Frank Bergmann, PhD - Publications

Affiliations: 
University of Heidelberg, Heidelberg, Baden-Württemberg, Germany 
Area:
Systems Biology, Software
Website:
http://frank-fbergmann.blogspot.com/

29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110  1
2020 Smith LP, Moodie SL, Bergmann FT, Gillespie C, Keating SM, König M, Myers CJ, Swat MJ, Wilkinson DJ, Hucka M. Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. Journal of Integrative Bioinformatics. PMID 32750035 DOI: 10.1515/Jib-2020-0018  0.68
2019 Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, et al. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics. PMID 31219795 DOI: 10.1515/Jib-2019-0021  0.68
2018 Bedaso Y, Bergmann FT, Choi K, Medley K, Sauro HM. A Portable Structural Analysis Library for Reaction Networks. Bio Systems. PMID 29857031 DOI: 10.1016/J.Biosystems.2018.05.008  1
2018 Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Journal of Integrative Bioinformatics. PMID 29522418 DOI: 10.1515/jib-2017-0081  0.68
2016 Lubitz T, Hahn J, Bergmann FT, Noor E, Klipp E, Liebermeister W. SBtab: a flexible table format for data exchange in systems biology. Bioinformatics (Oxford, England). PMID 27153616 DOI: 10.1093/bioinformatics/btw179  1
2015 Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics. 12: 731-901. PMID 29220970 DOI: 10.1515/jib-2015-271  0.68
2015 Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics. 12: 382-549. PMID 29220965 DOI: 10.1515/jib-2015-266  0.68
2015 Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics. 12: 271. PMID 26528569 DOI: 10.2390/Biecoll-Jib-2015-271  0.68
2015 Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Journal of Integrative Bioinformatics. 12: 266. PMID 26528564 DOI: 10.1038/Npre.2010.4959.1  0.68
2015 Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. Journal of Integrative Bioinformatics. 12: 262. PMID 26528560 DOI: 10.2390/biecoll-jib-2015-262  1
2015 Bergmann FT, Rodriguez N, Le Novère N. COMBINE Archive Specification Version 1. Journal of Integrative Bioinformatics. 12: 261. PMID 26528559 DOI: 10.2390/biecoll-jib-2015-261  1
2015 Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, et al. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Standards in Genomic Sciences. DOI: 10.4056/sigs.5279417  1
2014 Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, et al. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. Bmc Bioinformatics. 15: 369. PMID 25494900 DOI: 10.1186/S12859-014-0369-Z  1
2012 van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, et al. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (Oxford, England). 28: 2016-21. PMID 22581176 DOI: 10.1093/Bioinformatics/Bts270  1
2011 Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. Bmc Systems Biology. 5: 198. PMID 22172142 DOI: 10.1186/1752-0509-5-198  1
2011 Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, et al. Minimum Information About a Simulation Experiment (MIASE). Plos Computational Biology. 7: e1001122. PMID 21552546 DOI: 10.1371/Journal.Pcbi.1001122  1
2011 Hucka M, Bergmann FT, Keating SM, Smith LP. A profile of today's SBML-compatible software Proceedings - 7th Ieee International Conference On E-Science Workshops, Esciencew 2011. 143-150. DOI: 10.1109/eScienceW.2011.28  1
2010 Chandran D, Bergmann FT, Sauro HM. Computer-aided design of biological circuits using TinkerCell. Bioengineered Bugs. 1: 274-81. PMID 21327060 DOI: 10.4161/Bbug.1.4.12506  1
2010 Shen SY, Bergmann F, Sauro HM. SBML2TikZ: supporting the SBML render extension in LaTeX. Bioinformatics (Oxford, England). 26: 2794-5. PMID 20829443 DOI: 10.1093/Bioinformatics/Btq512  1
2010 Sauro HM, Bergmann FT. Software Tools for Systems Biology Systems Biomedicine. 289-314. DOI: 10.1016/B978-0-12-372550-9.00012-2  1
2009 Chandran D, Bergmann FT, Sauro HM. TinkerCell: modular CAD tool for synthetic biology. Journal of Biological Engineering. 3: 19. PMID 19874625 DOI: 10.1186/1754-1611-3-19  1
2009 Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model definition language. Bioinformatics (Oxford, England). 25: 2452-4. PMID 19578039 DOI: 10.1093/Bioinformatics/Btp401  1
2008 Sauro HM, Bergmann FT. Standards and ontologies in computational systems biology. Essays in Biochemistry. 45: 211-22. PMID 18793134 DOI: 10.1042/Bse0450211  1
2008 Bergmann FT, Sauro HM. Comparing simulation results of SBML capable simulators. Bioinformatics (Oxford, England). 24: 1963-5. PMID 18579569 DOI: 10.1093/Bioinformatics/Btn319  1
2006 Deckard A, Bergmann FT, Sauro HM. Supporting the SBML layout extension. Bioinformatics (Oxford, England). 22: 2966-7. PMID 17038346 DOI: 10.1093/Bioinformatics/Btl520  1
2006 Bergmann FT, Vallabhajosyula RR, Sauro HM. Computational tools for modeling protein networks Current Proteomics. 3: 181-197. DOI: 10.2174/157016406779475380  1
2006 Bergmann FT, Sauro HM. SBW - A modular framework for systems biology Proceedings - Winter Simulation Conference. 1637-1645. DOI: 10.1109/WSC.2006.322938  1
2005 Chickarmane V, Paladugu SR, Bergmann F, Sauro HM. Bifurcation discovery tool. Bioinformatics (Oxford, England). 21: 3688-90. PMID 16081475 DOI: 10.1093/Bioinformatics/Bti603  1
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