Update the publications

[cjmyers]

• 1. J. Mante, Z. Sents, D. Britt, W. Mo, C. Liao, R. Greer, C. Myers, “SeqImprove: Machine Learning Assisted Curation of Genetic Circuit Sequence Information”, in ACS Synthetic Biology, 13(9): 3051-3055, September, 2024.
• 2. L.Buecherl,C.Myers,andP.Fontanarrosa,“EvaluatingtheContributionofModelComplexity in Predicting Robustness in Synthetic Genetic Circuits”, , in ACS Synthetic Biology, 13(9): 2742-2752, September, 2024.
• 3. M. Golebiewski, G. Bader, P. Gleeson, T. Gorochowski, M. Hucka, S. Keating, M. Konig, C. Myers, D. Nickerson, B. Sommer, D. Waltemath, and F. Schreiber, “Specifications of Standards in Systems and Synthetic Biology: Status, Developments, and Tools in 2024”, in Journal of Integrative Bioinformatics, vol. 21, no. 1, 2024.
• 4. D. Albin, L. Buecherl, E. Kochavi, E. Niehaus, S. Novack, S. Uragoda, C. Myers, and M. Alistar, “PhageBox: An Open Source Digital Microfluidic Extension with Applications for Phage Discovery”, in Transactions on Biomedical Engineering (TBME), 71(1): 217-226, January, 2024.
• 5. C. Berezin, L. Aguilera, S. Billerbeck, P. Bourne, D. Densmore, P. Freemont, T. Gorochowski, S. Hernandez, N. Hillson, C. King, M. Kopke, S. Ma, K. Miller, T. Moon, J. Moore, B. Munsky, C. Myers, D.. Nicholas, S. Peccoud, W. Zhou, J. Peccoud, “Ten simple rules for managing laboratory information”, in PLOS Computational Biology, December 7, 2023.
• 6. S.Zilberzwige-Tal,P.Fontanarrosa,D.Bychenko,Y.Dorfan,E.Gazit,C.Myers,“Investigating and Modeling the Factors that Affect Genetic Circuit Performance”, in ACS Synthetic Biology, 12(11): 3189-3204, November 2, 2023.
• 7. D. Densmore, N. Hillson, E. Klavins, C. Myers, J. Peccoud, G. Stracquadanio, “Introduction to the Special Issue on BioFoundries and Cloud 1 Laboratories”, in Journal of Emerging Tech- nologies in Computing Systems, 19(3): 1-2, August 1, 2023.
• 8. J. Mante and C. Myers, “Advancing Reuse of Genetic Parts: Progress and Remaining Chal- lenges”, in Nature Communications, 14(1): 2953, May 23, 2023.
• 9. S. Samineni, G. Vidal, C. Vidal-Cespedes, G. Yanez, T. Rudge, C. Myers, and J. Mante, “Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories”, in ACS Synthetic Biology, 12(4): 1364-1370, March 30, 2023.
• 10. B. Cummins, J. Vrana, R. Moseley, H. Eramian, A. Deckard, P. Fontanarrosa, D. Bryce, M. Weston, G. Zheng, J. Nowak, F. Motta, M. Eslami, K. Johnson, R. Goldman, C. Myers, T. Johnson, M. Vaughn, N. Gaffney, J. Urrutia, S. Gopaulakrishnan, V. Biggers, T. Higa, L. Mosqueda, M. Gameiro, T. Gedeon, K. Mischaikow, J. Beal, B. Bartley, T. Mitchell, T. Nguyen, N. Roehner, and S. Haase, “Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop”, in Oxford Synthetic Biology, 8(1), March 28, 2023.
• 11. Z. Sents, T. Stoughton, L. Buecherl, P. Thomas, P. Fontanarrosa, and C. Myers, “SynBioSuite: a Tool for Improving the Workflow for Genetic Design and Modeling”, in ACS Synthetic Biology, 12(3): 892-897, March 8, 2023.
• 12. M. Konig, P. Gleeson, M. Golebiewski, T. Gorochowski, M. Hucka, S. Keating, C. Myers, D. Nickerson, B. Sommer, D. Waltemath, and F. Schreiber, “Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022”, in Journal of Integrative Bioinformatics, vol. 20, no. 1, 2023.
• 13. L. Buecherl, T. Mitchell, J. Scott-Brown, P. Vaidyanathan, G. Vidal, H. Baig, B. Bartley, J. Beal, M. Crowther, P. Fontanarrosa, T. Gorochowski, R. Grunberg, V. Kulkarni, J. McLaughlin, G. Misirli, E. Oberortner, A. Wipat, and C. Myers, “Synthetic Biology Open Language (SBOL) Version 3.1.0”, in Journal of Integrative Bioinformatics, vol. 20, no. 1, 2023.
• 14. J. Mante, J. Abam, S. Samineni, I. Potzsch, J. Beal, C. Myers, “Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa”, in ACS Synthetic Biology, 12(1): 340- 346, January 3, 2023.
• 15. M. Ahmadi, P. Thomas, L. Buecherl, C. Winstead, C. Myers, H. Zheng, “A Comparison of Weighted Stochastic Simulation Methods for the Analysis of Genetic Circuits”, in ACS Synthetic Biology, 12(1): 287-304, December 30, 2022.
• 16. R. Goldman, R. Moseley, B. Cummins, J. Vrana, N. Roehner, K. Clowers, D. Bryce, J. Beal, M. DeHaven, J. Nowak, T. Higa, V. Biggers, P. Lee, J. Hunt, L. Mosqueda, S. Haase, M. Weston, G. Zheng, A. Deckard, S. Gopaulakrishnan, J. Stubbs, N. Gaffney, M. Vaugn, N. Maheshri, E. Mihalev, B. Bartley, R. Markeloff, T. Mitchell, T. Nguyen, D. Sumorok, N. Walczak, C. Myers, Z. Zundel, B. Hatch, J. Scholz, J. Colonna-Romano, “Highly-Automated, High-Throughput Replication of Yeast-based Logic Circuit Design Assessments”, in Oxford Synthetic Biology, 7(1), October 6, 2022.
• 17. B. Shaikh, L. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S. Andrews, A. Anwar, M. Beber, F. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, J. Cooper, J. Detloff, B. Drawert, M. Dumontier, G. Ermentrout, J. Faeder, A. Freiburger, F. Fröhlich, A. Funahashi, A. Garny, J. Gennari, P. Gleeson, A. Goelzer, Z. Haiman, J. Hasenauer, J. Hellerstein, H. Hermjakob, S. Hoops, J. Ison, D. Jahn, H. Jakubowski, R. Jordan, M. Kalaš, M. König, W. Liebermeister, R. Sheriff, S. Mandal, R. McDougal, J. Medley, P. Mendes, R. Müller, C. Myers, A. Naldi, T. Nguyen, D. Nickerson, B. Olivier, D. Patoliya, L. Paulevé, L. Petzold, A. Priya, A. Rampadarath, J. Rohwer, A. Saglam, D. Singh, A. Sinha, J. Snoep, H. Sorby, R. Spangler, J. Starruß, P. Thomas, D. Niekerk, D. Weindl, F. Zhang, A. Zhukova, A. Goldberg, J. Schaff, M. Blinov, H. Sauro, I. Moraru, J. Karr, “BioSimulators: a central registry of simulation engines and services for recommending specific tools”, in Nucleic Acids Research, 50(W1):W108–14, May 7, 2022.
• 18. L. Buecherl and C. Myers, “Engineering Genetic Circuits: Advancements in Genetic Design Automation Tools and Standards for Synthetic Biology”, in Current Opinions in Microbiology, August, 2022.
• 19. T. Jones, S. Oliveira, W. Jackson, C. Myers, C. Voigt, and D. Densmore, “Genetic Circuit Design Automation with Cello 2.0”, in Nature Protocols, 17: 1097-1113, February 23, 2022.
• 20. D. Bryce, R. Goldman, M. DeHaven, J. Beal, B. Bartley, T. Nguyen, N. Walczak, M. Weston, G. Zheng, J. Nowak, P. Lee, J. Stubbs, N. Gaffney, M. Vaughn, C. Myers, R. Moseley, S. Haase, A. Deckard, B. Cummins, and N. Leiby, “Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis” in ACS Synthetic Biology, 11(2): 608-622, January 21, 2022.
• 21. E. Yu, J. Mante, and C. Myers, “Sequence-based Searching for SynBioHub Using VSEARCH”, in ACS Synthetic Biology, 11(2): 990-995, January 21, 2022.
• 22. N. Roehner, J. Mante, C. Myers, and J. Beal, “Synthetic Biology Curation Tools (SYNBICT)”, in ACS Synthetic Biology, 10(11): 3200-3204, November 19, 2021.
• 23. L. Buecherl, R. Roberts, P. Fontanarrosa, P. Thomas, J. Mante, Z. Zhang, and C. Myers, “Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA”, in ACS Synthetic Biology, 10(10): 2532-2540, October 15, 2021.
• 24. J. Mante, N. Roehner, K. Keating, J. Mclaughlin, E. Young, J. Beal, and C. Myers, “Curation Principles Derived from the Analysis of the SBOL iGEM Data Set”, in ACS Synthetic Biology, 10(10): 2592-2606, October 15, 2021.
• 25. J. Mante, Y. Hao, J. Jett, U. Joshi, K. Keating, X. Lu, G. Nakum, N. Rodriguez, J. Tang, L. Terry, X. Wu, E. Yu, J. Downie, B. McInnes, M. Nguyen, B. Sepulvado, E. Young, and C. Myers, “The Synthetic Biology Knowledge System”, in ACS Synthetic Biology, 10(9): 2276-2285, September 17, 2021.
• 26. F. Schreiber, P. Gleeson, M. Golebiewski, T. Gorochowski, M. Hucka, S. Keating, M. Konig, C. Myers, D. Nickerson, B. Sommer, and D. Waltemath, “Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2021”, in Journal of Integrative Bioinfor- matics, 18(3), September, 2021.
• 27. H. Baig, P. Fontanarossa, J. McLaughlin, J. Scott-Brown, P. Vaidyanathan, T. Gorochowski, G. Misirli, J. Beal, and C. Myers, “Synthetic Biology Open Language Visual (SBOL Visual) Version 3.0”, in Journal of Integrative Bioinformatics, 18(3), September, 2021.
• 28. H. Baig, P. Fontanarossa, V. Kulkarni, J. McLaughlin, P. Vaidyanathan, B. Bartley, S. Bhakta, S. Bhatia, M. Bissell, K. Clancy, R. Cox, A. Moreno, T. Gorochowski, R. Grunberg, J. Lee, A. Luna, C. Madsen, G. Misirli, T. Nguyen, N. Le Novere, Z. Palchick, M. Pocock, N. Roehner, H. Sauro, J. Scott-Brown, J. Sexton, G.-B. Stan, J. Tabor, L. Terry, M. Vilar, C. Voigt, A. Wipat, D. Zong, Z. Zundel, J. Beal, and C. Myers, “Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3”, in Journal of Integrative Bioinformatics, 18(3), September, 2021.
• 29. B. Hatch, L. Meng, J. Mante, J. McLaughlin, J. Scott-Brown, and C. Myers, “VisBOL2 - Improving Web-based Visualization for Synthetic Biology Designs”, in ACS Synthetic Biology, 10(8): 2111-2115, August 20, 2021.
• 30. L. Terry, J. Earl, S. Thayer, S. Bridge, and C. Myers, “SBOLCanvas: A Visual Editor for Genetic Designs”, in ACS Synthetic Biology, 10(7): 1792-1796, July 16, 2021.
• 31. K. Kiwimagi, J. Letendre, B. Weinberg, J. Wang, M. Chen, L. Watanabe, C. Myers, J. Beal, W. Wong, and R. Weiss, “Quantitative Characterization of Recombinase-Based Digitizer Circuits Enables Predictable Amplification of Biological Signals”, in Nature Communications Biology, 4(875), July 15, 2021.
• 1. M. Ahmadi, L. Buecherl, C. Myers, Z. Zhang, C. Winstead, and H. Zheng, “Rare-Event Guided Analysis of Infinite-State Chemical Reaction Networks”, in 21th International Conference on Quantitative Evaluation of SysTems (QEST 2023), September, 2024.
• 2. J. Jeppson, M. Volk, B. Israelsen, R. Roberts, A. Williams, L. Buecherl, C. Myers, H. Zheng, C. Winstead, and Z. Zhang, “STAMINA in C++: Modernizing an Infinite-State Probabilis- tic Model Checker”, in 20th International Conference on Quantitative Evaluation of SysTems (QEST 2023), September, 2023.
• 3. R. Roberts, T. Neupane, L. Buecherl, C. Myers, and Z. Zhang, “STAMINA 2.0: Improving Scalability of Infinite-State Stochastic Model Checking”, in 23rd International Conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2022, January, 2022.

[cjmyers]

@tayasherstyukova 2024
@Parkerack 2023
@doublergreer 2022
@Drock54651 2021

[doublergreer]

For anyone getting stuck manually entering the information of publications: this is not the best way to do it. In order to save yourself some time, you can use the academic import command line to autogenerate pages.
pip3 install -U academic
Download the .bib file from the cite feature on the journal website to the folder (.bibtex will work too, just change the extension to .bib).
Next, from inside the repository, run:
academic import [.bib file path] content/publication/[AuthorLastname-topic-year] --compact
This should generate a cite.bib file and an index.md file, used to generate the paper page on the site. It may put these files inside their own folder, so move them out to try to keep the same format as the other publications in the repository.