Publications

PAPERCATEGORYYEAR OF PUBLICATION
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.Standards Work2017
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.Calibrated Flow Cytometery2017
Biochemical complexity drives log-normal variation in genetic expression, Jacob Beal, Engineering Biology, 1.1 (2017), pp. 55-60, July 2017. (cached preprint)Science2017
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 2017standards Work2017
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)2017
Mathematical Foundations of Variation in Gene Expression, Jacob Beal, IET/SynBiCITE Engineering Biology Conference, December 2016.Science2016
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))Standards Work2016
Managing Bioengineering Complexity with AI Techniques, Jacob Beal, Aaron Adler, and Fusun Yaman, Elsevier BioSystems, 148, October 2016, pp. 40-46. (cached PDF)AI2016
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.Replicons2016
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.Standards Work2016
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.Standards Work2016
IWBDA 2015 (editorial) Jacob Beal, ACS Synthetic Biology, 5 (6), pp 443, June 2016.2016
ibSBOLj 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.Standards Work2016
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.Calibrated Flow Cytometery2016
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 2016.2016
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.Standards Work2015
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)2015
Design of Biological Circuits Using Signal-to-Noise Ratio, Jacob Beal, International Workshop on Bio-Design Automation (IWBDA), August 2015.Science2015
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.Standards Work2015
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 Standards Work2015
Associated abstract at IWBDA'15Standards Work2015
Copyright and Licensing of BBF RFCs, Jacob Beal, Drew Endy, David Grewal, Richard Johnson, Richard, and Linda Kahl, BioBricks Foundation Request for Comments (BBF RFC) #107, August 2015. Standards Work2015
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)Science2015
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)Predictions2015
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.Science2015
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).Replicons2015
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.Standards Work2015
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)2014
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.Replicons2014
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.Standards Work2014
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.Science2013
How can AI help Synthetic Biology?, Fusun Yaman, Aaron Adler, and Jacob Beal, abstract for senior member talk, AAAI, July 2013.AI2013
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.Standards Work2013
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.Predictions2013
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.Predictions2013
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.Standards Work2013
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.Standards Work2013
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/1721.1/78249standards Work2013
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.standards Work2012
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)Tool Chain2012
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)Tool Chain; AI2012
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.Tool Chain2012
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.Predictions; AI2012
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.Calibrated Flow Cytometery2012
Bridging Biology and Engineering Together with Spatial Computing, Jacob Beal, extended abstract for 12th International Conference on Membrane Computing, August 2011.Science2011
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.Tool Chain2011
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).Tool Chain2011
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.Tool Chain2011
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.Part Seclection2011
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.Tool Chain2011
Cells Are Plausible Targets for High-Level Spatial Languages, Jacob Beal and Jonathan Bachrach, Spatial Computing Workshop, October 2008.Tool Chain2008
IWBDA 2014 A Adler ACS synthetic biology 4 (8), 867-867Science2014
Adler; Aaron Daniel; Beal, Jacob Stuart Michael; Yaman-Sirin, Fusun; Weiss, Ron; and Davidsohn, Noah Justin, inventors, Raytheon BBN Technologies Corp., assignee. Methods of evaluating gene expression levels. US patent US8809057 B2. January 4, 2012.Patent; Calibrated Flow Cytometery2012