, 1998–2008.
• Principal Scientist, Science Commons project, Creative Commons, July 2007–December 2011. Fellow, 2006–07.
• Lead Software Engineer, Computational Biology group, Millennium Pharmaceuticals, Inc., 2002–05.
• Chief Technical Officer, Trenza Corp., 2000–01.
• Principal Research Scientist, Crystaliz, Inc., 1996–2000.
• Research Fellow, Collett lab, Centre for Neuroscience, University of Sussex, 1995–96.
• Research Assistant, Project for Mathematics and Computation, Department of Electrical Engineering and Computer Science, MIT, 1984–95.
• Computer Specialist, Computer Science Robotics and Vision Laboratory, Cornell University, 1991–93.
• Intern (research), Embedded Computation Area, Xerox Palo Alto Research Center, summer 1990.
• Consultant (LISP product development), Artificial Intelligence Technology Group, Digital Equipment Corporation, 1984–90.
• Teaching Assistant, Department of Electrical Engineering and Computer Science, MIT, 1986–89. (graduate core course in programming languages)
• Senior Programmer/Analyst, Computer Science Department, Yale University, 1981–84. ("T project")

Journal articles

• Jonathan A. Rees and Karen Cranston. Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal 5:e12581, 2017.
• Cody Hinchliff et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences 112:12764–12769, 2015.
• Brigitte Boeckmann et al. Quest for Orthologs entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biology and Evolution 7:1988–1999, 2015.
• Emily Jane McTavish et al. Phylesystem: a git-based data store for community curated-phylogenetic estimates. Bioinformatics 31:2794–2800, 2015.
• David J. Patterson et al. Scientific names of organisms: attribution, rights, and licensing. BMC Research Notes 7:79, 2014.
• Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald and M. Scott Marshall. Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings in Bioinformatics 10:193–204, 2009.
• Alan Ruttenberg et al. Advancing translational research with the Semantic Web. BMC Bioinformatics 2007, 8(Suppl 3):S2.
• Joël Pradines et al. Detection of centers of activity in transcript profiling data. Journal of Biopharmaceutical Statistics 14:701–721, 2004.
• Jonathan Rees, Sarah Ferguson, and Sankar Virdhagriswaran. Consistency management for distributed collaboration. ACM Computing Surveys 31(2es), 1999.
• T. S. Collett and J. A. Rees. View-based navigation in Hymenoptera: multiple strategies of landmark guidance in the approach to a feeder. Journal of Comparative Physiology A 181:47–58, 1997.
• Richard A. Kelsey and Jonathan A. Rees. A tractable Scheme implementation. Lisp and Symbolic Computation 7(4):315–335, 1994.

Conference papers

• Alan Ruttenberg, Jonathan Rees, and Jeremy Zucker. What BioPAX communicates and how to extend OWL to help it. OWL: Experiences and Directions Workshop, 2006.
• Alan Ruttenberg, Jonathan Rees, and Joanne Luciano. Experience using OWL DL for the exchange of biological pathway information. OWL: Experiences and Directions Workshop, 2005.
• Jonathan A. Rees and Bruce R. Donald. Program mobile robots in Scheme. Proceedings of the 1992 IEEE International Conference on Robotics and Automation 2681–2688.
• William Clinger and Jonathan Rees. Macros that work. Conference Record of the Eighteenth Annual ACM Symposium on Principles of Programming Languages 155–162, 1991.
• Jonathan A. Rees and Norman I. Adams IV. Object-oriented programming in Scheme. Proceedings of the 1988 ACM Conference on Lisp and Functional Programming 277–288.
• David Kranz, Richard Kelsey, Jonathan Rees, Paul Hudak, James Philbin, and Norman Adams. Orbit: An optimizing compiler for Scheme. Proceedings of the SIGPLAN '86 Symposium on Compiler Construction, pages 219–233. Chosen for reissue in Kathryn S. McKinley (editor), 20 Years of the ACM SIGPLAN Conference on Programming Language Design and Implementation (1979–1999): A Selection, SIGPLAN Notices 39(4), 2004.
• Alan Bawden and Jonathan Rees. Syntactic closures. Proceedings of the 1988 ACM Conference on Lisp and Functional Programming, pages 86–95.
• Jonathan A. Rees and Norman I. Adams IV. T: A dialect of Lisp or, Lambda: The ultimate software tool. Conference Record of the 1982 ACM Symposium on Lisp and Functional Programming, pages 114–122.

Other publications

• Addressing the technical friction points in open science. Creative Commons white paper. Prepared for Workshop on Research and Resource Commons in Scientific Research, Washington College of Law, American University, 17 November 2011. Alternate URL: neurocommons.org/report/techlandscape.pdf
• Recommendations for independent scholarly publication of data sets. Creative Commons white paper, 2010.
• Dan Connolly, Alan Ruttenberg, and Jonathan Rees. Semantic Web technologies applied to interpretation of HLA structure variation. Science Commons, 2009.
• Phil Cryer et al. Adoption of Persistent Identifiers for Biodiversity Informatics. Global Biodiversity Information Facility, 2009.
• Contributor to: Franklyn Turbak, David Gifford, and Mark Sheldon. Design Concepts in Programming Languages. MIT Press, 2008.
• Options for future publication of Psyche. Cambridge Entomological Club, 2004.
• A Security Kernel Based on the Lambda-Calculus. PhD dissertation, MIT, 1995. Reprinted in part as MIT AI Memo 1564, 1996.
• The Scheme of Things (column): Implementing lexically scoped macros; User-defined data types. Lisp Pointers 6(1–3), ACM, 1993.
• William Clinger and Jonathan Rees, editors. The revised⁴ report on the algorithmic language Scheme. Lisp Pointers 4(3), ACM, 1991.
• Modular macros. SM dissertation, MIT, 1989.
• Jonathan Rees and William Clinger, editors. The revised³ report on the algorithmic language Scheme. ACM SIGPLAN Notices 21(12), December 1986.
• Jonathan A. Rees, Norman I. Adams IV and James R. Meehan. The T manual. Yale University Computer Science Department, fourth edition 1984.

Invited presentations

• A data store for community-curated phylogenetic estimates. Pierce lab, Museum of Comparative Zoology, Harvard University, 4 December 2015.
• 'Open' as a strategy for durability, reproducibility, and scalability. Bioinformatics Open Source Conference, Boston, MA, 12 July 2014.
• Taxonomic data exchange as expression and synthesis of phylogenetic claims. iEvoBio, Raleigh, N.C., 25 June 2014.
• Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases. Harvard University Herbaria, Cambridge, MA, 9 July 2014.
• Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases. TDWG 2013 Annual Conference, Florence, Italy, 31 October 2013.
• Digital data repositories. Cochrane Colloqium, Quebec City, 23 September 2013.
• From scientific values to software architecture and back. National Evolutionary Synthesis Center, Durham, N.C., 4 September 2012.
• Data ungovernance. DataONE Data Governance Workshop, Washington, D.C., 15 December 2011.
• What any persistent identifier system has to do. IDCC11 Workshop on Domain Names and Persistence, Bristol, UK, 8 December 2011.
• Addressing the technical friction points in open science. Workshop on Research and Resource Commons in Scientific Research, Washington College of Law, American University, 17 November 2011.
• Happy infrastructure means a happy commons. Creative Commons Global Summit, Warsaw, 16 September 2011.
• Open source knowledge management. Creative Commons Tech Summit, Cambridge, MA, 8 December 2008.
• Novel methods for sharing and integrating web-based data. Workshop on Geospatial knowledge infrastructures. Welsh e-Science Centre, Cardiff University, 26 November 2007.
• Science Commons. Creative Commons China launch, Renmin University, Beijing, 29 April 2006.
• Data analysis using structured biological knowledge: Experience with a database of functional interactions. Children's Hospital Informatics Program, Boston, 28 June 2004.
• Algorithmic chemistry. Operational Models of Complex Adaptive Systems (workshop), University of Neuchâtel, Switzerland, 10 December 1998.
• Visually controlled flight trajectories in insects. Robot Café seminar, Cornell University Computer Science Department, 17 November 1992.
• Embedded Scheme, parts I and II. Xerox Palo Alto Research Center, 25 July 1991 and 29 June 1992.
• Program mobile robots in Scheme. Oxford University Robotics Laboratory, 20 May 1992.

Service

• Member of Technical Architecture Group (TAG) of TDWG (biodiversity information standards organization), appointed 2017.
• Treasurer, Cambridge Entomological Club, 2005–2013.
• Member of Technical Architecture Group (TAG), World Wide Web Consortium, 2008–2012.
• Co-organizer, IDCC11 Workshop: Domain names and persistence, International Digital Curation Conference, 2011.
• Member of LSID-GUID Task Group, Global Biodiversity Information Facility (GBIF), 2009.
• Member of Scheme Programming Language Steering Committee, 2008–present.
• Program committee member, ACM SIGPLAN 2005 Workshop on Scheme and Functional Programming.

Other experience

• Participant, Advancing conservation with articial intelligence (workshop), MIT Enironmental Solutions Initiative, September 2017.
• A reference taxonomy for phylogenetic data aggregation. Poster at TDWG 2016 (Biodiversity Information Standards), Santa Clara de San Carlos, Costa Rica, December 2016.
• Participant, NESCent Phyloinformatics VoCamp, Montpellier, France, November 2009.
• Visitor, Algorithmic Chemistry project, Santa Fe Institute, summers 1998, 1999, and 2004.
• The PARIS project at Millennium Pharmaceuticals, of which I was a member, won the Bio-IT World Best Practices Award in 2003.
• Creator of Scheme 48 and Pre-Scheme, free/libre software projects, 1986–2000 (with Richard Kelsey).