Publications

PAPERCATEGORYYEAR OF PUBLICATION
Engineered yeast genomes accurately assembled from pure and mixed samples, Joseph H. Collins, Kevin W. Keating, Trent R. Jones, Shravani Balaji, Celeste B. Marsan, Marina Çomo, Zachary J. Newlon, Tom Mitchell, Bryan Bartley, Aaron Adler, Nicholas Roehner & Eric M. Young. Nature Communications volume 12, Article number: 1485, March 2021
2021
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, online May 2019. (cached PDF)Tool Chain2019
Standards to Enable Genome-Scale Engineering, Bryan Bartley, Jacob Beal, Jonathan R. Karr, Elizabeth A. Strychalski, GP-Write Consortium, March 2019.Standards Work2019
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.Science2018
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/10.1101/463844Standards Work2018
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.AI2018
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 20182018
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 2018.2018
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.Standard Works2018
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.Standard Works2018
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 2018Calibrated2018
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 2018.2018
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, 20182018
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.
Standard Works2018
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.
Standard Works2018
Managing Bioengineering Complexity, Fusun Yaman, Aaron Adler, Jacob Beal. 30th innovative Applications of Artificial Intelligence (IAAI-18), February 2018AI2018
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
IWBDA 2014 A Adler ACS synthetic biology 4 (8), 867-867Science2014
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
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
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
Synthetic Biology Open Language (SBOL) Version 2.3, Curtis Madsen, Angel Goñi Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox, Thomas Gorochowski, Raik Grünberg, 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 ORCID logo, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris Myers, Ernst Oberortner, Herbert Sauro and Anil Wipat, De Gruyter, June 13, 2019.
2019
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 ORCID logo and Anil Wipat, De Gruyter, June 13, 2019.
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 Publications, June 17, 2019.
2019
Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL) RETURN TO ISSUEPREVRESEARCH ARTICLENEXT
Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)
Bradley Brown, Bryan Bartley, Jacob Beal, Jasmine E. Bird, Ángel Goñi-Moreno, James Alastair McLaughlin, Göksel Mısırlı, Nicholas Roehner, David James Skelton, Chueh Loo Poh, Irina Dana Ofiteru, Katherine James, and Anil Wipat, ACS Publications, July 31, 2020.
2020
Verification of genetic engineering in yeasts with nanopore whole genome sequencing Joseph H. Collins, Kevin W. Keating, Trent R. Jones, Shravani Balaji, Celeste B. Marsan, Marina Çomo, Zachary J. Newlon, Tom Mitchell, Bryan Bartley, Aaron Adler, Nicholas Roehner, View ORCID ProfileEric M. Young, BioRxiv, March 5, 2020.2020
CMOS electrochemical imaging arrays for the detection and classification of microorganisms, Christopher E. Arcadia; Kangping Hu; Slava Epstein; Meni Wanunu; Aaron Adler; Jacob K. Rosenstein, IEEE, April 27, 2021.2021
Opportunities and Challenges in Applying Artificial Intelligence to Bioengineering, Fusun Yaman, Aaron Adler, Jacob Beal, Automated Reasoning for Systems Biology and Medicine pp 425-452, June 12, 2019.
2019
The long journey towards standards for engineering biosystems , 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, 6 May 2020.2020
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 Güell, Leslie A. Mitchell, Alec A. K. Nielsen, Bill Peck, Alexander C. Smith, C. Neal Stewart Jr., Hille Tekotte, Science Magazine, 18 Oct 2019.
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 & Wilson W. Wong, Nature Communications, 24 October 2019.2019
Organizing genome engineering for the gigabase scale, Bryan A. Bartley, Jacob Beal, Jonathan R. Karr & Elizabeth A. Strychalski, Nature Communications, 04 February 20202020
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 & iGEM Interlab Study Contributors, Nature, 17 September 2020.
2020
Embrace experimentation in biosecurity governance, Sam Weiss Evans, Jacob Beal, Kavita Berger, Diederik A. Bleijs, Alessia Cagnetti, Francesca Ceroni, Gerald L. Epstein, Natàlia Garcia-Reyero, David R. Gillum, Graeme Harkess, Nathan J. Hillson, Petra A. M. Hogervorst, Jacob L. Jordan, Geneviève Lacroix, Rebecca Moritz, Seán S. ÓhÉigeartaigh, Megan J. Palmer, Mark W. J. van Passel, Science Magazine, 10 Apr 2020.2020
Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability, Jesse Tordoff, Matej Krajnc, Nicholas Walczak, Matthew Lima, JacobBeal, Stanislav Shvartsman, Ron Weiss, Science Direct, January 20, 2021.2021
Levels of autonomy in synthetic biology engineering, Jacob Beal, Miles Rogers, Molecular Systems Biology, 1 December 2020.2020
Communicating Structure and Function in Synthetic Biology Diagrams, Jacob Beal, Tramy Nguyen, Thomas E. Gorochowski, Angel Goñi-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 Novère, Zach Palchick, Matthew Pocock, Herbert Sauro, John T. Sexton, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris Myers, and Anil Wipat, ACS Publications, July 26, 2019.2019
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering, James Alastair McLaughlin,Jacob Beal, Göksel Mısırlı, Raik Grünberg, Bryan A. Bartley, James Scott-Brown, Prashant Vaidyanathan, Pedro Fontanarrosa, Ernst Oberortner, Anil Wipat, Thomas E. Gorochowski, and Chris J. Myers, Frontiers in Bioengineering and Biotechnology, 2020.2020
TASBEImage Analytics: A Processing Pipeline for Quantifying Cell Organization from Fluorescent Microscopy, Nicholas Walczak, Jacob Beal, Jesse Tordoff, Ron Weiss, Programmed Morphogenesis pp 3-15, 20 December 2020.2020
Calibration Protocol-Plate Reader Fluorescence Calibration V. 3, Geoff Baldwin , Traci Haddock-Angelli , Jacob Beal , Ari Dwijayanti , Marko Storch , Natalie Farny , Cheryl Telmer, Alejandro Vignoni , Richard Tennant , Paul Rutten, iGEM, 2019.2019