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2020 – today
- 2024
[j72]Martin Golebiewski
, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. 21(1) (2024)- [j71]Dreycey Albin, Lukas Buecherl, Eitan Kochavi, Elise Niehaus, Sasha M. Novack, Shenali Uragoda, Chris J. Myers, Mirela Alistar:
PhageBox: An Open Source Digital Microfluidic Extension With Applications for Phage Discovery. IEEE Trans. Biomed. Eng. 71(1): 217-226 (2024) - [c73]Mohammad Ahmadi, Lukas Buecherl, Chris J. Myers, Zhen Zhang, Chris Winstead, Hao Zheng:
Rare-Event Guided Analysis of Infinite-State Chemical Reaction Networks. QEST+FORMATS 2024: 196-212 - 2023
- [j70]Douglas Densmore, Nathan J. Hillson, Eric Klavins, Chris J. Myers, Jean Peccoud, Giovanni Stracquadanio:
Introduction to the Special Issue on BioFoundries and Cloud Laboratories. ACM J. Emerg. Technol. Comput. Syst. 19(3): 26:1-26:2 (2023) - [j69]Lukas Buecherl, Thomas Mitchell, James Scott-Brown, Prashant Vaidyanathan, Gonzalo Vidal, Hasan Baig, Bryan Bartley, Jacob Beal, Matthew Crowther, Pedro Fontanarrosa, Thomas E. Gorochowski, Raik Grünberg, Vishwesh Kulkarni, James Alastair McLaughlin, Göksel Misirli, Ernst Oberortner, Anil Wipat, Chris J. Myers:
Synthetic biology open language (SBOL) version 3.1.0. J. Integr. Bioinform. 20(1) (2023) - [j68]Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J. Integr. Bioinform. 20(1) (2023) - [j67]Casey-Tyler Berezin, Luis U. Aguilera, Sonja Billerbeck, Philip E. Bourne, Douglas Densmore, Paul S. Freemont, Thomas E. Gorochowski, Sarah I. Hernandez, Nathan J. Hillson, Connor R. King, Michael Köpke, Shuyi Ma, Katie M. Miller, Tae Seok Moon, Jason H. Moore, Brian Munsky, Chris J. Myers, Dequina A. Nicholas, Samuel J. Peccoud, Wen Zhou, Jean Peccoud:
Ten simple rules for managing laboratory information. PLoS Comput. Biol. 19(12) (2023) - [c72]Joshua Jeppson, Matthias Volk, Bryant Israelsen, Riley Roberts, Andrew Williams, Lukas Buecherl, Chris J. Myers, Hao Zheng, Chris Winstead, Zhen Zhang:
STAMINA in C++: Modernizing an Infinite-State Probabilistic Model Checker. QEST 2023: 101-109 - 2022
- [j66]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [c71]Riley Roberts, Thakur Neupane, Lukas Buecherl, Chris J. Myers, Zhen Zhang:
STAMINA 2.0: Improving Scalability of Infinite-State Stochastic Model Checking. VMCAI 2022: 319-331 - [i6]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - [i5]Mohammad Ahmadi, Zhen Zhang, Chris J. Myers, Chris Winstead, Hao Zheng:
Counterexample Generation for Infinite-State Chemical Reaction Networks. CoRR abs/2207.05207 (2022) - 2021
- [j65]Hasan Baig, Pedro Fontanarossa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. 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 J. Myers:
Synthetic biology open language visual (SBOL Visual) version 2.3. J. Integr. Bioinform. 18(3) (2021) - [j64]Hasan Baig, Pedro Fontanarossa, James Alastair McLaughlin, James Scott-Brown, Prashant Vaidyanathan, Thomas E. Gorochowski, Goksel Misirli, Jacob Beal, Chris J. Myers:
Synthetic biology open language visual (SBOL visual) version 3.0. J. Integr. Bioinform. 18(3) (2021) - [j63]Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2021. J. Integr. Bioinform. 18(3) (2021) - 2020
- [j62]Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Michael Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. 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 J. Myers:
Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinform. 17(2-3) (2020) - [j61]Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Jacob Beal, Matthew Crowther, Thomas E. Gorochowski, Raik Grünberg, Goksel Misirli, James Scott-Brown, Ernst Oberortner, Anil Wipat, Chris J. Myers:
Synthetic biology open language (SBOL) version 3.0.0. J. Integr. Bioinform. 17(2-3) (2020) - [j60]Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2020. J. Integr. Bioinform. 17(2-3) (2020) - [j59]Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka:
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J. Integr. Bioinform. 17(2-3) (2020) - [j58]Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers:
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17(2-3) (2020) - [i4]Hao Zheng, Yingying Zhang, Chris J. Myers:
Local State Space Analysis to Assist Partial Order Reduction. CoRR abs/2004.14971 (2020) - [i3]Hao Zheng, Andrew Price, Chris J. Myers:
Using Decision Diagrams to Compactly Represent the State Space for Explicit Model Checking. CoRR abs/2004.14995 (2020)
2010 – 2019
- 2019
- [j57]Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - [j56]Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16(2) (2019) - [j55]Curtis Madsen, Ángel Goñi-Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox III, Thomas E. Gorochowski, Raik Grünberg, Chris Macklin, James Alastair McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew R. 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 J. Myers, Ernst Oberortner, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.3. J. Integr. Bioinform. 16(2) (2019) - [j54]Curtis Madsen, Ángel Goñi-Moreno, Zachary Palchick, Umesh P, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Mike Bissell, Kevin Clancy, Robert Sidney Cox III, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, James Alastair McLaughlin, Tramy Nguyen, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat:
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. J. Integr. Bioinform. 16(2) (2019) - [j53]Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16(2) (2019) - [j52]Tramy Nguyen, Timothy S. Jones, Pedro Fontanarrosa, Jeanet V. Mante, Zach Zundel, Douglas Densmore, Chris J. Myers:
Design of Asynchronous Genetic Circuits. Proc. IEEE 107(7): 1356-1368 (2019) - [j51]Leandro H. Watanabe, Jacob Barhak, Chris J. Myers:
Toward reproducible disease models using the Systems Biology Markup Language. Simul. 95(10) (2019) - [c70]Thakur Neupane, Chris J. Myers, Curtis Madsen, Hao Zheng, Zhen Zhang:
STAMINA: STochastic Approximate Model-Checker for INfinite-State Analysis. CAV (1) 2019: 540-549 - [p1]Thakur Neupane, Zhen Zhang, Curtis Madsen, Hao Zheng, Chris J. Myers:
Approximation Techniques for Stochastic Analysis of Biological Systems. Automated Reasoning for Systems Biology and Medicine 2019: 327-348 - [i2]Thakur Neupane, Zhen Zhang, Curtis Madsen, Hao Zheng, Chris J. Myers:
Approximation Techniques for Stochastic Analysis of Biological Systems. CoRR abs/1901.07857 (2019) - [i1]Thakur Neupane, Chris J. Myers, Curtis Madsen, Hao Zheng, Zhen Zhang:
STAMINA: STochastic Approximate Model-checker for INfinite-state Analysis. CoRR abs/1906.03978 (2019) - 2018
- [j50]Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grünberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.2.0. J. Integr. Bioinform. 15(1) (2018) - [j49]Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat:
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. J. Integr. Bioinform. 15(1) (2018) - [j48]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15(1) (2018) - [j47]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15(1) (2018) - [j46]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15(1) (2018) - 2017
- [c69]Vladimir Dubikhin, Chris J. Myers, Danil Sokolov, Ioannis Syranidis, Alexandre Yakovlev:
Advances in Formal Methods for the Design of Analog/Mixed-Signal Systems: Invited. DAC 2017: 36:1-36:6 - [c68]Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath:
A brief history of COMBINE. WSC 2017: 884-895 - 2016
- [j45]Xin Li, Chandramouli V. Kashyap, Chris J. Myers:
Guest Editors' Introduction Challenges and Opportunities in Analog/Mixed-Signal CAD. IEEE Des. Test 33(5): 5-6 (2016) - [j44]Vladimir Dubikhin, Danil Sokolov, Alex Yakovlev, Chris J. Myers:
Design of Mixed-Signal Systems With Asynchronous Control. IEEE Des. Test 33(5): 44-55 (2016) - [j43]Jacob Beal, Robert Sidney Cox III, Raik Grünberg, James Alastair McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.1.0. J. Integr. Bioinform. 13(3) (2016) - [j42]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13(3) (2016) - [j41]Zhen Zhang, Wendelin Serwe, Jian Wu, Tomohiro Yoneda, Hao Zheng, Chris J. Myers:
An improved fault-tolerant routing algorithm for a Network-on-Chip derived with formal analysis. Sci. Comput. Program. 118: 24-39 (2016) - [j40]Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber:
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63(10): 2007-2014 (2016) - 2015
- [j39]Nicolas Rodriguez, Alex Thomas, Leandro H. Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, Andreas Dräger:
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinform. 31(20): 3383-3386 (2015) - [j38]Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew R. Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris J. Myers, Anil Wipat, Herbert M. Sauro:
Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integr. Bioinform. 12(2) (2015) - [j37]Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson:
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12(2) (2015) - [j36]Falk Schreiber, Gary D. Bader, Martin Golebiewski, Michael Hucka, Benjamin Kormeier, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Stephan Weise:
Specifications of Standards in Systems and Synthetic Biology. J. Integr. Bioinform. 12(2) (2015) - [j35]Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion I. Moraru, Wolfram Liebermeister:
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. J. Integr. Bioinform. 12(2) (2015) - [j34]Hao Zheng, Zhen Zhang, Chris J. Myers, Emmanuel Rodriguez, Yingying Zhang:
Compositional Model Checking of Concurrent Systems. IEEE Trans. Computers 64(6): 1607-1621 (2015) - [j33]Chris J. Myers:
Computational Synthetic Biology: Progress and the Road Ahead. IEEE Trans. Multi Scale Comput. Syst. 1(1): 19-32 (2015) - [c67]Andrew N. Fisher, Chris J. Myers, Peng Li:
Reachability Analysis Using Extremal Rates. NFM 2015: 158-172 - 2014
- [j32]Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Introduction to the Special Issue on Computational Synthetic Biology. ACM J. Emerg. Technol. Comput. Syst. 11(3): 20:1-20:5 (2014) - [j31]Curtis Madsen, Zhen Zhang, Nicholas Roehner, Chris Winstead, Chris J. Myers:
Stochastic Model Checking of Genetic Circuits. ACM J. Emerg. Technol. Comput. Syst. 11(3): 23:1-23:21 (2014) - [c66]Zhen Zhang, Wendelin Serwe, Jian Wu, Tomohiro Yoneda, Hao Zheng, Chris J. Myers:
Formal Analysis of a Fault-Tolerant Routing Algorithm for a Network-on-Chip. FMICS 2014: 48-62 - [c65]Andrew N. Fisher, Satish Batchu, Kevin R. Jones, Dhanashree Kulkarni, Scott Little, David Walter, Chris J. Myers:
LEMA: A tool for the formal verification of digitally-intensive analog/mixed-signal circuits. MWSCAS 2014: 1017-1020 - [c64]Leandro H. Watanabe, Chris J. Myers:
Hierarchical stochastic simulation of genetic circuits. SpringSim (TMS-DEVS) 2014: 37 - 2013
- [c63]Honghuang Lin, Peng Li, Chris J. Myers:
Verification of digitally-intensive analog circuits via kernel ridge regression and hybrid reachability analysis. DAC 2013: 66:1-66:6 - [c62]Dhanashree Kulkarni, Andrew N. Fisher, Chris J. Myers:
A new assertion property language for analog/mixed-signal circuits. FDL 2013: 1-8 - 2012
- [j30]Curtis Madsen, Chris J. Myers, Tyler Patterson, Nicholas Roehner, Jason T. Stevens, Chris Winstead:
Design and Test of Genetic Circuits Using ${\tt iBioSim}$iBioSim. IEEE Des. Test Comput. 29(3): 32-39 (2012) - [c61]Chris J. Myers:
Formal Verification of Genetic Circuits. CAV 2012: 5 - [c60]Curtis Madsen, Chris J. Myers, Nicholas Roehner, Chris Winstead, Zhen Zhang:
Utilizing stochastic model checking to analyze genetic circuits. CIBCB 2012: 379-386 - [c59]Hao Zheng, Andrew Price, Chris J. Myers:
Using decision diagrams to compactly represent the state space for explicit model checking. HLDVT 2012: 17-24 - [c58]Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro:
Modeling and design automation of biological circuits and systems. ICCAD 2012: 291-293 - [c57]Chris J. Myers, Jian Wu, Zhen Zhang, Hao Zheng, Yingying Zhang:
Poster Abstract: Methods and Tools for Verification of Cyber-Physical Systems. ICCPS 2012: 232 - [c56]Yingying Zhang, Emmanuel Rodriguez, Hao Zheng, Chris J. Myers:
An Improvement in Partial Order Reduction Using Behavioral Analysis. ISVLSI 2012: 100-107 - [c55]Hao Zheng, Emmanuel Rodriguez, Yingying Zhang, Chris J. Myers:
A Compositional Minimization Approach for Large Asynchronous Design Verification. SPIN 2012: 62-79 - 2011
- [j29]Scott Little, David Walter, Chris J. Myers, Robert A. Thacker, Satish Batchu, Tomohiro Yoneda:
Verification of Analog/Mixed-Signal Circuits Using Labeled Hybrid Petri Nets. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 30(4): 617-630 (2011) - [j28]Nathan A. Barker, Chris J. Myers, Hiroyuki Kuwahara:
Learning Genetic Regulatory Network Connectivity from Time Series Data. IEEE ACM Trans. Comput. Biol. Bioinform. 8(1): 152-165 (2011) - [c54]Hiroyuki Kuwahara, Chris J. Myers:
Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. BCB 2011: 425-429 - [c53]Yingying Zhang, Emmanuel Rodriguez, Hao Zheng, Chris J. Myers:
A Behavioral Analysis Approach for Efficient Partial Order Reduction. HASE 2011: 49-56 - 2010
- [j27]Scott Little, David Walter, Kevin R. Jones, Chris J. Myers, Alper Sen:
Analog/Mixed-Signal Circuit Verification Using Models Generated from Simulation Traces. Int. J. Found. Comput. Sci. 21(2): 191-210 (2010) - [j26]Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov:
Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. PLoS Comput. Biol. 6(3) (2010) - [c52]Haiqiong Yao, Hao Zheng, Chris J. Myers:
State space reductions for scalable verification of asynchronous designs. HLDVT 2010: 17-24 - [c51]Robert A. Thacker, Kevin R. Jones, Chris J. Myers, Hao Zheng:
Automatic abstraction for verification of cyber-physical systems. ICCPS 2010: 12-21 - [c50]Chris Winstead, Curtis Madsen, Chris J. Myers:
iSSA: An incremental stochastic simulation algorithm for genetic circuits. ISCAS 2010: 553-556
2000 – 2009
- 2009
- [j25]Chris J. Myers, Nathan A. Barker, Kevin R. Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam-Phuong D. Nguyen:
iBioSim: a tool for the analysis and design of genetic circuits. Bioinform. 25(21): 2848-2849 (2009) - [j24]Naohiro Hamada, Yuki Shiga, Takao Konishi, Hiroshi Saito, Tomohiro Yoneda, Chris J. Myers, Takashi Nanya:
A Behavioral Synthesis System for Asynchronous Circuits with Bundled-data Implementation. Inf. Media Technol. 4(2): 211-226 (2009) - [j23]Naohiro Hamada, Yuki Shiga, Takao Konishi, Hiroshi Saito, Tomohiro Yoneda, Chris J. Myers, Takashi Nanya:
A Behavioral Synthesis System for Asynchronous Circuits with Bundled-data Implementation. IPSJ Trans. Syst. LSI Des. Methodol. 2: 64-79 (2009) - [c49]Chris J. Myers, Nathan A. Barker, Hiroyuki Kuwahara, Kevin R. Jones, Curtis Madsen, Nam-Phuong D. Nguyen:
Genetic design automation. ICCAD 2009: 713-716 - [c48]Robert A. Thacker, Chris J. Myers, Kevin R. Jones, Scott Little:
A new verification method for embedded systems. ICCD 2009: 193-200 - 2008
- [j22]Frédéric Béal, Tomohiro Yoneda, Chris J. Myers:
Hazard Checking of Timed Asynchronous Circuits Revisited. Fundam. Informaticae 88(4): 411-435 (2008) - [j21]Frédéric Béal, Tomohiro Yoneda, Chris J. Myers:
A Conservative Framework for Safety-Failure Checking. IEICE Trans. Inf. Syst. 91-D(3): 642-654 (2008) - [j20]Hiroyuki Kuwahara, Chris J. Myers:
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions. J. Comput. Biol. 15(7): 779-792 (2008) - [j19]David Walter, Scott Little, Chris J. Myers, Nicholas Seegmiller, Tomohiro Yoneda:
Verification of Analog/Mixed-Signal Circuits Using Symbolic Methods. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 27(12): 2223-2235 (2008) - [c47]Naohiro Hamada, Yuki Shiga, Hiroshi Saito, Tomohiro Yoneda, Chris J. Myers, Takashi Nanya:
A behavioral synthesis method for asynchronous circuits with bundled-data implementation (Tool paper). ACSD 2008: 50-55 - 2007
- [j18]Hiroshi Saito, Naohiro Hamada, Nattha Jindapetch, Tomohiro Yoneda, Chris J. Myers, Takashi Nanya:
Scheduling Methods for Asynchronous Circuits with Bundled-Data Implementations Based on the Approximation of Start Times. IEICE Trans. Fundam. Electron. Commun. Comput. Sci. 90-A(12): 2790-2799 (2007) - [j17]Curtis A. Nelson, Chris J. Myers, Tomohiro Yoneda:
Efficient Verification of Hazard-Freedom in Gate-Level Timed Asynchronous Circuits. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 26(3): 592-605 (2007) - [j16]Tomohiro Yoneda, Chris J. Myers:
Synthesis of Timed Circuits Based on Decomposition. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 26(7): 1177-1195 (2007) - [c46]Frédéric Béal, Tomohiro Yoneda, Chris J. Myers:
Hazard Checking of Timed Asynchronous Circuits Revisited. ACSD 2007: 51-60 - [c45]David Walter, Scott Little, Nicholas Seegmiller, Chris J. Myers, Tomohiro Yoneda:
Symbolic Model Checking of Analog/Mixed-Signal Circuits. ASP-DAC 2007: 316-323 - [c44]Nam-Phuong D. Nguyen, Hiroyuki Kuwahara, Chris J. Myers, James P. Keener:
The Design of a Genetic Muller C-Element. ASYNC 2007: 95-104 - [c43]David Walter, Scott Little, Chris J. Myers:
Bounded Model Checking of Analog and Mixed-Signal Circuits Using an SMT Solver. ATVA 2007: 66-81 - [c42]Scott Little, David Walter, Kevin R. Jones, Chris J. Myers:
Analog/Mixed-Signal Circuit Verification Using Models Generated from Simulation Traces. ATVA 2007: 114-128 - [c41]Scott Little, Alper Sen, Chris J. Myers:
Application of Automated Model Generation Techniques to Analog/Mixed-Signal Circuits. MTV 2007: 109-115 - [c40]