Jacob Beal Engineering Fellow Raytheon BBN Technologies 10 Moulton Street Cambridge, MA, USA 02138 I am also a Research Affiliate of University of Iowa Electrical and Computer Engineering.

Primary E-mail: jakebeal@ieee.org Corporate E-mail: jake.beal@raytheon.com - Unreliable Raytheon's email handling is in flux, so I cannot depend on this address. Phone: (617) 873-7676 CV (last updated March, 2023)

My blog, Jake Beal's Next Step, is where I post general thinking about my research, plus updates regarding publications and talks.

Key Ongoing Projects

• Synthetic Biology: using high-level languages, design automation, and predictive modeling to control the behavior of living cells
  • FAST-NA pathogen sequence screening: high-performance detection of biological threats in nucleic acid or protein sequences.
  • TASBE Flow Analytics: free tools for calibrated flow cytometry analysis (GitHub link)
  • Synthetic Biology Open Language: representing biological designs in a form suitable for engineering (replacement for GenBank and GFF formats)
  • iGEM Engineering committee: genetic device engineering, cellular measurement guidance, software tools, and interlaboratory studies
  • Biological Protocols Working Group: open community organization developing a free and open standard for representation of biological protocols, the Protocol Activity Modeling Language (PAML)
  • NIST Flow Cytometry Standards Consortium: developing standards and reference materials for flow cytometry applictions
• Protelis: an aggregate programming language based on computational fields and embedded in Java.

Other Useful Links

• International Gene Synthesis Consortium (IGSC)
• International Workshop on Bio Design Automation (IWBDA)
• IEEE International Conference on Autonomic Computing and Self-Organizing Systems (ACSOS)
  
• Proto: a spatial computing language for programming networks using a continuous space abstraction (largely superseded by Protelis)

About Me

I am an Engineering Fellow at Raytheon BBN Technologies. I am also a research affiliate of the University of Iowa. Previously, I was also a research affiliate of MIT, where I did my graduate and postdoctoral work.

The uniting theme of my research is "engineered self-organization," which is the production of predictable aggregate behavior from locally interacting elements. At present, my investigations are mainly in the domains of synthetic biology (the predictive engineering of desired behaviors in living cells), and aggregate and spatial computing (the description and control of systems of many weakly connected computing devices, and an extension of amorphous computing). Previous research subjects have included work on human-like intelligence and various learning and reasoning systems.

At BBN, I am a member of the Synthetic Biology group in the Intelligent Software & Systems business unit. At the University of Iowa, I collaborate with members of the Electrical and Computer Engineering department.

I don't plan to post any significant amount of my non-professional life on this web page.

Publications

Publications most likely to be of interest are marked with a . This is a fairly complete list, including early and obsolete work.

• Flow Cytometry Quantification of Transient Transfections in Mammalian Cells Jacob Beal, to appear, Methods in Molecular Biology (MIMB): Mammalian Synthetic Systems.
  Preprint available at: https://doi.org/10.48550/arXiv.2305.07948
• Standardized Representation of Parts and Assembly for Build Planning Jacob Beal, Vinoo Selvarajah, Gaël Chambonnier, Traci Haddock, Alejandro Vignoni, Gonzalo Vidal, and Nicholas Roehner, ACS Synthetic Biology 12, no. 12 (2023): 3646-3655., December 2023.
• Securing Fieldable Bioinformatics Daniel Wyschogrod, Steven T. Murphy, Jacob Beal, and Allison Taggart, In Workshop on High Performance Computing on Bioinformatics (HPCB) at 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 3390-3397. IEEE, December, 2023.
• Retrobiosynthesis, Biosecurity, and Large Language Models Prasanna Muthukumar, Nicholas Roehner, Kemper Talley, Sean Colbath and Jacob Beal, AI4Synbio Symposium at AAAI 2023 Fall Symposia, November 2023.
• Splicing-based Biocontainment Devices Allison Taggart, Miles Rogers and Jacob Beal, 15th International Workshop on Bio-Design Automation (IWBDA), September 2023.
• Biological Malware Detector Muntaha Samad, Dan Wyschogrod and Jacob Beal, 15th International Workshop on Bio-Design Automation (IWBDA), September 2023.
• Building an Open Representation for Biological Protocols Bryan Bartley, Jacob Beal, Miles Rogers, Daniel Bryce, Robert P Goldman, Benjamin Keller, Peter Lee, Vanessa Biggers, Joshua Nowak, Mark Weston, ACM Journal on Emerging Technologies in Computing Systems 19, no. 3, pp1-21, June 2023.
  bioRxiv preprint: https://doi.org/10.1101/2022.07.05.498808
• Studying Pathogens Degrades BLAST-based Pathogen Identification Jacob Beal, Adam Clore, Jeff Manthey, Scientific Reports, 13(1), p.5390, April, 2023
  bioRxiv preprint: https://doi.org/10.1101/2022.07.12.499705
• Functional Synthetic Biology Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard, Gael Chambonnier, Nikolaos Ntelkis, Isaac Guerreiro, Martin Holub, Paul Ross, Vinoo Selvarajah, Noah Sprent, Gonzalo Vidal, Alejandro Vignoni Synthetic Biology, Volume 8, Issue 1, April, 2023, https://doi.org/10.1093/synbio/ysad006
  arXiv preprint: https://doi.org/10.48550/arXiv.2207.00538
• Synthetic biology open language (SBOL) version 3.1. 0. Lukas Buecherl, Thomas Mitchell, James Scott-Brown, Prashant Vaidyanathan, Gonzalo Vidal, Hasan Baig, Bryan Bartley, Jacob Beal, Matthew Crowther, Pedro Fontanarrosa, Thomas Gorochowski, Raik Grünberg, Vishwesh Kulkarni, James McLaughlin, Goksel Misirli, Ernst Oberortner, Anil Wipat, and Chris Myers. Journal of integrative bioinformatics 20, no. 1, 20220058, March 2023.
• Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop Breschine Cummins, Justin Vrana, Robert C Moseley, Hamed Eramian, Anastasia Deckard, Pedro Fontanarrosa, Daniel Bryce, Mark Weston, George Zheng, Joshua Nowak, Francis C Motta, Mohammed Eslami, Kara Layne Johnson, Robert P Goldman, Chris J Myers, Tessa Johnson, Matthew W Vaughn, Niall Gaffney, Joshua Urrutia, Shweta Gopaulakrishnan, Vanessa Biggers, Trissha Higa, Lorraine Mosqueda, Marcio Gameiro, Tomas Gedeon, Konstantin Mischaikow, Jacob Beal, Bryan Bartley, Tom Mitchell, Tramy T Nguyen, Nicholas Roehner, Steven B Haase, Synthetic Biology, Volume 8, Issue 1, March 2023, https://doi.org/10.1093/synbio/ysad005
  bioRxiv preprint: https://doi.org/10.1101/2022.06.10.495560
• Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa Jeanet Mante, Julian Abam, Sai P Samineni, Isabel M Potzsch, Jacob Beal, Chris J Myers, ACS Synthetic Biology, 12 (1), pp. 340--346, January 2023, https://doi.org/10.1021/acssynbio.2c00521
  bioRxiv preprint: https://doi.org/10.1101/2022.08.31.505873
• Stability and Resilience of Distributed Information Spreading in Aggregate Computing, Yuanqiu Mo, Soura Dasgupta, Jacob Beal. IEEE Transactions on Automatic Control, 68 (1), January 2023. doi: 10.1109/TAC.2022.3140253.
  Preprint available at: https://arxiv.org/abs/2102.10319
• Workshop Report: Testing Sequence Screening Jacob Beal, Sarah Carter, Adam Clore, Christina LaPosa, December, 2022. https://zenodo.org/doi/10.5281/zenodo.10214844
• Near-optimal knowledge-free resilient leader election Yuanqiu Mo, Giorgio Audrito, Soura Dasgupta, and Jacob Beal. Automatica 146, Paper 110583, December 2022. https://doi.org/10.1016/j.automatica.2022.110583
• Adapting Malware Detection to DNA Screening Dan Wyschogrod, Jeff Manthey, Tom Mitchell, Steven Murphy, Adam Clore, Jacob Beal, 14th International Workshop on Bio-Design Automation (IWBDA), October 2022.
• Standardizing the Representation of Parts and Devices for Build Planning Jacob Beal, Vinoo Selvarajah, Gael Chambonnier, Traci Haddock-Angelli, Alejandro Vignoni, Gonzalo Vidal, Nicholas Roehner, 14th International Workshop on Bio-Design Automation (IWBDA), October 2022.
• Steps Towards Functional Synthetic Biology Ibrahim Aldulijan, Jacob Beal, Sonja Billerbeck, Jeff Bouffard, Gael Chambonnier, Nikolaos Delkis, Isaac Guerreiro, Martin Holub, Daisuke Kiga, Jacky Loo, Paul Ross, Vinoo Selvarajah, Noah Sprent, Gonzalo Vidal, Alejandro Vignoni, 14th International Workshop on Bio-Design Automation (IWBDA), October 2022.
• Implementing Cross-Platform Protocol Execution with the Protocol Activity Modeling Language Bryan Bartley, Jacob Beal, Alexis Casas, Jeremy Cahill, Timothy Fallon, Daniel Bryce, Robert P. Goldman, Luiza Hesketh, Tim Dobbs, Alejandro Vignoni, 14th International Workshop on Bio-Design Automation (IWBDA), October 2022.
• Highly-automated, high-throughput replication of yeast-based logic circuit design assessments Robert P Goldman, Robert Moseley, Nicholas Roehner, Breschine Cummins, Justin D Vrana, Katie J Clowers, Daniel Bryce, Jacob Beal, Matthew DeHaven, Joshua Nowak, Trissha Higa, Vanessa Biggers, Peter Lee, Jeremy P Hunt, Lorraine Mosqueda, Steven B Haase, Mark Weston, George Zheng, Anastasia Deckard, Shweta Gopaulakrishnan, Joseph F Stubbs, Niall I Gaffney, Matthew W Vaughn, Narendra Maheshri, Ekaterina Mikhalev, Bryan Bartley, Richard Markeloff, Tom Mitchell, Tramy Nguyen, Daniel Sumorok, Nicholas Walczak, Chris Myers, Zach Zundel, Benjamin Hatch, James Scholz, John Colonna-Romano, Synthetic Biology 7, no. 1 (2022): ysac018, October 2022. https://doi.org/10.1093/synbio/ysac018
• Multicolor plate reader fluorescence calibration Jacob Beal, Cheryl A Telmer, Alejandro Vignoni, Yadira Boada, Geoff S Baldwin, Liam Hallett, Taeyang Lee, Vinoo Selvarajah, Sonja Billerbeck, Bradley Brown, Guo-nan Cai, Liang Cai, Edward Eisenstein, Daisuke Kiga, David Ross, Nina Alperovich, Noah Sprent, Jaclyn Thompson, Eric M Young, Drew Endy, Traci Haddock-Angelli, Synthetic Biology, 7 (1), ysac010, August 2022. https://doi.org/10.1093/synbio/ysac010
• Building the Plant SynBio Toolbox through Combinatorial Analysis of DNA Regulatory Elements Alexander C Pfotenhauer, Alessandro Occhialini, Mary-Anne Nguyen, Helen Scott, Lezlee T Dice, Stacee A Harbison, Li Li, D Nikki Reuter, Tayler M Schimel, C Neal Stewart Jr, Jacob Beal, Scott C Lenaghan, ACS Synthetic Biology, 11 (8), pp. 2741-2755, August 2022. https://doi.org/10.1021/acssynbio.2c00147
• pySBOL3: SBOL3 for Python Programmers Tom Mitchell, Jacob Beal, and Bryan Bartley, ACS Synthetic Biology, 11 (7), pp. 2523-2526, July 2022. https://doi.org/10.1021/acssynbio.2c00249
• Computational prediction of synthetic circuit function across growth conditions Breschine Cummins, Robert C Moseley, Anastasia Deckard, Mark Weston, George Zheng, Daniel Bryce, Joshua Nowak, Marcio Gameiro, Tomas Gedeon, Konstantin Mischaikow, Jacob Beal, Tessa Johnson, Matthew Vaughn, Niall I Gaffney, Shweta Gopaulakrishnan, Joshua Urrutia, Robert P Goldman, Bryan Bartley, Tramy T Nguyen, Nicholas Roehner, Tom Mitchell, Justin D Vrana, Katie J Clowers, Narendra Maheshri, Diveena Becker, Ekaterina Mikhalev, Vanessa Biggers, Trissha Higa, Lorraine Mosqueda, Steven B Haase, bioRxiv preprint, June 2022. https://doi.org/10.1101/2022.06.13.495701
• Simulation-Based Engineering of Time-Delayed Safety Switches for Safer Gene Therapies Helen Scott, Dashan Sun, Jacob Beal, and Samira Kiani, ACS Synthetic Biology, 11 (5), pp. 1782-1789, May 2022. https://doi.org/10.1021/acssynbio.1c00621
• Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks, Jacob Beal, Brian Teague, John T. Sexton, Sebastian Castillo-Hair, Nicholas A. DeLateur, Meher Samineni, Jeffery J. Tabor, Ron Weiss, and the Calibrated Flow Cytometry Study Consortium. ACS Synthetic Biology, 11 (3), pp. 1196-1207, March 2022.
  Preprint available at https://doi.org/10.1101/2021.10.10.460840
• Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis Daniel Bryce, Robert P Goldman, Matthew DeHaven, Jacob Beal, Bryan Bartley, Tramy T Nguyen, Nicholas Walczak, Mark Weston, George Zheng, Josh Nowak, Peter Lee, Joe Stubbs, Niall Gaffney, Matthew W Vaughn, Chris John Myers, Robert C Moseley, Steven Haase, Anastasia Deckard, Bree Cummins, Nick Leiby, ACS Synthetic Biology, 11 (2), pp. 608-622, February 2022. https://doi.org/10.1021/acssynbio.1c00305
• Intent Parser: A Tool for Codification and Sharing of Experimental Design, Tramy Nguyen, Nicholas Walczak, Daniel Sumorok, Mark Weston, Jacob Beal. ACS Synthetic Biology, January 2022. https://doi.org/10.1021/acssynbio.1c00285
• Development and transition of FAST-NA screening technology Jacob Beal, Dan Wyschogrod, Tom Mitchell, Susan Katz, Jeff Manthey and Adam Clore, BBN Technical Report 8622, Raytheon BBN Technologies, December 2021. https://zenodo.org/doi/10.5281/zenodo.10214869
• Synthetic Biology Curation Tools (SYNBICT), Nicholas Roehner, Jeanet Mante, Chris J Myers, Jacob Beal. ACS Synthetic Biology, 10 (11), pp. 3200--3204, November 2021.
• Curation Principles Derived from the Analysis of the SBOL iGEM Data Set, Jeanet Mante, Nicholas Roehner, Kevin Keating, James Alastair McLaughlin, Eric Young, Jacob Beal, Chris J Myers. ACS Synthetic Biology, 10 (10), pp. 2592--2606, October 2021.
• Synthetic biology open language visual (SBOL visual) version 3.0, Hasan Baig, Pedro Fontanarossa, James McLaughlin, James Scott-Brown, Prashant Vaidyanathan, Thomas Gorochowski, Goksel Misirli, Jacob Beal, Chris Myers. Journal of Integrative Bioinformatics, 18 (3), Article 20210013, October 2021. https://doi.org/10.1515/jib-2021-0013
• Towards collaborative and automated development of resources for data standards in synthetic biology, Jake Sumner Ajibode, Jacob Beal, James Scott-Brown, Thomas Gorochowski, Chris Myers and Goksel Misirli. 13th International Workshop on Bio-Design Automation (IWBDA), September 2021.
• Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa, Julian Abam, Jeanet Mante, Isabel Potzsch, Jake Beal and Chris Myers. 13th International Workshop on Bio-Design Automation (IWBDA), September 2021.
• Data Representation in the DARPA SD2 Program, Nicholas Roehner, Jacob Beal, Bryan Bartley, Richard Markeloff, Tom Mitchell, Tramy Nguyen, Daniel Sumorok, Nicholas Walczak, Chris Myers, Zach Zundel, James Scholz, Benjamin Hatch, Mark Weston and John Colonna-Romano. 13th International Workshop on Bio-Design Automation (IWBDA), September 2021.
• Cyberbiosecurity and Public Health in the Age of COVID-19, Aaron Adler, Jacob Beal, Mary Lancaster, Daniel Wyschogrod. chapter in ``Emerging Threats of Synthetic Biology and Biotechnology: Addressing Security and Resilience Issues,'' ed. Benjamin D Trump, Marie-Valentine Florin, Edward J Perkins, Igor Linkov, Springer Publishing, pp. 103--115, September, 2021 https://doi.org/10.1007/978-94-024-2086-9_7
• Effect of Monotonic Filtering on Graph Collection Dynamics, , Hunza Zainab, Giorgio Audrito, Soura Dasgupta, Jacob Beal. Workshop on Engineering Collective Adaptive Systems (eCAS), September 2021.
  Extended arXiv version entitled ``Monotonic filtering for distributed collection'' at: https://arxiv.org/abs/2107.05791
• Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals, Katherine A. Kiwimagi, Justin H. Letendre, Benjamin H. Weinberg, Junmin Wang, Mingzhe Chen, Leandro Watanabe, Chris J. Myers, Jacob Beal, Wilson W. Wong, Ron Weiss. Communications Biology, 4, Article 875, July 2021
• Synthetic biology open language visual (SBOL Visual) version 2.3, Hasan Baig, Pedro Fontanarossa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox, Angel Goni Moreno, Thomas Gorochowski, Raik Grunberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novere, Zachary Palchick, Matthew Pocock, Nicholas Roehner, Herbert Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Logan Terry, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris Myers. Journal of Integrative Bioinformatics, 18 (3), Article 20200045, June 2021. https://doi.org/10.1515/jib-2020-0045
• Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs, Jacob Beal, Geoff S Baldwin, Natalie G Farny, Markus Gershater, Traci Haddock-Angelli, Russell Buckley-Taylor, Ari Dwijayanti, Daisuke Kiga, Meagan Lizarazo, John Marken, Kim de Mora, Randy Rettberg, Vishal Sanchania, Vinoo Selvarajah, Abigail Sison, Marko Storch, Christopher T. Workman and the iGEM Interlab Study Contributors. PLoS ONE, 16 (6): e0252263, June 2021, https://doi.org/10.1371/journal.pone.0252263
• A Lyapunov Analysis of a Most Probable Path Finding Algorithm, Yuanqiu Mo, Soura Dasgupta, Jacob Beal. IEEE Control Systems Letters, 6, pp. 1052--1057, June 2021.
• Priority-enabled Load Balancing for Dispersed Computing, Aaron Paulos, Soura Dasgupta, Jacob Beal, Yuanqiu Mo, Jon Schewe, Alexander Wald, Partha Pal, Richard Schantz, J Bryan Lyles. IEEE 5th International Conference on Fog and Edge Computing (ICFEC), May 2021.
• Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability, Jesse Tordoff, Matej Krajnc, Nicholas Walczak, Matthew Lima, Jacob Beal, Stanislav Shvartsman, Ron Weiss. Cell Reports Physical Science 2 (1), 100305, January 2021. (preprint version)
• TASBE Image Analytics: A Processing Pipeline for Quantifying Cell Organization from Fluorescent Microscopy Nicholas Walczak, Jacob Beal, Jesse Tordoff, Ron Weiss, chapter in ``Programmed Morphogenesis'', ed. Mo R Ebrahimkhan, Joshua Hislop, Series: Methods in Molecular Biology, vol 2258. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1174-6_1, 2021 (online December 2020).
  (preprint version)
• Levels of Autonomy in Synthetic Biology Engineering Jacob Beal and Miles Rogers. Molecular Systems Biology, 16(12), e10019, December 2020.
• Field-based Coordination with the Share Operator Giorgio Audrito, Jacob Beal, Ferruccio Damiani, Danilo Pianini, and Mirko Viroli. Logical Methods in Computer Science, vol 16, October 2020.
  arXiv preprint, October 2019. https://arxiv.org/abs/1910.02874 (cached)
• Robust Estimation of Bacterial Cell Count from Optical Density Jacob Beal, Natalie G. Farny, Traci Haddock-Angelli, Vinoo Selvarajah, Geoff S. Baldwin, Russell Buckley-Taylor, Markus Gershater, Daisuke Kiga, John Marken, Vishal Sanchania, Abigail Sison, Christopher T. Workman, and the iGEM Interlab Study Contributors. Nature Communications Biology, 3(1), pp. 1--29, September 2020.
  bioRxiv preprint, October 2019. https://doi.org/10.1101/803239
• The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering James Alastair McLaughlin, Jacob Beal, Goksel Misirli, Raik Grunberg, Bryan A Bartley, James Scott-Brown, Prashant Vaidyanathan, Pedro Fontanarrosa, Ernst Oberortner, Anil Wipat, Thomas E Gorochowski, Chris J Myers. Frontiers in Bioengineering and Biotechnology, 8:1009, https://doi.org/10.3389/fbioe.2020.01009, September 2020.
• Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL) Bradley Brown, Bryan Bartley, Jacob Beal, Jasmine E Bird, Angel Goni-Moreno, James Alastair McLaughlin, Goksel Misirli, Nicholas Roehner, David James Skelton, Chueh Loo Poh, Irina Dana Ofiteru, Katherine James, Anil Wipat. ACS Synthetic Biology, 9(9), pp. 2410--2417, September, 2020. (preprint version)
• Improving Collection Dynamics by Monotonic Filtering Hunza Zainab, Giorgio Audrito, Soura Dasgupta, Jacob Beal. Workshop on Engineering Collective Adaptive Systems (eCAS), August 2020.
• Round-Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis Daniel Bryce, Robert P. Goldman, Matthew DeHaven, Jacob Beal, Tramy Nguyen, Nicholas Walczak, Mark Weston, George Zheng, Josh Nowak, Joe Stubbs, Niall Gaffney, Matthew Vaughn, Chris Myers. 12th International Workshop on Bio-Design Automation (IWBDA), August 2020.
• Intent Parser: a tool for codifying experiment design Tramy Nguyen, Nicholas Walczak, Jacob Beal, Daniel Sumorok, Mark Weston. 12th International Workshop on Bio-Design Automation (IWBDA), August 2020.
• Collaborative Terminology: SBOL Project Dictionary Jacob Beal, Daniel Sumorok, Bryan Bartley, Tramy Nguyen. 12th International Workshop on Bio-Design Automation (IWBDA), August 2020.
• Describing engineered biological systems with SBOL3 and ShortBOL2 Matthew Crowther, Lewis Grozinger, James McLaughlin, Goksel Misirli, Jacob Beal, Bryan A. Bartley, Angel Goñi-Moreno, Anil Wipat. 12th International Workshop on Bio-Design Automation (IWBDA), August 2020.
• A resilient leader election using aggregate programming blocks Yuanqiu Mo, Giorgio Audrito, Soura Dasgupta, and Jacob Beal. International Federation of Automatic Control World Congress (IFAC) 2020, July 2020.
• Synthetic Biology Open Language (SBOL) Version 3.0.0 Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Jacob Beal, Matthew Crowther, Thomas E Gorochowski, Raik Grunberg, Goksel Misirli, James Scott-Brown, Ernst Oberortner, Anil Wipat, Chris J Myers. Journal of Integrative Bioinformatics, 17(2-3), 20200017. https://doi.org/10.1515/jib-2020-0017, June, 2020.
• Synthetic Biology Open Language Visual (SBOL Visual) Version 2.2 Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Michael Bissell, Kevin Clancy, Robert Sidney Cox, Angel Goni Moreno, Thomas Gorochowski, Raik Grunberg, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novere, Zachary Palchick, Matthew Pocock, Nicholas Roehner, Herbert Sauro, James Scott-Brown, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Marta Vazquez Vilar, Christopher A Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris Myers. Journal of Integrative Bioinformatics, 17(2-3), 20200014. https://doi.org/10.1515/jib-2020-0014, June 2020.
• The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise? Jacob Beal, Angel Goñi Moreno, Chris Myers, Ariel Hecht, María del Carmen de Vicente, Maria Parco, Markus Schmidt, Kenneth Timmis, Geoff Baldwin, Steffi Friedrichs, Paul Freemont, Daisuke Kiga, Elena Ordozgoiti, Maja Rennig, Leonardo Rios, Kristie Tanner, Víctor de Lorenzo, Manuel Porcar, EMBO Reports, 21(5), e50521, May 2020. (preprint version)
• Embrace experimentation in biosecurity governance Sam Weiss Evans, Jacob Beal, Kavita Berger, Diederik A Bleijs, Alessia Cagnetti, Francesca Ceroni, Gerald L Epstein, Natalia Garcia-Reyero, David R Gillum, Graeme Harkess, Nathan J Hillson, Petra AM Hogervorst, Jacob L Jordan, Geneviève Lacroix, Rebecca Moritz, Sean S OhEigeartaigh, Megan J Palmer, Mark WJ van Passel. Science, 368(6487), pp. 138--140, April 2020. (preprint version)
• SBOL Visual 2 Ontology Goksel Misirli, Jacob Beal, Thomas E Gorochowski, Guy-Bart Stan, Anil Wipat, Chris J Myers, ACS Synthetic Biology, 9(4), pp. 972--977, March 2020.
• ShortBOL: A language for scripting designs for engineered biological systems using Synthetic Biology Open Language (SBOL) Matthew Crowther, Lewis Grozinger, Matthew Pocock, Christopher PD Taylor, James A McLaughlin, Goksel Misirli, Bryan A Bartley, Jacob Beal, Angel Goñi-Moreno, Anil Wipat. ACS Synthetic Biology, 9(4), pp. 962--966, March 2020.
• Organizing Genome Editing for the Gigabase Scale Bryan Bartley, Jacob Beal, Jonathan Karr, and Elizabeth Strychalski. Nature Communications, February 2020, doi:10.1038/s41467-020-14314-z
  Prior arXiv version: https://arxiv.org/abs/1909.01468
• Highly Distinguished Amino Acid Sequences of 2019-nCoV, Jacob Beal, Thomas Mitchell, Daniel Wyschogrod, Jeff Manthey, Adam Clore, bioRxiv preprint, January, 2020. https://doi.org/10.1101/2020.01.31.929497
• From Distributed Coordination to Field Calculus and Aggregate Computing Mirko Viroli, Jacob Beal, Ferruccio Damiani, Giorgio Audrito, Roberto Casadei, Danilo Pianini. Journal of Logical and Algebraic Methods in Programming, vol. 109, article 100486, December 2019.
• Global Uniform Asymptotic Stability of a Generalized Adaptive Bellman-Ford Algorithm Yuanqiu Mo, Soura Dasgupta, and Jacob Beal. IEEE Conference on Decision and Control (CDC), December 2019.
• Technological challenges and milestones for writing genomes Nili Ostrov, Jacob Beal, Tom Ellis, D. Benjamin Gordon, Bogumil J. Karas, Henry H. Lee, Scott C. Lenaghan, Jeffery A. Schloss, Giovanni Stracquadanio, Axel Trefzer, Joel S. Bader, George M. Church, Cintia M. Coelho, J. William Efcavitch, Marc Guell, Leslie A. Mitchell, Alec A. K. Nielsen, Bill Peck, Alexander C. Smith, C. Neal Stewart Jr., and Hille Tekotte. Science, 366(6463), pp. 310--312, October 2019.
• High-performance chemical-and light-inducible recombinases in mammalian cells and mice Benjamin H. Weinberg, Jang Hwan Cho, Yash Agarwal, N. T. Hang Pham, Leidy D. Caraballo, Maciej Walkosz, Charina Ortega, Micaela Trexler, Nathan Tague, Billy Law, William K. J. Benman, Justin Letendre, Jacob Beal, and Wilson W. Wong. Nature Communications 10, Article 4845, October 2019.
• Robustness of the Adaptive Bellman-Ford Algorithm: Global Stability and Ultimate Bounds Yuanqiu Mo, Soura Dasgupta, and Jacob Beal. IEEE Transactions on Automatic Control, 64(10), pp. 4121--4136, October 2019.
• New Distributed Constraint Reasoning Algorithms for Load Balancing in Edge Computing Khoi D. Hoang, Christabel Wayllace, William Yeoh, Jacob Beal, Soura Dasgupta, Yuanqiu Mo, Aaron Paulos, and Jon Schewe. 22nd International Conference on Principles and Practice of Multi-Agent Systems (PRIMA '19), October 2019.
• Communicating Structure and Function in Synthetic Biology Diagrams, Jacob Beal, Tramy Nguyen, Thomas E. Gorochowski, Angel Goni-Moreno, James Scott-Brown, James Alastair McLaughlin, Curtis Madsen, Benjamin Aleritsch, Bryan Bartley, Shyam Bhakta, Mike Bissell, Sebastian Castillo Hair, Kevin Clancy, Augustin Luna, Nicolas Le Novere, Zach Palchick, Matthew Pocock, Herbert Sauro, John T. Sexton, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris Myers, and Anil Wipat. ACS Synthetic Biology, 8(8), pp. 1818-1825, August 2019.
• Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) Nicholas Roehner, Bryan Bartley, Jacob Beal, James McLaughlin, Matthew Pocock, Michael Zhang, Zach Zundel, and Chris J. Myers. ACS Synthetic Biology, 8(7), pp. 1519-1523 July 2019.
• TASBE Flow Analytics: A Package for Calibrated Flow Cytometry Analysis, Jacob Beal, Cassandra Overney, Aaron Adler, Fusun Yaman, Lisa Tiberio, and Meher Samineni. ACS Synthetic Biology, 8(7), pp 1524--1529, July 2019. (cached PDF)
• The Morphogen Circuit Builder and Compiler Bryan Bartley, Brian Basnight, Jesse Tordoff, Jacob Beal, Ron Weiss. 11th International Workshop on Bio-Design Automation (IWBDA), July 2019.
• SBOL Visual 2 Ontology Goksel Misirli, Jacob Beal, Thomas E. Gorochowski, Guy-Bart Stan, Anil Wipat, Chris Myers. 11th International Workshop on Bio-Design Automation (IWBDA), July 2019.
• Synthetic Biology Open Language (SBOL) Version 2.3 Curtis Madsen, Angel Goni Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox, Thomas Gorochowski, Raik Grunberg, Chris Macklin, James McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris Myers, Ernst Oberortner, Herbert Sauro, Anil Wipat. Journal of Integrative Bioinformatics, June 2019, from doi:10.1515/jib-2019-0025
• Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1 Curtis Madsen, Angel Goni Moreno, Zachary Palchick, Umesh P, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Mike Bissell, Kevin Clancy, Robert Sidney Cox, Thomas Gorochowski, Raik Grunberg, Augustin Luna, James McLaughlin, Tramy Nguyen, Nicolas Le Novere, Matthew Pocock, Herbert Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris Myers, Jacob Beal, Anil Wipat. Journal of Integrative Bioinformatics, June 2019, from doi:10.1515/jib-2018-0101
• Opportunities and Challenges in Applying Artificial Intelligence to Bioengineering Fusun Yaman, Aaron Adler, and Jacob Beal. chapter in ``Automated Reasoning for Systems Biology and Medicine,'' ed. Petro Lio, Paolo Zuliani, Springer Publishing, pp 425--452, June 2019.
• The share operator for field-based coordination Giorgio Audrito, Jacob Beal, Ferruccio Damiani, Danilo Pianini, and Mirko Viroli. International Conference on Coordination Languages and Models (COORDINATION '19), June 2019.
• A Framework for Self-Adaptive Dispersal of Computing Services Aaron Paulos, Soura Dasgupta, Jacob Beal, Yuanqiu Mo, Khoi Hoang, J. Bryan Lyles, Partha Pal, Richard Schantz, Jon Schewe, Ramesh Sitaraman, Alexander Wald, Christabel Wayllace, and William Yeoh. Workshop on Engineering Collective Adaptive Systems (eCAS), June 2019.
• New Distributed Constraint Satisfaction Algorithms for Load Balancing in Edge Computing: A Feasibility Study Khoi D. Hoang, Christabel Wayllace, William Yeoh, Jacob Beal, Soura Dasgupta, Yuanqiu Mo, Aaron Paulos, and Jon Schewe. International Workshop on Optimization In Multi-Agent Systems (OptMAS-19), May 2019.
• Standards to Enable Genome-Scale Engineering, Bryan Bartley, Jacob Beal, Jonathan R. Karr, Elizabeth A. Strychalski, GP-Write Consortium, March 2019.
• A Higher-Order Calculus of Computational Fields, Giorgio Audrito, Mirko Viroli, Ferruccio Damiani, Danilo Pianini, and Jacob Beal. ACM Transactions on Computational Logic (TOCL), 20(1), Article 5, January 2019.
  An associated journal-first abstract was also presented at FORTE '19
• Selecting and assessing challenge problems, Jared Freeman, Drew Leins, Conrad Bell IV, and The SD2 Research Consortium. Theoretical Issues in Ergonomics Science, 20(1), pp. 27-38, January 2019.
• Robust Stability of Spreading Blocks in Aggregate Programming, Yuanqiu Mo, Soura Dasgupta and Jacob Beal, IEEE Conference on Decision and Control (CDC), December 2018.
  Received Outstanding Student Paper Award.
• Small molecule-based regulation of gene expression for RNA-delivered circuits in mammalian cells, Tyler E Wagner, Jacob R Becraft, Katie Bodner, Brian Teague, Xin Zhang, Amanda Woo, Ely Porter, Bremy Alburquerque, Brian Dobosh, Oliwia Andries, Niek N Sanders, Jacob Beal, Douglas Densmore, Tasuku Kitada, and Ron Weiss. Nature Chemical Biology, 14 (11), pp. 1043?1050, November 2018.
• Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL), Bradley Brown, Christian Atallah, James Alastair McLaughlin, Goksel Misirli, Angel Goni-Moreno, Nicholas Roehner, David James Skelton, Bryan Bartley, Jacob Beal, Chueh Loo Poh, Irina Dana Ofiteru, and Anil Wipat. bioRxiv preprint, November, 2018. http://dx.doi.org/10.1101/463844
• 2018 Semiconductor Synthetic Biology Roadmap, Victor Zhrinov, et al., Semiconductor Research Corporation, October, 2018.
• Formalizing Sample Transformation Plans, Daniel Bryce, Robert Goldman, Ugur Kuter, Alex Plotnick, Matt DeHaven, Chris Geib, Jake Beal, Nic Roehner and Bryan Bartley. AAAI Fall Symposium on AI for Synthetic Biology, October 2018.
• Time to get serious about measurement in synthetic biology, Jacob Beal, Traci Haddock-Angelli, Natalie Farny, Randy Rettberg. Trends in Biotechnology, 36 (9), pp. 869?871, September 2018
• An Aggregate Computing Approach to Self-Stabilizing Leader Election, Yuanqiu Mo, Jake Beal and Soura Dasgupta. Workshop on Engineering Collective Adaptive Systems (eCAS), September 2018.
• Toward Programming 3D Shape Formation in Mammalian Cells, Jesse Tordoff, Jacob Beal, Ron Weiss, Bryan Bartley, Gizem Gumuskaya, Katherine Kiwimagi, Matej Krajnc, Kevin Lebo, Stanislav Shvartsman, Allen Tseng and Nicholas Walczak. 10th International Workshop on Bio-Design Automation (IWBDA), August 2018.
• The Synthetic Biology Open Language Supports Integration of the Engineering Life-Cycle for Synthetic Biologists, Bryan Bartley, Christian Atallah, Alasdair Humphries, Vishwesh Kulkarni, Curtis Madsen, Goksel Misirli, Angel Goni-Moreno, Tramy Nguyen, Ernst Oberortner, Nicholas Roehner, Meher Samineni, Zach Zundel, Jacob Beal, Chris Myers, Herbert Sauro, Anil Wipat. 10th International Workshop on Bio-Design Automation (IWBDA), August 2018.
• Specifying Combinatorial Designs with the Synthetic Biology Open Language, Nicholas Roehner, Bryan Bartley, Jacob Beal, James McLaughlin, Matthew Pocock, Michael Zhang, Zach Zundel, Chris Myers and Anil Wipat. 10th International Workshop on Bio-Design Automation (IWBDA), August 2018.
• Quantification of Bacterial Fluorescence using Independent Calibrants, , Jacob Beal, Traci Haddock-Angelli, Geoff Baldwin, Markus Gershater, Ari Dwijayanti, Marko Storch, Kim de Mora, Meagan Lizarazo, Randy Rettberg, and the iGEM Interlab Study Contributors. PLoS ONE, 13 (6): e0199432, June 2018
• Space-Time Universality of Field Calculus, Giorgio Audrito, Jacob Beal, Ferruccio Damiani, Mirko Viroli, International Conference on Coordination Languages and Models (COORDINATION '18), June 2018.
• From Field-Based Coordination to Aggregate Computing, Mirko Viroli, Jacob Beal, Ferruccio Damiani, Giorgio Audrito, Roberto Casadei, Danilo Pianini, International Conference on Coordination Languages and Models (COORDINATION '18), June 2018.
• XPlan: Experiment Planning for Synthetic Biology, Ugur Kuter, Robert P Goldman, Daniel Bryce, Jacob Beal, Matthew DeHaven, Christopher S. Geib, Alexander F. Plotnick, Tramy Nguyen, Nicholas Roehner. Hierarchical Planning, June 2018.
• Engineering modular intracellular protein sensor-actuator devices, Velia Siciliano, Breanna DiAndreth, Blandine Monel, Jacob Beal, Jin Huh, Kiera L Clayton, Liliana Wroblewska, AnneMarie McKeon, Bruce D Walker, Ron Weiss. Nature Communications, 9(1), Article 1881. May, 2018
• Adaptive Opportunistic Airborne Sensor Sharing, Jacob Beal, Kyle Usbeck, Joseph Loyall, Mason Rowe, James Metzler. ACM Transactions on Autonomous and Adaptive Systems (TAAS), 13(1): Article 6, April 2018
• Synthetic Biology Open Language (SBOL) Version 2.2.0, Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grunberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris Myers, Herbert Sauro, Anil Wipat. Journal of Integrative Bioinformatics, 15 (1), April, 2018. (cached PDF)
  Also published as: BioBricks Foundation Request for Comments (BBF RFC) #114.
• Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0, Robert Sidney Cox, Curtis Madsen, James McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas Gorochowski, Raik Grunberg, Augustin Luna, Nicolas Le Novere, Matthew Pocock, Herbert Sauro, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris Myers, Jacob Beal, and Anil Wipat, Journal of Integrative Bioinformatics, March, 2018. (cached PDF)
  Also published as: BioBricks Foundation Request for Comments (BBF RFC) #115.
• Engineering Resilient Collective Adaptive Systems by Self-Stabilisation Mirko Viroli, Giorgio Audrito, Jacob Beal, Ferruccio Damiani, and Danilo Pianini. ACM Transactions on Modeling and Computer Simulation (TOMACS), 18 (2), Article 16, March 2018. (cached PDF)
• Managing Bioengineering Complexity, Fusun Yaman, Aaron Adler, Jacob Beal. 30th innovative Applications of Artificial Intelligence (IAAI-18), February 2018
• Self-Adaptation to Device Distribution in the Internet of Things, Jacob Beal, Mirko Viroli, Danilo Pianini, and Ferruccio Damiani. ACM Transactions on Autonomous and Adaptive Systems, 12 (3), Article 12, September 2017.
• Error in Self-Stabilizing Spanning-Tree Estimation of Collective State Yuanqiu Mo, Jacob Beal, and Soura Dasgupta, Workshop on Engineering Collective Adaptive Systems (eCAS), September 2017.
• Towards a Foundational API for Resilient Distributed Systems Design Matteo Francia, Danilo Pianini, Jacob Beal, and Mirko Viroli, Workshop on Engineering Collective Adaptive Systems (eCAS), September 2017.
• A Visual Language for Protein Design, Robert Sidney Cox, James Alastair McLaughlin, Raik Grunberg, Jacob Beal, Anil Wipat, and Herbert M Sauro. ACS Synthetic Biology, August, 2017.
• Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads, Jacob Beal, Nicholas DeLateur, Brian Teague, Ron Weiss, John Sexton, Sebastian Castillo-Hair, and Jeffrey J. Tabor. peer-reviewed abstract in 9th International Workshop on Bio-Design Automation, August 2017.
• Biochemical complexity drives log-normal variation in genetic expression, Jacob Beal, Engineering Biology, 1.1 (2017), pp. 55-60, July 2017. (cached preprint)
• A Standard-Enabled Workflow for Synthetic Biology, Chris J. Myers, Jacob Beal, Thomas E. Gorochowski, Hiroyuki Kuwahara, Curtis Madsen, James Alastair McLaughlin, Goksel Misirli, Tramy Nguyen, Ernst Oberortner, Meher Samineni, Anil Wipat, Michael Zhang, and Zach Zundel. Biochemical Society Transactions, 45 (3) 793-803, June 2017
• Summary Report for the SemiSynBio Workshop on an EDA/BDA Interaction Roadmap, Jacob Beal and Brian Bramlett, Semiconductor Research Corporation, May 2017.
• Reducing DNA context dependence in bacterial promoters, Swati Banerjee Carr, Jacob Beal, and Douglas M. Densmore. PLoS ONE 12(4): e0176013, April 2017. (cached PDF)
• Mathematical Foundations of Variation in Gene Expression, Jacob Beal, IET/SynBiCITE Engineering Biology Conference, December 2016.
• A Lyapunov Analysis for the Robust Stability of an Adaptive Bellman-Ford Algorithm, Soura Dasgupta and Jacob Beal, IEEE Conference on Decision and Control (CDC), December 2016.
• Synthetic Biology Open Language (SBOL) Version 2.1.0, Jacob Beal, Robert Sidney Cox, Raik Grunberg, James McLaughlin, Tramy Nguyen, Chris Macklin, Michael Bissell, Curtis Madsen, Nicholas Roehner, Ernst Oberortner, Goksel Misirli, Kevin Clancy, Matthew Pocock, Zhen Zhang, Chris Myers, Michael Zhang, Meher Samineni, Zach Zundel, Bryan Bartley, Kiri Choi, John H. Gennari, Herbert Sauro. Journal of Integrative Bioinformatics, 13(3):291, December, 2016. (cached PDF)
  Also published as: BioBricks Foundation Request for Comments (BBF RFC) #112. doi:1721.1/105278, October 2016 (cached PDF))
• Managing Bioengineering Complexity with AI Techniques, Jacob Beal, Aaron Adler, and Fusun Yaman, Elsevier BioSystems, 148, October 2016, pp. 40-46. (cached PDF)
• Self-adaptation to Device Distribution Changes in Situated Computing Systems Jacob Beal, Mirko Viroli, Danilo Pianini, and Ferruccio Damiani, IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), September 2016.
  Received Best Paper Award
• Adaptive Task Reallocation for Airborne Sensor Sharing Jacob Beal, Kyle Usbeck, Joseph Loyall, Mason Rowe, and James Metzler, Workshop on Engineering Collective Adaptive Systems (eCAS), September 2016.
• Combining Self-Organisation and Autonomic Computing in CASs with Aggregate-MAPE Mirko Viroli, Antonio Bucchiarone, Danilo Pianini, and Jacob Beal, Workshop on Engineering Collective Adaptive Systems (eCAS), September 2016.
• Trading Accuracy for Speed in Approximate Consensus Jacob Beal, Knowledge Engineering Review: Special Issue on Spatial Computing, 31 (4), pp 325--342, September 2016.
• Design for Improved Repression in RNA Replicons, Jacob Beal and Ron Weiss, peer-reviewed abstract in 8th International Workshop on Bio-Design Automation, August 2016.
• Resiliency with Aggregate Computing: State of the Art and Roadmap Mirko Viroli and Jacob Beal, Workshop on FORmal methods for the quantitative Evaluation of Collective Adaptive SysTems (FORECAST), July 2016.
• Aggregate Programming: From Foundations to Applications, Jacob Beal and Mirko Viroli. chapter in "Formal Methods for the Quantitative Evaluation of Collective Adaptive Systems." ed. Marco Bernardo, Rocco De Nicola, and Jane Hillston, Springer International Publishing, pp 233-260, June 2016.
• Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs, Nathan J. Hillson, Hector A. Plahar, Jacob Beal, and Ranjini Prithviraj, ACS Synthetic Biology, 5 (6), pp 449--451, June 2016.
• Sharing Structure and Function in Biological Design with SBOL 2.0, Nicholas Roehner, Jacob Beal, Kevin Clancy, Bryan Bartley, Goksel Misirli, Raik Grunberg, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Michael Zhang, Zhen Zhang, Zach Zundel, Douglas Densmore, John H. Gennari, Anil Wipat, Herbert M. Sauro, and Chris J. Myers, ACS Synthetic Biology, 5 (6), pp 498--506, June 2016.
• IWBDA 2015 (editorial) Jacob Beal, ACS Synthetic Biology, 5 (6), pp 443, June 2016.
• Improving gossip dynamics through overlapping replicates, Danilo Pianini, Jacob Beal, and Mirko Viroli, International Conference on Coordination Languages and Models, June 2016.
• Opportunistic Sharing of Airborne Sensors Jacob Beal, Kyle Usbeck, Joseph Loyall, and James Metzler, International Conference on Distributed Computing in Sensor Systems (DCOSS), May, 2016.
• libSBOLj 2.0: A Java Library to Support SBOL 2.0, Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Goksel Misirli, Matthew Pocock, Ernst Oberortner, Meher Samineni, Zach Zundel, Jacob Beal, Kevin Clancy, Anil Wipat, and Chris Myers, IEEE Life Sciences Letters, 1 (4), pp 34--37, April 2016.
• Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli, Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Kim de Mora, Meagan Lizarazo, Jim Hollenhorst, Randy Rettberg, with the iGEM Interlab Study Contributors, PLoS ONE 11(3): e0150182. doi:10.1371/journal.pone.0150182. March 2016.
• A Type-Sound Calculus of Computational Fields Ferruccio Damiani, Mirko Viroli, Jacob Beal, Science of Computer Programming, Volume 117, pp 17--44, doi:10.1016/j.scico.2015.11.005, February 2016.
• CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology, Sonya V. Iverson, Traci L. Haddock, Jacob Beal, and Douglas M. Densmore, ACS Synthetic Biology, 5 (1), pp 99-103, January 2016.
• SBOL Visual: Standard Schematics for Synthetic Genetic Constructs, Jacqueline Quinn, Robert Sidney Cox III, Aaron Adler, Jacob Beal, Swapnil Bhatia, Yizhi Cai, Joanna Chen, Kevin Clancy, Michal Galdzicki, Nathan J. Hillson, Nicolas Le Novere, Akshay J Maheshwari, James Alastair McLaughlin, Chris J. Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Larisa Soldatova, Guy-Bart V Stan, Neil Swainston, Anil Wipat, and Herbert M Sauro, PLoS Biology 13(12): e1002310. doi:10.1371/journal.pbio.1002310, December 2015.
• Cas9 gRNA engineering for selectable genome editing, activation and repression, Samira Kiani, Alejandro Chavez, Marcelle Tuttle, Richard N Hall, Raj Chari, Dmitry Ter-Ovanesyan, Jason Qian, Benjamin W Pruitt, Jacob Beal, Suhani Vora, Joanna Buchthal, Emma J K Kowal, Mohammad R Ebrahimkhani, James J Collins, Ron Weiss, and George Church, Nature Methods, Nature Methods 12(11), pp 1051-1054, November 2015. (supplementary information)
• Engineering multi-agent systems with aggregate computing, Danilo Pianini, Mirko Viroli, and Jacob Beal, Principles and Practice of Multi-Agent Systems (PRIMA 2015), October 2015.
• Aggregate Programming for the Internet of Things, Jacob Beal, Danilo Pianini, and Mirko Viroli, IEEE Computer, 48(9), pp 22-30, September 2015.
• Efficient Engineering of Complex Self-Organizing Systems by Self-Stabilising Fields, Mirko Viroli, Jacob Beal, Ferruccio Damiani, and Danilo Pianini, IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), September 2015.
• Distributed Recovery for Enterprise Services, Shane S. Clark, Jacob Beal, and Partha Pal, IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), September 2015.
• Toward Predicting Distributed Systems Dynamics, Amy Kumar, Jacob Beal, Soura Dasgupta, Raghuraman Mudumbai, Spatial and COllective PErvasive Computing Systems (SCOPES) workshop at IEEE SASO, September 2015.
• Design of Biological Circuits Using Signal-to-Noise Ratio, Jacob Beal, International Workshop on Bio-Design Automation (IWBDA), August 2015.
• Copyright and Licensing of BBF RFCs, Jacob Beal, Drew Endy, David Grewal, Richard Johnson, Richard, Linda Kahl, BioBricks Foundation Request for Comments (BBF RFC) #107, August 2015. http://hdl.handle.net/1721.1/98266
  I noticed that the BBF RFC copyright licensing in BBF RFC #0 needed an update, and this document enacts it.
• Synthetic Biology Open Language (SBOL) Version 2.0.0, Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris Myers, Anil Wipat and Herbert Sauro. Journal of Integrative Bioinformatics, 12(2):272, September, 2015. http://dx.doi.org/10.2390/biecoll-jib-2015-272
  Also published as: BioBricks Foundation Request for Comments (BBF RFC) #108. doi:1721.1/98369
  Associated abstract at IWBDA'15
• Formal Foundations of Sensor Network Applications, Jacob Beal and Mirko Viroli, SIGSPATIAL Special, Volume 7, Number 2, pp. 36 - 42, July 2015.
• Signal-to-noise ratio measures efficacy of biological computing devices and circuits, Jacob Beal, Frontiers in Bioengineering and Biotechnology, Volume 3, Article #93, June 2015. (cached PDF)
• Space-time Programming, Jacob Beal and Mirko Viroli, Philosophical Transactions of the Royal Society A, Volume 373, Issue 2046, pages 20140220, June 2015.
• Superdiffusive Dispersion and Mixing of Swarms, Jacob Beal, ACM Transactions on Autonomous and Adaptive Systems, Volume 10, Issue 2, Article #10, June 2015.
• Code Mobility Meets Self-Organisation: a Higher-order Calculus of Computational Fields, Ferruccio Damiani, Mirko Viroli, Danilo Pianini, and Jacob Beal, Formal Techniques for Distributed Objects, Components, and Systems, pp. 113-128, June 2015.
• Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition, Noah Davidsohn, Jacob Beal, Samira Kiani, Aaron Adler, Fusun Yaman, Yinqing Li, Zhen Xie, and Ron Weiss, ACS Synthetic Biology, doi: dx.doi.org/10.1021/sb500263b, 4 (6), pp 673-681, June 2015 (online November 2014). (supplementary information)
  
• Protelis: Practical Aggregate Programming, Danilo Pianini, Mirko Viroli, Jacob Beal, ACM Symposium on Applied Computing 2015, April 2015.
• Bridging the Gap: A Roadmap to Breaking the Biological Design Barrier, Jacob Beal, Frontiers in Bioengineering and Biotechnology, 2:87. doi:10.3389/fbioe.2014.00087, January 2015.
• Model-Driven Engineering of Gene Expression from RNA Replicons, Jacob Beal, Tyler E. Wagner, Tasuku Kitada, Odisse Azizgolshani, Jordan Moberg Parker, Douglas Densmore, and Ron Weiss, ACS Synthetic Biology, dx.doi.org/10.1021/sb500173f, 4 (1), pp 48--56, January 2015 (supplementary information).
  
• Proposed Data Model for the Next Version of the Synthetic Biology Open Language, Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Jacob Beal, Kevin Clancy, Curtis Madsen, Goksel Misirli, Anil Wipat, Herbert Sauro, and Chris J. Myers, ACS Synthetic Biology, dx.doi.org/10.1021/sb500176h, 4 (1), pp 57--71, January 2015.
  
• Managing Design Change with Functional Blueprints, Jacob Beal, Aaron Adler, Fusun Yaman, Jeffrey Cleveland, Hala Mostafa, Annan Mozeika, Kyle Usbeck, Gretchen Markiewicz, and Benjamin Axelrod, in "Through-life Engineering Services" ed. Louis Redding and Rajkumar Roy, Springer International Publishing, pp 269-284, doi: http://dx.doi.org/10.1007/978-3-319-12111-6_16, December 2014.
• Building blocks for aggregate programming of self-organising applications, Jacob Beal and Mirko Viroli, Workshop on Fundamental of Collective Adaptive Systems (FoCAS), September 2014.
• CRISPR transcriptional repression devices and layered circuits in mammalian cells, Samira Kiani, Jacob Beal, Mohammad R Ebrahimkhani, Jin Huh, Richard N Hall, Zhen Xie, Yinqing Li and Ron Weiss. Nature Methods, 11 (7), pp. 723-726, July 2014. (supplementary information)
  
• Precision Design of Expression from RNA Replicons, Jacob Beal, Tyler E. Wagner, Tasuku Kitada, Andrey Krivoy, Odisse Azizgolshani, Jordan Moberg Parker, Douglas Densmore, and Ron Weiss, International Workshop on Bio-Design Automation (IWBDA), June 2014.
  
• The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology, Michal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grunberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Chris J Myers, and Herbert M Sauro, Nature Biotechnology, 32(6), June 2014.
• Towards a Unified Model of Spatial Computing, Jacob Beal, Mirko Viroli, and Ferruccio Damiani, 7th Spatial Computing Workshop (SCW'14), May 2014.
  
• On the Evaluation of Space-Time Functions, Jacob Beal, Kyle Usbeck, and Brett Benyo, The Computer Journal, December 2013.
• Functional synthesis of genetic regulatory networks, Jacob Beal and Aaron Adler, Workshop on Functional Programming Concepts in Domain-Specific Languages at 18th ACM SIGPLAN International Conference on Functional Programming (ICFP 2013), pp. 3-10, September 2013.
• QuaFL: A typed DSL for quantum programming, Andrei Lapets, Marcus Da Silva, Michael Thome, Aaron Adler, Jacob Beal, and Martin Roetteler, Workshop on Functional Programming Concepts in Domain-Specific Languages at 18th ACM SIGPLAN International Conference on Functional Programming (ICFP 2013), pp. 19-26, September 2013.
  
• Superdiffusive Dispersion and Mixing of Swarms with Reactive Levy Walks, Jacob Beal, IEEE SASO, September 2013.
  
• WebProto: Aggregate Programming for Everyone, Kyle Usbeck and Jacob Beal, demonstration abstract, IEEE SASO, September 2013.
• Spatial Computing Meets Realistic Mobile Wireless Problems, Bernat Wiandt, Vilmos Simon, Andras Kokuti, and Jacob Beal, demonstration abstract, IEEE SASO, September 2013.
• A Calculus of Computational Fields, Mirko Viroli, Ferruccio Damiani, and Jacob Beal, 12th International Workshop on
  Foundations of Coordination Languages and Self Adaptive Systems (FOCLASA'13), September 2013.
• Precise Mass-Market Energy Demand Management Through Stochastic Distributed Computing, Alex Papalexopoulos, Jacob Beal, and Steven Florek, IEEE Transactions on Smart Grid, online publication August 2013.
• A Morphogenetically Assisted Design Variation Tool, Aaron Adler, Fusun Yaman, Jacob Beal, Jeffrey Cleveland, Hala Mostafa, and Annan Mozeika, AAAI, July 2013.
• How can AI help Synthetic Biology?, Fusun Yaman, Aaron Adler, and Jacob Beal, abstract for senior member talk, AAAI, July 2013.
• Synthetic Biology Open Language Visual: an ontological use case, Jacqueline Quinn, Michal Galdzicki, Robert Sidney Cox III, Jacob Beal, Kevin Clancy, Nathan Hillson, and Larisa Soldatova, extended abstract at Bio-Ontologies, July 2013.
  
• Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition, Noah Davidsohn, Jacob Beal, Aaron Adler, Fusun Yaman, Yinqing Li, Zhen Xie, and Ron Weiss, peer-reviewed abstract in 5th International Workshop on Bio-Design Automation, July 2013.
• Online Tools for Characterization, Design, and Debugging, Aaron Adler, Fusun Yaman, and Jacob Beal, peer-reviewed abstract in 5th International Workshop on Bio-Design Automation, July 2013.
• Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology, Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Robert Sidney Cox III, Michal Galdzicki, Nathan Hillson, Akshay Maheshwari, Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Herbert M Sauro, Larisa Soldatova, Guy-Bart Stan, Mandy Wilson, and Drew Endy, peer-reviewed abstract in 5th International Workshop on Bio-Design Automation, July 2013.
• Recent Advances in the Synthetic Biology Open Language, Michal Galdzicki, Ernst Oberortner, Matthew Pocock, Jacqueline Quinn, Mandy Wilson, Evan Appleton, Bryan Bartley, Jacob Beal, Swapnil Bhatia, Robert Cox, Raik Gruunberg, Goksel Misirli, Hector Plahar, Nicholas Roehner, Larisa Soldotova, Guy-Bart Stan, Doug Densmore, Chris J. Myers, Herbert Sauro, and Anil Wipat, peer-reviewed abstract in 5th International Workshop on Bio-Design Automation, July 2013.
• Mixed Geometric-Topological Representation for Electromechanical Design, Jacob Beal, Aaron Adler, and Hala Mostafa, GECCO 2013, July 2013.
• Accelerating Approximate Consensus with Self-Organizing Overlays, Jacob Beal, 6th Spatial Computing Workshop, May 2013.
• Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0,  Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Nathan Hillson, Michal Galdzicki, Akshay Maheshwari, Umesh P, Matthew Pocock, Cesar Rodriguez, Guy-Bart Stan, Drew Endy, BioBricks Foundation Request for Comments (BBF RFC) #93. March 2013. http://hdl.handle.net/1721.1/78249
  
• Operational Semantics of Proto, Mirko Viroli, Jacob Beal, and Kyle Usbeck, Science of Computer Programming, 78(6), pp. 633-656, 2013. (cached preprint)
  
• Better Living Through Manifold Geometry, Jacob Beal, Stefan Dulman, Olivier Michel, and Antoine Spicher, editorial introduction to Special Issue on Spatial Computing, The Computer Journal, online publication December 2012.
  
• Organizing the Aggregate: Languages for Spatial Computing, Jacob Beal, Stefan Dulman, Kyle Usbeck, Mirko Viroli, and Nikolaus Correll, chapter in "Formal and Practical Aspects of Domain-Specific Languages: Recent Developments", ed. Marjan Mernik, IGI Global, December 2012.
  Preprint available on arXiv, CoRR, abs/1202.5509v2, April 2012.
• A Tactical Command Approach to Human Control of Vehicle Swarms, Jacob Beal, AAAI 2012 Fall Symposium "Human Control of Bio-Inspired Swarms," November, 2012.
  
• Engineered Self-Organization Approaches to Adaptive Design, Jacob Beal, 2012 Conference on Through-Life Engineering Services, November 2012.
  
• Synthetic Biology Open Language (SBOL) Version 1.1.0, Michal Galdzicki, Mandy Wilson, Cesar A. Rodriguez, Matthew R. Pocock, Ernst Oberortner, Laura Adam, Aaron Adler, J. Christopher Anderson, Jacob Beal, Yizhi Cai, Deepak Chandran, Douglas Densmore, Omri A. Drory, Drew Endy, John H. Gennari, Raik Grunberg, Timothy S. Ham, Nathan J. Hillson, Jeffrey D. Johnson, Allan Kuchinsky, Matthew W. Lux, Curtis Madsen, Goksel Misirli, Chris J. Myers, Carlos Olguin, Jean Peccoud, Hector Plahar, Darren Platt, Nicholas Roehner, Evren Sirin, Trevor F. Smith, Guy-Bart Stan, Alan Villabos, Anil Wipat, and Herbert M. Sauro, BioBricks Foundation Request for Comments (BBF RFC) #87, October 2012.
  Prior version: SBOL Version 1.0.0, BBF RFC #84, October 2011.
• Fast Precise Distributed Control for Energy Demand Management, Jacob Beal, Jeff Berliner, and Kevin Hunter, IEEE SASO 2012, September 2012.
  
• A Dimensionless Graceful Degradation Metric for Quantifying Resilience, Jacob Beal, Workshop on Evaluation of Self-Adaptive and Self-Organizing Systems, IEEE SASO, September, 2012.
  
• An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications, Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman, ACS Synthetic Biology, online publication July 2012. (cached preprint)
• Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks, Fusun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob Beal, ACS Synthetic Biology, online publication July 2012. (cached preprint)
  
• A Manifold Operator Representation for Adaptive Design, Jacob Beal, Hala Mostafa, Benjamin Axelrod, Annan Mozeika, Aaron Adler, Gretchen Markiewicz, and Kyle Usbeck, GECCO 2012, July 2012.
  
• Linda in Space-Time: An Adaptive Coordination Model for Mobile Ad-Hoc Environments, Mirko Viroli, Danilo Pianini, and Jacob Beal, Coordination 2012, June 2012.
  
• Lightweight Simulation Scripting with Proto, Jacob Beal, Kyle Usbeck and Brian Krisler, 5th Spatial Computing Workshop (SCW'12) at AAMAS 2012, June 2012.
  Kyle's talk is available here.
  
• Results from TASBE, Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman, peer-reviewed abstract in 4th International Workshop on Bio-Design Automation, June 2012.
• Toward Automated Design of Cell State Detectors, Jacob Beal and Fusun Yaman, peer-reviewed abstract in 4th International Workshop on Bio-Design Automation, June 2012.
• A Method for Fast, High-Precision Characterization of Synthetic Biology Devices, Jacob Beal, Ron Weiss, Fusun Yaman, Noah Davidsohn, and Aaron Adler, MIT CSAIL Tech Report 2012-008, April, 2012.
  
• Cross Domain Identity Management and Entitlement, Michael Atighetchi, Jonathan Webb, Jacob Beal, Brian Krisler, and Michael Mayhew, Military Communications Conference (MILCOM), November 2011.
  Note: not publicly distributed.
• An Agent Framework for Agent Societies, Kyle Usbeck and Jacob Beal, Actors and Agents Reloaded (AGERE) workshop at SPLASH 2011, October 2011.
  
• On the Evaluation of Space-Time Functions, Jacob Beal and Kyle Usbeck, 4th Spatial Computing Workshop (SCW'11) at IEEE SASO 2011, October 2011.
• Using Morphogenetic Models to Develop Spatial Structures, Jacob Beal, Jessica Lowell, Annan Mozeika, and Kyle Usbeck, 4th Spatial Computing Workshop (SCW'11) at IEEE SASO 2011, October 2011.
  
• Morphogenetically Assisted Design Variation, Aaron Adler, Fusun Yaman, Jeffrey Cleveland, and Jacob Beal, 2nd International Conference on Morphological Computation, September 2011.
  
• Bridging Biology and Engineering Together with Spatial Computing, Jacob Beal, extended abstract for 12th International Conference on Membrane Computing, August 2011.
  
• Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks, Jacob Beal, Ting Lu, Ron Weiss, PLoS ONE 6(8): e22490. doi:10.1371/journal.pone.0022490, August 2011.
  
• Functional Blueprints: An Approach to Modularity in Grown Systems, Jacob Beal, Swarm Intelligence Journal, 5(3-4), p257-281, June 2011 (preprint, supplementary information).
  A book chapter version also appears in the book "Morphogenetic Engineering: Toward Programmable Complex Systems", edited by Rene Doursat, Hiroki Sayama, and Olivier Michel, Springer, December 2012. Prior conference version in 7th International Conference on Swarm Intelligence (ANTS 2010), September 2010.
• High-Level Programming Languages for Bio-Molecular Systems, Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai, chapter in "Design and Analysis of Bio-Molecular Circuits", edited by Heinz Koeppl, Douglas Densmore, Mario di Bernardo, Gianluca Setti, Springer, 2011 (preprint).
  
• TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering, Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Fusun Yaman, Richard Schantz, Joseph Loyall, peer-reviewed abstract in 3rd International Workshop on Bio-Design Automation, June 2011.
• Toward Automated Selection of Parts for Genetic Regulatory Networks, Fusun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, Jacob Beal, Ron Weiss, and Noah Davidsohn, peer-reviewed abstract in 3rd International Workshop on Bio-Design Automation, June 2011.
  
• A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering, Viktor Vasilev, Chenkai Liu, Traci Haddock, Swapnil Bhatia, Aaron Adler, Fusun Yaman, Jacob Beal, Jonathan Babb, Ron Weiss, and Douglas Densmore, peer-reviewed abstract in 3rd International Workshop on Bio-Design Automation, June 2011.
  
• Core Operational Semanics of Proto, Mirko Viroli, Jacob Beal, and Matteo Casadei, ACM Symposium on Applied Computing 2011, March 2011.
  
• A Spatial Computing Approach to Distributed Algorithms, Jacob Beal and Richard Schantz, 44th Asilomar Conference on Signals, Systems, and Computers, November 2010.
• Adjustable Autonomy for Cross-Domain Entitlement Decisions, Jacob Beal, Jonathan Webb, and Michael Atighetchi, 3rd ACM workshop on Artificial Intelligence and Security (AISec), October 2010.
  
• Distributed Control for Small Customer Energy Demand Management, Vinayak V. Ranade, and Jacob Beal, IEEE SASO 2010, September 2010.
  Vinayak's presentation is available here
• A Basis Set of Operators for Space-Time Computations, Jacob Beal, 3rd Spatial Computing Workshop, September 2010.
  
• Composable Continuous Space Programs for Robotic Swarms, Jonathan Bachrach, Jacob Beal, and James McLurkin, Neural Computing and Applications, Special Issue on Swarms, Volume 19, Issue 6 (2010), pages 825-847.
• Spectrum Curricula: Design and Initial Results, Jacob Beal, Alice Leung, and Robert Laddaga, Learning By Demonstration section of 2010 AAAI Robotics Exhibition, July 2010.
  
• Spectrum Curricula for Measuring Teachability, Jacob Beal, Alice Leung, and Robert Laddaga, Workshop on Agents Learning Interactively from Human Teachers, at AAMAS 2010, May 2010.
• Laplacian-Based Consensus on Spatial Computers, Nelson Elhage and Jacob Beal, 9th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2010), May 2010.
• Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems Sagar Indurkhya and Jacob Beal, in PLoS ONE 5(1): e8125. doi:10.1371/journal.pone.0008125, January 2010.
  Code for the LOLCAT algorithm is available in MIT DSpace
• LTML - A Language for Representing Semantic Web Service Workflow Procedures, Mark Burstein, Robert P. Goldman, Drew V. McDermott, David McDonald, Jacob Beal, and John Maraist, workshop on "Semantics for the Rest of Us -- Variants of Semantic Web Languages in the Real World", at 8th International Semantic Web Conference, October 2009
• Dynamically Defined Processes for Spatial Computers, Jacob Beal, Spatial Computing Workshop 2009, September 2009.
• Enhancing Methodological Rigor for Computational Cognitive Science: Complexity Analysis Jacob Beal and Jennifer Roberts, Cognitive Science Conference, July 2009.
• Enhancing Methodological Rigor for Computational Cognitive Science: Core Tenets and Ad Hoc Residuals Jennifer Roberts and Jacob Beal, Cognitive Science Conference, July 2009.
• Self-Managing Associative Memory for Dynamic Acquisition of Expertise in High-Level Domains, Jacob Beal, IJCAI 2009, July 2009.
• Programming Manifolds, Jacob Beal and Jonathan Bachrach, Dagstuhl Seminar 06361: Computing Media and Languages for Space-Oriented Computation, Andre DeHon, Jean-Louis Giavitto, and Frederic Gruau eds, December, 2006. Updated version published as MIT CSAIL Tech Report 2009-023, June, 2009.
• Research Challenges in Information Systems for the Next Generation Electric Grid, Richard Schantz, Jacob Beal, Joseph Loyall, Partha Pal, Kurt Rohloff, and Azer Bestavros, NITRD Workshop on New Research Directions for Future Cyber-Physical Energy Systems, June 2009.
  
• Fast Self-Stabilization for Gradients, Jacob Beal, Jonathan Bachrach, Dan Vickery, and Mark Tobenkin, IEEE DCOSS 2009, June 2009.
  An extension and discrete-network proof tightening the bounds from our previous Constraint and Restoring Force gradient paper.
• Behavior Modes for Randomized Robotic Coverage, Jacob Beal, Nikolaus Correll, Leonardo Urbina, and Jonathan Bachrach, Second International Conference on Robot Communication and Coordination, April 2009.
• Curricula and Metrics to Investigate Human-Like Learning Jacob Beal, Paul Robertson, and Robert Laddaga, AAAI 2009 Spring Symposium "Agents that Learn from Human Teachers", March, 2009.
• Amorphous Computing, Hal Abelson, Jacob Beal, and Gerald Jay Sussman, article in "Encyclopedia of Complexity and System Science" Springer-Verlag, March 2009.
  Draft available as MIT CSAIL Tech Report 2007-030, June 2007
•  Flexible Self-Healing Gradients, Jacob Beal, ACM Symposium on Applied Computing 2009, March 2009.
• Engineered Robustness by Controlled Hallucination, Jacob Beal and Gerald Jay Sussman, AAAI 2008 Fall Symposium "Naturally-Inspired Artificial Intelligence", November 2008.
• Cells Are Plausible Targets for High-Level Spatial Languages, Jacob Beal and Jonathan Bachrach, Spatial Computing Workshop, October 2008.
• Empirical Characterization of Discretization Error in Gradient-based Algorithms, Jonathan Bachrach, Jacob Beal, Joshua Horowitz, and Dany Qumsiyeh, IEEE SASO 2008, October 2008.
• Cognitive Security for Personal Devices, Rachel Greenstadt and Jacob Beal, First ACM workshop on AISec, October 2008.
  This is a position paper on attaining more human-like security by having a device imprint on a broad-spectrum collection of passively available biometrics. A prior version was published as MIT CSAIL Tech Report 2008-016, in March 2008.
• PACEM: Cooperative Control for Citywide Energy Management, Jacob Beal and Hal Abelson, whitepaper, August 2008.
• Analyzing Composability in a Sparse Encoding Model of Memorization and Association, Jacob Beal and Thomas F. Knight, Jr, IEEE 7th International Conference on Development and Learning (ICDL 2008), August 2008.
• Learning Composable Signals for a Cognitive Substrate, Jacob Beal, Cognitive Science Conference, July 2008.
• Autonomy in Spatial Computing, Jonathan Bachrach and Jacob Beal, Third Workshop on Hot Topics in Autonomic Computing, June 2008.
• Shared Focus of Attention for Heterogeneous Agents, Jacob Beal, Short Paper, 7th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2008), May 2008.
• Fast Self-Healing Gradients, Jacob Beal, Jonathan Bachrach, Dan Vickery, and Mark Tobenkin, ACM Symposium on Applied Computing 2008, March 2008.
  Received Best Paper Award (Artificial Intelligence & Agents Theme); Also available as MIT CSAIL Tech Report 2007-050
• Learning by Learning to Communicate, Jacob Beal, PhD Thesis, August 2007.
  Also listed as Tech Report MIT-CSAIL-TR-2007-042. If you have difficulty with the PDF, try it in postscript
• Constraint and Restoring Force, Jacob Beal, Jonathan Bachrach, and Mark Tobenkin, MIT CSAIL Tech Report 2007-044, August 2007.
• Continuous Space-Time Semantics Allow Adaptive Program Execution, Jonathan Bachrach, Jacob Beal, and Takeshi Fujiwara. IEEE SASO 2007, July 2007.
  Also available as MIT CSAIL Tech Report 2007-038
• Developmental Cost for Models of Intelligence, Jacob Beal, AAAI 2007 Workshop on Evaluating Architectures for Intelligence, July 2007.
  Also listed as Tech Report MIT-CSAIL-TR-2007-026
• Building Spatial Computers, Jonathan Bachrach and Jacob Beal, MIT CSAIL Tech Report 2007-017, March 2007.
• Sidestepping Impossibility: Combat Consensus in the Assassins' Guild., Jacob Beal, MIT CSAIL Student Workshop 2006, September 2006.
  Followup to the first Assassins' Guild paper, this one examines carefully how combat consensus gets around an impossibility result.
• What the Assassins' Guild Taught Me About Distributed Computing, Jacob Beal, International Conference on Complex Systems (ICCS) 2006, June 2006. (Also MIT CSAIL Technical Report MIT-CSAIL-TR-2006-038)
  The deeper I look at how live action roleplaying runs distributed simulations, the more surprises I find. I think there's something here for computer scientists to pay attention to.
• Programming a Sensor Network as an Amorphous Medium, Jonathan Bachrach and Jacob Beal, extended abstract for poster at IEEE DCOSS 2006, June 2006.
  Our poster at DCOSS.
• Infrastructure for Engineered Emergence on Sensor/Actuator Networks, Jacob Beal and Jonathan Bachrach, IEEE Intelligent Systems, (Vol. 21, No. 2) pp. 10-19, March/April 2006.
  Preprint version of the article and sidebar.
• CogSci to AI: It's the Brainware, Stupid!, Jacob Beal and Gerald Jay Sussman, AAAI 2006 Spring Symposium "Between a Rock and a Hard Place: Cognitive Science Principles Meet AI-Hard Problems", Stanford, March 2006.
• Amorphous Medium Language, Jacob Beal, Large-Scale Multi-Agent Systems Workshop at AAMAS 2005, July 2005.
• Learning From Snapshot Examples, Jacob Beal, MIT AI Memo 2005-012, April 2005.
  The ideas in this memo need more contextualizion w.r.t. other machine learning work. As it stands, it documents an abstraction barrier and learning heuristic I needed and was unable to find elsewhere. Obsoleted by the IIES mechanism in my PhD thesis.
• Shrinking the Leap of Faith, Jacob Beal and Tim Shepard, unpublished draft, March 2005.
  This sketches some ideas about exploiting the locality of wireless connections to make it easier to establish trust with distant servers on the Internet.
• Biologically-Inspired Robust Spatial Programming, Jacob Beal and Gerald Sussman, MIT AI Memo 2005-001, January 2005.
• Programming an Amorphous Computational Medium, Jacob Beal, in Unconventional Programming Paradigms International Workshop, September 2004. Updated version in LNCS Vol. 3566, August 2005.
• Deamplification of DoS Attacks via Puzzles, Jacob Beal and Tim Shepard, unpublished draft, October 2004.
  Tim was trying to figure out whether the puzzles in the IETF's proposed Host Identity Protocol were actually a useful defense against an attacker with a large network of hijacked computers. We found out that it is.
• Predictive Modelling for Fisheries Management in the Colombian Amazon, Jacob Beal and Sara Bennett, International Conference on Complex Systems (ICCS) 2004, June 2004.
  
• RamboNodes for the Metropolitan Ad Hoc Network, Jacob Beal and Seth Gilbert, MIT AI Memo 2003-027.
  A tightened version was published in Workshop on Dependability in Wireless Ad Hoc Networks and Sensor Networks, part of the International Conference on Dependable Systems and Networks, June 2004.
• Leveraging Language into Learning, PhD Proposal, February 2004.
  Previously partially developed in AI Memo 2003-007
• Near-Optimal Distributed Failure Circumscription, Jacob Beal, AI Memo 2003-017, August 2003.
• A Robust Amorphous Hierarchy from Persistent Nodes, Jacob Beal, AI Memo 2003-012, May 2003.
• Persistent Nodes for Reliable Memory in Geographically Local Networks, Jacob Beal, AI Memo 2003-011, April 2003.
• Leaderless Distributed Hierarchy Formation, Jacob Beal, AI Memo 2002-021, December 2002.
  This didn't work as well as I wanted, and led me to start working with Persistent Nodes for hierarchy formation instead.
• Amorphous Infrastructure for Language Implementation, Ryan Newton and Jacob Beal, MIT CSAIL Tech Report 2006-015, December 2002.
  Written as a project in an Amorphous Computing seminar, this work was the origin of the Persistent Node algorithm. We made an official recording of it in 2006 to make referencing easier.
• An Algorithm for Bootstrapping Communications, Jacob Beal, International Conference on Complex Systems (ICCS), June 2002.
  A longer version appears as AI Memo 2001-016, August 2001.
• Generating Communications Systems Through Shared Context, Jacob Beal, Master's Thesis, AI Tech Report 2002-002, January 2002.
• The Development of a Small Autonomous Helicopter Robot for Search and Rescue in Hostile Environments, Jacob Beal, Carl Blaurock, Keith Bonawitz, Kyrilian Dyer, Paul Elliott, Paul Eremenko, Eric Feron, Emilio Frazzoli, Benjamin Ingram, Michael Lester, Manway Liu, Stefan Marti, Joshua Napoli, Kailas Narendran, and Scott Rasmussen, Proceedings of the AUVSI Annual Symposium, July, 1999.
  

Tutorials and Survey Talks

General Interest

• Building an Open Bioeconomy, iGEM Open Talks, September 2021.
• Surviving Life as a Researcher, presented at IEEE SASO 2016 Doctoral Symposium, September 2016. An updated version was presented in the Biomedical Engineering Seminar, University of Iowa, February 2018 (PowerPoint version)
  

Synthetic Biology

• Synthetic Biology Open Language: Data Model version 3, 15th International Workshop on Bio-Design Automation (IWBDA), September, 2023.
• Integrating DBTL with Agile Data Curation, EMSL Integration 2022: AI/ML for advancing discoveries in biological and environmental sciences, Richland, Washington, October 2022.
• Automating Laboratory Protocols with the Protocol Activity Modeling Language, 14th International Workshop on Bio-Design Automation (IWBDA), October, 2022.
• SBOL Version 3: Data Exchange throughout the Bioengineering Lifecycle, 14th International Workshop on Bio-Design Automation (IWBDA), October, 2022.
  Prior version given in 13th IWBDA in September, 2021.
• Introduction to the Protocol Activity Modeling Language (PAML), HARMONY 2022, April 2022.
• Quantifying fluorescence and cell count with plate readers, iGEM 2021 Summer Webinar Series, June 2021.
  Prior version given in iGEM 2020 Summer Webinar Series in July 2020.
• Quantifying fluorescence and cell phenotypes with flow cytometry, iGEM 2021 Summer Webinar Series, June 2021.
  Prior version given in iGEM 2020 Summer Webinar Series in July 2020.
• Analysis and visualisation of gene expression data, After iGEM Academic Publishing Workshops, May, 2021. (PowerPoint version)
• Precision genetic device engineering with TASBE Flow Analytics, NIST Flow Cytometry Standards Consortium Workshop, February, 2021.
• From Art to Engineering in Synthetic Biology, Build-a-Cell Workshop, January 2021.
• SBOL Version 3: Simplified Data Exchange for Bioengineering, COMBINE, October, 2020.
• Introductory SBOL Workshop, 12th International Workshop of Bio-Design Automation, August 2020.
  Prior versions given at 11th IWBDA in July 2019, 10th IWBDA in August 2018, 9th IWBDA in August 2017, 8th IWBDA in August 2016.
• Biological Information Processing: From Experimentation to Engineering, Given 3 times, at Microsoft Research UK, University of Bristol, and Imperial College London, March 2020.
• SBOL Visual: Diagrams for Synthetic Biology, International Genetically Engineered Machine Jamboree (iGEM 19), November 2019.
• Paths to Resilient Biological Information Processing CalTech, October, 2019.
  Similar talks were given at the Workshop on Bio-Design for Portability (BD4P), July 2019 and University College London, July 2019.
• Software Tools for Synthetic Biology Workflows, International Genetically Engineered Machine Jamboree (iGEM 18), October 2018.
• Engineering Complex Behaviors in Biological Organisms, University of Arizona, June, 2018.
• Software Workflows for Synthetic Biology, Synthetic Biology: Engineering, Evolution and Design (SEED 18), June 2018
• Foundations for Engineered Biomolecular Circuits, Newcastle University, May, 2018.
• Foundational Metrology for Engineering Biomolecular Circuits, Dagstuhl Seminar 18082, “Formal Methods for the Synthesis of Biomolecular Circuits”, February 2018
• Engineering Complex Behaviors in Biological Organisms, ACM Boston, May 2017.
  Similar talks were given at the 26th GLSVLSI Conference, May 2016, the National Institute of Standards and Technology in April 2016, and at the University of Iowa in December 2015.
• High-Level Genetic Circuit Design: The Proto BioCompiler, MIT, March 2014.
• TASBE Synthetic Biology Tools, Boston University, June 2013. Also given at MIT in July 2013 and June 2014.

Aggregate Computing

Note: many of the aggregate computing / spatial computing talks break to demonstration in Proto partway through, using a sequence of examples. This collection of demonstration code may be used to execute the examples.

• Aggregate Programming: From Theory to Resilient IoT Services, University of Iowa, March 2017.
• Morphogenetic Engineering: the Bilateria approach to design, Morphogenetic Prototyping Workshop, Adelaide, Australia, November 2016.
• Aggregate Programming (PowerPoint with Animations)
  Plenary talk at 10th International Conference on Swarm Intelligence, September 2016.
• Engineering Complex Behaviors in Biological Organisms (PowerPoint with Animations)
  Seminar at University of Iowa, December 2015.
• Engineering Self-Organization: From Networking to Synthetic Biology (PowerPoint with Animations)
  Dagstuhl Seminar Talk, October 2015.
• Ensuring Safe Composition of Distributed Processes (PowerPoint with Animations)
  Invited Talk at QA4SASO Workshop, September 2015.
• Metrology and Predictive Design for Synthetic Biology (PowerPoint with Animations), updated November 2013.
  
• Fast, Scalable Demand-Shaping with ColorPower (PowerPoint with Animations)
  Invited talk at Washington State University, January 2013, reprised in several other locations.
  
• Spatial Computing: From Manifold Geometry to Networking and Biology (PowerPoint with Animations)
  Invited talk at University of Iowa, February 2012.
• Spatial Computing: From Manifold Geometry to Biology; associated demonstration file.
  Presented at AMORPH 2010.
• Lecture Series: Spatial Computing: From global to local and back again
  • Lecture 1: Spatial Computers and Fields
  • Lecture 2: Continuous Space-Time Programs
  • Lecture 3: Discrete Approximation and Self-Healing
  • Lecture 4: Moving Devices
  • Lecture 5: Current Frontiers
  Presented at Third French Complex Systems Summer School, August 2009.
• Spatial Computing for Swarms; associated demonstration file.
  Presentation locations include IEEE SASO 2009 and RoboComm 2009.
• Pervasive Computing Focused: Spatial Approaches to Pervasive Computing; associated demonstration file.
  Presented with Marco Mamei and Christian Borcea at IEEE SASO 2008; proto-specific portions begin on page 110.
• Collaborative Networks Focused: Spatial Computing for Networked Collaboration; associated demonstration file.
  Presented at CTS 2010.

Other Talks

• Spatial computing: a unifying approach to computational materials, presented at Royal Society Meeting on Heterotic Computing, November 2013. (PowerPoint)
  
• Superdiffusive Dispersion and Mixing of Swarms with Reactive Levy Walks, presented at IEEE SASO, September 2013.
  
• The Importance of Asymmetry for Rapidly Reaching Consensus, presented at Socio-Technical Systems Workshop at IEEE SASO, September 2013. 
• Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition, presented at 5th International Workshop on Bio-Design Automation, July 2013.
  
• Accelerating Approximate Consensus with Self-Organizing Overlays, presented at 6th Spatial Computing Workshop, May 2013.
• SBOL in Action: The BBN BioCompiler, presented at SBOL Workshop, April 2013.
  
• High-Level BioDesign Automation, presented at Workshop on Semiconductor Concepts from Synthetic Biology (SemiSynBio), February, 2013. (PDF)
• From Spatial Computing to Tactical Command of Swarms, presented at AAAI 2012 Fall Symposium "Human Control of Bio-Inspired Swarms," November, 2012.
  Code for associated live Proto demonstration.
• Engineered Self-Organization Approaches to Adaptive Design, presented at 2012 Conference on Through-Life Engineering Services, November 2012. (pdf version)
  
• From Inspiration to Quantification, presented for IEEE SASO 2012 panel on New Research Directions, September 2012 (pdf).
  
• Fast Precise Distributed Control for Energy Demand Management, presented at IEEE SASO 2012, September 2012.
• A Dimensionless Graceful Degradation Metric for Quantifying Resilience, presented at Workshop on Evaluation of Self-Adaptive and Self-Organizing Systems, IEEE SASO, September, 2012.
• Organizing the Aggregate: Languages for Spatial Computing, presented at 5th Spatial Computing Workshop (SCW'12) at AAMAS 2012, June 2012.
  
• Problems of First-Class Functions over Space-Time, presented at New England Programming Language and Systems Symposium, June 2012.  OpenOffice version with animations.
  
• Automated Design of Synthetic Biology Feedback Circuits, presented at 2012 Institute of Biological Engineering Conference, March 2012.
  The abstract associated with the talk.
  
• On the Evaluation of Space-Time Functions, presented at 4th Spatial Computing Workshop (SCW'11) at IEEE SASO 2011, October 2011.
• Toward Breaking the Complexity Barrier for Synthetic Biology Therapeutics, presented at IEEE Engineering in Medicine and Biology, August 2011.
  
• Morphogenesis as a Reference Architecture for Engineered Systems, presented at 3rd International Workshop on Morphogenetic Engineering, August 2011.
  The two-page abstract associated with the talk.
• TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering, presented at 3rd International Workshop on Bio-Design Automation, June 2011.
• Core Operational Semanics of Proto, presented at ACM Symposium on Applied Computing 2011, March 2011.
  
• High-Level Languages for Synthetic Biology, presented at MIT Synthetic Biology Lunch seminar series, November 2010.
  
• Spatial Computing, Synthetic Biology, and Emerging IP Challenges, presented at Creative Commons, November 2010.
  
• A Spatial Computing Approach to Distributed Algorithms, presented at 44th Asilomar Conference on Signals, Systems, and Computers, November 2010.
• PACEM: The Colored Power Approach to Energy Demand Management, presented at MIT Energy Initiative Fall 2010 Conference, October 2010.
  
• Adjustable Autonomy for Cross-Domain Entitlement Decisions, presented at 3rd ACM workshop on Artificial Intelligence and Security (AISec), October 2010.
  
• A Basis Set of Operators for Space-Time Computations, presented at 3rd Spatial Computing Workshop, September 2010.
  
• Functional Blueprints: An Approach to Modularity in Grown Systems, presented at 7th International Conference on Swarm Intelligence (ANTS 2010), September 2010.
• Automatic Compilation from High-Level Languages to Genetic Regulatory Networks, presented at 2nd International Workshop on Bio-Design Automation, June 2010.
  The two-page abstract associated with the talk. A prior version was presented at the 2010 Institute of Biological Engineering Conference.
• Laplacian-Based Consensus on Spatial Computers, presented at 9th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2010), May 2010.
• Spectrum Curricula for Measuring Teachability, presented at Workshop on Agents Learning Interactively from Human Teachers, at AAMAS 2010, May 2010. A smaller, updated version of this talk was presented at the Robotics Exhibition Workshop at AAAI 2010 in July 2010.
• Dynamically Defined Processes for Spatial Computers, presented at Spatial Computing Workshop 2009, September, 2009.
• Enhancing Methodological Rigor for Computational Cognitive Science: Complexity Analysis, presented at Cognitive Science Conference, July 2009.
• Self-Managing Associative Memory for Dynamic Acquisition of Expertise in High-Level Domains, presented at IJCAI 2009, July 2009.
• Functional blueprints: a means of adaptive integration?, presented at First International Workshop on Morphogenetic Engineering, June 2009.
  The one-page abstract associated with the talk.
• Behavior Modes for Randomized Robotic Coverage, presented at Second International Conference on Robot Communication and Coordination, April, 2009.
• Flexible Self-Healing Gradients, presented at ACM Symposium on Applied Computing 2009, March 2009.
• Curricula and Metrics to Investigate Human-Like Learning, presented at AAAI 2009 Spring Symposium "Agents that Learn from Human Teachers", March, 2009.
• Empirical Characterization of Discretization Error in Gradient-based Algorithms, presented at IEEE SASO 2008, October 2008.
• Grand Challenge: Spatial Computing, presented for IEEE SASO 2008 panel on Grand Challenges, October 2008.
• Cells Are Plausible Targets for High-Level Spatial Languages, presented at Spatial Computing Workshop, October 2008. Also presented at 2009 Institute of Biological Engineering Conference.
• Spatial Computing and the Challenge of Engineered Emergence, presented at Harvard CRCS Privacy and Security Lunch Seminar, April 2008.
  A shorter, related talk, Autonomy in Spatial Computing was presented at the Third Workshop on Hot Topics in Autonomic Computing, June 2008.
• Fast Self-Healing Gradients, presented at ACM SAC 2008, March 2008.
  Associated paper won the Best Paper Award (Artificial Intelligence & Agents Theme).
• Programming Cell Aggregates, presented to the MIT Synthetic Biology Lunch, January 2008.
• Learning by Learning to Communicate, PhD Thesis Defense, MIT CSAIL, August, 2007. Material after page 43 is supplementary slides that were not used in the talk, but could be brought up to help respond to questions.
• Developmentally Inspired Cognitive Architectures, presented at AAAI 2007 Workshop on Evaluating Architectures for Intelligence, July 2007.
• Continuous Time Programming, presented at IEEE SASO 2007, July 2007.
• A Brief History of Amorphous Computing, internal presentation, April 2007.
  An informal talk explaining how my work fits into the larger context of amorphous computing. Take the categories with a grain of salt.
• Principles for Engineered Emergence, presented at Unconventional Computation: Quo Vadis?, March 2007. (Published as a CSAIL Work Product).
  The first talk explicitly about engineered self-organization. A shorter but more recent version was presented at ICCS in November, 2007
• Programming Spatial Computers, internal presentation, September 2006.
  A 5-minute summary of what the Amorphous Medium approach is all about, for new students at CSAIL.
• Programming Manifolds, presented at Dagstuhl Seminar 06361, "Computing Media and Languages for Space-Oriented Computation," Germany, September 2006.
  An expansion and update on the continuous semantics of Proto.
• Sidestepping Impossibility: Combat Consensus in the Assassins' Guild., presented at MIT CSAIL Student Workshop 2006, September 2006.
  See note above on the associated publication.
• What the Assassins' Guild Taught Me About Distributed Computing, presented at International Conference on Complex Systems (ICCS) 2006, June 2006.
  See note above on the associated publication.
• CogSci to AI: It's the Brainware, Stupid!, presented at AAAI 2006 Spring Symposium "Between a Rock and a Hard Place: Cognitive Science Principles Meet AI-Hard Problems", Stanford, March 2006.
• Integration by Coincidence: Status and Speculation, presented at MIT Biologically Inspired Cognitive Architectures (BICA) workshop, January 2006.
• Continuous Semantics of Proto, internal presentation, January 2006.
• Implementing Valiant's Neuro-Logic, internal presentation, December 2005.
• Amorphous Medium Language, presented at the Large-Scale Multi-Agent Systems (LSMAS) Workshop in AAMAS-05, Netherlands, July 2005.
  Contains a good overview of AML abstraction layers, execution model, and language concepts.
• Leveraging Language into Learning, presented at AAAI 2005 Doctoral Consortium, Pittsburgh, July 2005.
• Amorphous Computing's Programming Languages, internal presentation, April 2005.
• Learning from Snapshot Examples, presented in CSAIL Student Seminar, MIT, April 2005.
  See note above on the associated publication.
• Programming an Amorphous Medium, invited talk at Unconventional Programming Paradigms workshop, France, September 2004.
• Generating Communication Systems Through Shared Context, MIT RQE presentation, Spring 2004.
• Analyzing Failures as Noise Presented with Seth Gilbert at LIDS Student Conference 2004, MIT, January 2004.
  
• Near-Optimal Distributed Failure Circumscription, presented at PDCS 2003, Los Angeles, November 2003.

• Stability of Aggregate Computing Yuanqiu Mo, Ph.D. Thesis, University of Iowa, December 2019
• Software Compliance Testing for Workflows Using the Synthetic Biology Open Language Meher Samineni, M.S. Thesis, University of Utah, August 2018 &
• A Foundational Library for Aggregate Programming Matteo Francia, M.S. Thesis, Universita Bologna, March 2017.
• Reliable Gene Expression and Assembly for Synthetic Biological Devices in E. Coli Through Customized Promoter Insulator Elements and Automated DNA Assembly, Swati Banerjee Carr, Ph.D. Thesis, Boston University, July, 2016.
• Foundational Platform for Mammalian Synthetic Biology, Noah Davidsohn, Ph.D. Thesis, MIT, January, 2013.
  
• Model and Control for Cooperative Energy Management, Vinayak V. Ranade, M.Eng. Thesis, MIT, June 2010.
• A Distributed Building Evacuation System, Dany M. Qumsiyeh, M.Eng. Thesis, MIT, June 2008.

Rants & Ramblings

These are old and written informally, impolitely, and imprecisely, with the arrogance of a young grad student. Don't take them seriously unless they happen to inspire you...

• Human-Like vs. Complementary Intelligence
  I sometimes think that AI is incoherent because we mean different things when we say "intelligence". This rant tries to pry the definitions apart and figure out what human-like intelligence might mean. (October, 2004)
• How do we know when we're winning?
  Thoughts on AI research methodology presented during the Genesis Group's internal workshop in 2003.

Just for Fun

• Definitive Guide to Writing Guild Games for the Rest of Eternity, Jacob Beal and Joe Foley, in The Mechanicomicon Project, version 96, June 2010 (original publication in 2000).
  Not actually scientific writing at all, but an enjoyable (to me) rant on the writing of live action roleplaying games in the exceding particular culture of the MIT Assassin's Guild, written in the style of an extended flame back when I had just finished my undergraduate and updated a couple of times since. Mature content advisory.