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Dräger A, Supper J, Planatscher H, Magnus JB, Oldiges M, Zell A. Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum. In: Srinivasan D, Wang L, editors. IEEE Congress on Evolutionary Computation (CEC 2007); 2007 September; Singapore, Singapore. IEEE Press; c00.
Dräger A, Kronfeld M, Supper J, Planatscher H, Magnus JB, Oldiges M, Zell A. Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum. In: Srinivasan D, Wang L, editors. IEEE Congress on Evolutionary Computation (CEC 2007); 2007 September; Singapore, Singapore. IEEE Press; c00.
Lambeck S, Dräger A, Guthke R. Network Inference by Considering Multiple Objectives: Insights from In Vivo Transcriptomic Data Generated by a Synthetic Network. In: Arabnia HR, Tran Q, Chang R, He M, Marsh A, editors. International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010; 2010 July; Las Vegas, NV, USA. CSREA Press; c00.
Kronfeld M, Dräger A, Aschoff M, Zell A. On the Benefits of Multimodal Optimization for Metabolic Network Modeling. In: Grosse I, Neumann S, Posch S, Schreiber F, Stadler P, editors. German Conference on Bioinformatics (GCB 2009); 2009 September; Halle (Saale), Germany. German Informatics Society; c00.
Schröder A, Wrzodek C, Wollnik J, Dräger A, Wanke D, Berendzen KW. Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization. IEEE Congress on Evolutionary Computation (CEC 2011); 2011 June; New Orleans, LA, USA. IEEE; c00.
Supper J, Fröhlich H, Spieth C, Dräger A, Zell A. Inferring Gene Regulatory Networks by Machine Learning Methods. In: Sankoff D, Wang L, Chin F, editors. Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007). 5th Asia-Pacific Bioinformatics Conference (APBC 2007); 2007 January; Hong Kong, China. 57 Shelton Street, Govent Garden, London WC2H 9HE, UK: Imperial College Press; c00.
Dräger A, Hassis N, Supper J, Schröder A, Zell A. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39. PubMed PMID: 18447902; PubMed Central PMCID: PMC2412839.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8. PubMed PMID: 18689808; PubMed Central PMCID: PMC2530884.
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol. 2009 Jan 14;3:5. doi: 10.1186/1752-0509-3-5. PubMed PMID: 19144170; PubMed Central PMCID: PMC2661887.
Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A. SBML2L(A)T(E)X: conversion of SBML files into human-readable reports. Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23. PubMed PMID: 19307240; PubMed Central PMCID: PMC2682517.
Supper J, Spangenberg L, Planatscher H, Dräger A, Schröder A, Zell A. BowTieBuilder: modeling signal transduction pathways. BMC Syst Biol. 2009 Jun 30;3:67. doi: 10.1186/1752-0509-3-67. PubMed PMID: 19566957; PubMed Central PMCID: PMC2712453.
Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A. ModuleMaster: a new tool to decipher transcriptional regulatory networks. Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9. PubMed PMID: 19819296.
Dräger A, Schröder A, Zell A. Automating mathematical modeling of biochemical reaction networks. In: Choi S, editor. Systems Biology for Signaling Networks New York: Springer; 2010. p.159-205.
Büchel F, Wrzodek C, Mittag F, Dräger A, Schröder A, Zell A. ProDGe: investigating protein-protein interactions at the domain level. [Internet]. Nature Precedings; 2011 August. Available from: DOI: 10.1038/npre.2011.6188.1.
Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M. JSBML: a flexible Java library for working with SBML. Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22. PubMed PMID: 21697129; PubMed Central PMCID: PMC3137227.
Wrzodek C, Dräger A, Zell A. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23. PubMed PMID: 21700675; PubMed Central PMCID: PMC3150042.
Schröder A, Wollnik J, Wrzodek C, Dräger A, Bonin M, Burk O, Thomas M, Thasler WE, Zanger UM, Zell A. Inferring statin-induced gene regulatory relationships in primary human hepatocytes. Bioinformatics. 2011 Sep 15;27(18):2473-7. doi: 10.1093/bioinformatics/btr416. Epub 2011 Jul 14. PubMed PMID: 21757465.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Controlled vocabularies and semantics in systems biology. Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77. PubMed PMID: 22027554; PubMed Central PMCID: PMC3261705.
König M, Dräger A, Holzhütter HG. CySBML: a Cytoscape plugin for SBML. Bioinformatics. 2012 Sep 15;28(18):2402-3. doi: 10.1093/bioinformatics/bts432. Epub 2012 Jul 5. PubMed PMID: 22772946.
Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics. 2012 Oct 15;28(20):2648-53. doi: 10.1093/bioinformatics/bts508. Epub 2012 Aug 24. PubMed PMID: 22923304; PubMed Central PMCID: PMC3467751.
Dräger A, Planatscher H. Metabolic Network Modeling. In: Dubitzky W, Wolkenhauer O, Yokota H, Cho K, editors. Encyclopedia of Systems Biology New York: Springer-Verlag; 2013. 1249-1251p.
Dräger A, Planatscher H. Parameter Estimation, Metabolic Network Modeling. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, editors. Encyclopedia of Systems Biology New York: Springer; 2013. p.1627-1631.
Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A. Precise generation of systems biology models from KEGG pathways. BMC Syst Biol. 2013 Feb 21;7:15. doi: 10.1186/1752-0509-7-15. PubMed PMID: 23433509; PubMed Central PMCID: PMC3623889.
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. The systems biology simulation core algorithm. BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55. PubMed PMID: 23826941; PubMed Central PMCID: PMC3707837.
Vlaic S, Hoffmann B, Kupfer P, Weber M, Dräger A. GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinformatics. 2013 Sep 1;29(17):2216-7. doi: 10.1093/bioinformatics/btt370. Epub 2013 Jun 26. PubMed PMID: 23803467.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116. PubMed PMID: 24180668; PubMed Central PMCID: PMC4228421.
Büchel F, Saliger S, Dräger A, Hoffmann S, Wrzodek C, Zell A, Kahle PJ. Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. BMC Neurosci. 2013 Nov 6;14:136. doi: 10.1186/1471-2202-14-136. PubMed PMID: 24195591; PubMed Central PMCID: PMC3871002.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135. PubMed PMID: 24321545; PubMed Central PMCID: PMC3892043.
Eichner J, Topf F, Dräger A, Wrzodek C, Wanke D, Zell A. TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. PLoS One. 2013;8(12):e82238. doi: 10.1371/journal.pone.0082238. eCollection 2013. PubMed PMID: 24349230; PubMed Central PMCID: PMC3861411.
Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol. 2014;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014. Review. PubMed PMID: 25538939; PubMed Central PMCID: PMC4259112.
Dörr A, Keller R, Zell A, Dräger A. SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. Computation (Basel). 2014 Dec;2(4):246-257. doi: 10.3390/computation2040246. Epub 2014 Dec 18. PubMed PMID: 32211200; PubMed Central PMCID: PMC7093077.
Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10. PubMed PMID: 26261351; PubMed Central PMCID: PMC4553782.
King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol. 2015 Aug;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug. PubMed PMID: 26313928; PubMed Central PMCID: PMC4552468.
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. J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271. PubMed PMID: 26528569; PubMed Central PMCID: PMC5457286.
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. J Integr Bioinform. 2015 Sep 4;12(2):266. doi: 10.2390/biecoll-jib-2015-266. PubMed PMID: 26528564; PubMed Central PMCID: PMC5451324.
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A. SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9. PubMed PMID: 26452770; PubMed Central PMCID: PMC4600286.
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do genome-scale models need exact solvers or clearer standards?. Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. PubMed PMID: 26467284; PubMed Central PMCID: PMC4631202.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16. PubMed PMID: 26079347; PubMed Central PMCID: PMC4595895.
Keller R, Klein M, Thomas M, Dräger A, Metzger U, Templin MF, Joos TO, Thasler WE, Zell A, Zanger UM. Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling. PLoS Comput Biol. 2016 Jan;12(1):e1004431. doi: 10.1371/journal.pcbi.1004431. eCollection 2016 Jan. PubMed PMID: 26727233; PubMed Central PMCID: PMC4699813.
King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2016 Jan 4;44(D1):D515-22. doi: 10.1093/nar/gkv1049. Epub 2015 Oct 17. PubMed PMID: 26476456; PubMed Central PMCID: PMC4702785.
Römer M, Eichner J, Dräger A, Wrzodek C, Wrzodek F, Zell A. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PLoS One. 2016;11(2):e0149263. doi: 10.1371/journal.pone.0149263. eCollection 2016. PubMed PMID: 26882475; PubMed Central PMCID: PMC4801062.
Scranton MA, Ostrand JT, Georgianna DR, Lofgren SM, Li D, Ellis RC, Carruthers DN, Dräger A, Masica DL, Mayfield SP. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii. Algal research. 2016 February; 15:135-142. doi: 10.1016/j.algal.2016.02.011.
Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Syst Biol. 2016 Jun 6;10(1):40. doi: 10.1186/s12918-016-0283-2. PubMed PMID: 27266508; PubMed Central PMCID: PMC4895898.
Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. A Padawan Programmer's Guide to Developing Software Libraries. Cell Syst. 2017 Nov 22;5(5):431-437. doi: 10.1016/j.cels.2017.08.003. Epub 2017 Oct 4. PubMed PMID: 28988801.
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. PubMed PMID: 29457794; PubMed Central PMCID: PMC5840010.
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. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J Integr Bioinform. 2018 Mar 9;15(1). doi: 10.1515/jib-2017-0081. PubMed PMID: 29522418; PubMed Central PMCID: PMC6167032.
Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Res. 2018 Nov 16;46(20):10682-10696. doi: 10.1093/nar/gky752. PubMed PMID: 30137486; PubMed Central PMCID: PMC6237786.
Mostolizadeh R, Dräger A, Jamshidi N. Insights into Dynamic Network States Using Metabolomic Data. Methods Mol Biol. 2019;1978:243-258. doi: 10.1007/978-1-4939-9236-2_15. PubMed PMID: 31119667.
Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Review. PubMed PMID: 30462164; PubMed Central PMCID: PMC6433895.
Romano P, Céol A, Dräger A, Fiannaca A, Giugno R, La Rosa M, Milanesi L, Pfeffer U, Rizzo R, Shin SY, Xia J, Urso A. The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):125. doi: 10.1186/s12859-019-2681-0. PubMed PMID: 30999855; PubMed Central PMCID: PMC6472292.
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