Frank T. Bergmann

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Herbert M SauroUniversity of WashingtonVerified email at u.washington.edu
Michael HuckaCalifornia Institute of TechnologyVerified email at caltech.edu
Dagmar WaltemathProfessor of Medical InformaticsVerified email at uni-greifswald.de
David Phillip NickersonAuckland Bioengineering Institute, University of AucklandVerified email at auckland.ac.nz
Brett G. OlivierVU AmsterdamVerified email at vu.nl
Sven SahleUniversität HeidelbergVerified email at bioquant.uni-heidelberg.de
Lucian SmithUniversity of WashingtonVerified email at uw.edu
Martin GolebiewskiHITS gGmbH, Heidelberg (Germany)Verified email at h-its.org
Jonathan CooperUniversity College LondonVerified email at ucl.ac.uk
Nicolas RodriguezSenior Software Systems and Database Architect, Babraham InstituteVerified email at babraham.ac.uk
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Chris MyersUniversity of UtahVerified email at ece.utah.edu
Stefan HoopsResearch Associate Professor, Biocomplexity Institute & Initiative, University of VirginiaVerified email at virginia.edu
Sarah KeatingUCLVerified email at ucl.ac.uk
Huaiyu MiPreventive Medicine, University of Southern CaliforniaVerified email at usc.edu
Tobias CzaudernaUniversity of Applied Sciences MittweidaVerified email at hs-mittweida.de
Emek DemirOHSUVerified email at ohsu.edu
Snoep JLStellenbosch University; Manchester University; Vrije Universiteit AmsterdamVerified email at sun.ac.za
Akira FunahashiProfessor of Systems Biology, Keio UniversityVerified email at bio.keio.ac.jp
Anatoly SorokinOkinawa Institute of Science and TechnologyVerified email at oist.jp

Frank T. Bergmann

BioQUANT/COS, Heidelberg University, Heidelberg, Germany

Verified email at caltech.edu

Systems Biology Computational Biology


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Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language D Waltemath, R Adams, FT Bergmann, M Hucka, F Kolpakov, AK Miller, ... BMC systems biology 5 (1), 1-10, 2011	275	2011
TinkerCell: modular CAD tool for synthetic biology D Chandran, FT Bergmann, HM Sauro Journal of biological engineering 3 (1), 1-17, 2009	232	2009
Minimum information about a simulation experiment (MIASE) D Waltemath, R Adams, DA Beard, FT Bergmann, US Bhalla, R Britten, ... PLoS computational biology 7 (4), e1001122, 2011	149	2011
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project FT Bergmann, R Adams, S Moodie, J Cooper, M Glont, M Golebiewski, ... BMC bioinformatics 15 (1), 1-9, 2014	133	2014
Antimony: a modular model definition language LP Smith, FT Bergmann, D Chandran, HM Sauro Bioinformatics 25 (18), 2452-2454, 2009	115	2009
Software support for SBGN maps: SBGN-ML and LibSBGN MP Van Iersel, AC Villéger, T Czauderna, SE Boyd, FT Bergmann, A Luna, ... Bioinformatics 28 (15), 2016-2021, 2012	106	2012
SBW-a modular framework for systems biology FT Bergmann, HM Sauro Proceedings of the 2006 Winter Simulation Conference, 1637-1645, 2006	90	2006
COPASI and its applications in biotechnology FT Bergmann, S Hoops, B Klahn, U Kummer, P Mendes, J Pahle, S Sahle Journal of biotechnology 261, 215-220, 2017	76	2017
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ... Frontiers in bioengineering and biotechnology 3, 19, 2015	75	2015
Bifurcation discovery tool V Chickarmane, SR Paladugu, F Bergmann, HM Sauro Bioinformatics 21 (18), 3688-3690, 2005	71	2005
The Systems Biology Markup Language (SBML): language specification for level 3 version 1 core M Hucka, FT Bergmann, S Hoops, SM Keating, S Sahle, JC Schaff, ... Journal of integrative bioinformatics 12 (2), 382-549, 2015	67	2015
Toward community standards and software for whole-cell modeling D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ... IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016	59	2016
Computer-aided design of biological circuits using TinkerCell D Chandran, FT Bergmann, HM Sauro Bioengineered bugs 1 (4), 276-283, 2010	39	2010
Comparing simulation results of SBML capable simulators FT Bergmann, HM Sauro Bioinformatics 24 (17), 1963-1965, 2008	39	2008
Supporting the SBML layout extension A Deckard, FT Bergmann, HM Sauro Bioinformatics 22 (23), 2966-2967, 2006	35	2006
SBtab: a flexible table format for data exchange in systems biology T Lubitz, J Hahn, FT Bergmann, E Noor, E Klipp, W Liebermeister Bioinformatics 32 (16), 2559-2561, 2016	34	2016
The systems biology markup language (SBML) level 3 package: flux balance constraints BG Olivier, FT Bergmann Journal of integrative bioinformatics 12 (2), 660-690, 2015	33	2015
Standards and ontologies in computational systems biology O Wolkenhauer, P Wellstead, KH Cho, HM Sauro, FT Bergmann Essays in biochemistry 45, 211-222, 2008	33	2008
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) D Waltemath, FT Bergmann, C Chaouiya, T Czauderna, P Gleeson, ... Standards in genomic sciences 9 (3), 1285-1301, 2014	30	2014
Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis R Großeholz, CC Koh, N Veith, T Fiedler, M Strauss, B Olivier, BC Collins, ... NPJ systems biology and applications 2 (1), 1-9, 2016	27	2016

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