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2020 – today
- 2022
[j20]Benjamin D. Maier
, Luis U. Aguilera, Sven Sahle, Pascal Mutz, Priyata Kalra, Christopher Dächert, Ralf Bartenschlager, Marco Binder, Ursula Kummer:
Stochastic dynamics of Type-I interferon responses. PLoS Comput. Biol. 18(10): 1010623 (2022)- 2021
- [j19]Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina A. Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez-Álvarez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl:
PEtab - Interoperable specification of parameter estimation problems in systems biology. PLoS Comput. Biol. 17(1) (2021)
2010 – 2019
- 2019
- [j18]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) - 2018
- [j17]Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath:
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J. Integr. Bioinform. 15(1) (2018) - [j16]Frank T. Bergmann, Sarah M. Keating, Ralph Gauges, Sven Sahle, Katja Wengler:
SBML Level 3 package: Render, Version 1, Release 1. J. Integr. Bioinform. 15(1) (2018) - [j15]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) - [j14]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) - 2016
- [j13]Frank T. Bergmann, Sven Sahle, Christoph Zimmer:
Piecewise parameter estimation for stochastic models in COPASI. Bioinform. 32(10): 1586-1588 (2016) - [j12]Christoph Zimmer, Sven Sahle:
Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. Comput. Biol. Chem. 61: 75-85 (2016) - [i1]Christoph Zimmer, Frank T. Bergmann, Sven Sahle:
Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. CoRR abs/1601.04458 (2016) - 2015
- [j11]Christoph Zimmer, Sven Sahle:
A termination criterion for parameter estimation in stochastic models in systems biology. Biosyst. 137: 55-63 (2015) - [j10]Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler, Frank Thomas Bergmann:
The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - [j9]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) - [j8]Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12(2) (2015) - 2012
- [j7]Irina Surovtsova, Natalia Simus, Katrin Hübner, Sven Sahle, Ursula Kummer:
Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Syst. Biol. 6: 14 (2012) - 2011
- [j6]Dagmar Waltemath, Richard R. Adams, Frank T. Bergmann, Michael Hucka, Fedor A. Kolpakov, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (2011) - [j5]Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011)
2000 – 2009
- 2009
- [j4]Irina Surovtsova, Natalia Simus, Thomas Lorenz, Artjom König, Sven Sahle, Ursula Kummer:
Accessible methods for the dynamic time-scale decomposition of biochemical systems. Bioinform. 25(21): 2816-2823 (2009) - 2008
- [j3]Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph Gauges, Razif R. Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno Besson, Isabel Rojas, Rebecca C. Wade, Ursula Kummer:
SYCAMORE - a systems biology computational analysis and modeling research environment. Bioinform. 24(12): 1463-1464 (2008) - 2006
- [j2]Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wegner:
A model diagram layout extension for SBML. Bioinform. 22(15): 1879-1885 (2006) - [j1]Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer:
COPASI - a COmplex PAthway SImulator. Bioinform. 22(24): 3067-3074 (2006) - [c2]Irina Surovtsova, Sven Sahle, Jürgen Pahle, Ursula Kummer:
Approaches to complexity reduction in a systems biology research environment (SYCAMORE). WSC 2006: 1683-1689 - [c1]Sven Sahle, Ralph Gauges, Jürgen Pahle, Natalia Simus, Ursula Kummer, Stefan Hoops, Christine Lee, Mudita Singhal, Liang Xu, Pedro Mendes:
Simulation of biochemical networks using COPASI: a complex pathway simulator. WSC 2006: 1698-1706
Coauthor Index
aka: Frank Thomas Bergmann
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