Publikationen
2021
Begutachteter Zeitschriftenartikel
Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells
Pretschner, Anna; Pabel, Sophie; Haas, Markus; Heiner, Monika; Marwan, Wolfgang
In: Frontiers in genetics - Lausanne: Frontiers Media, Bd. 11 (2021), insges. 17 S.
Begutachteter Zeitschriftenartikel
Quantifying 35 transcripts in a single tube - model-based calibration of the GeXP multiplex RT-PCR assay
Marquardt, Pauline; Werthmann, Britta; Rätzel, Viktoria; Haas, Markus; Marwan, Wolfgang
In: BMC biotechnology - London: BioMed Central, 2001, Bd. 21 (2021), insges. 15 S.
2020
Begutachteter Zeitschriftenartikel
Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets
Rätzel, Viktoria; Werthmann, Britta; Haas, Markus; Strube, Jan; Marwan, Wolfgang
In: Biosystems: journal of biological and information processing sciences - Amsterdam [u.a.]: Elsevier Science, Volume 189 (2020), article 104092
2019
Begutachteter Zeitschriftenartikel
Disentangling a complex response in cell reprogramming and probing the waddington landscape by automatic construction of petri nets
Rätzel, Victoria; Werthmann, Britta; Haas, Markus; Strube, Jan; Marwan, Wolfgang
In: bioRxiv beta - Cold Spring Harbor: Cold Spring Harbor Laboratory, NY, 2013 . - 2019, S. 38
Dissertation
Biologische Variabilität bei der Musterbildung von 'Dictyostelium discoideum'
Hilgardt, Christiane; Marwan, Wolfgang
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010, X, 168 S., Ill., graph. Darst., 30 cm
2018
Dissertation
Modellbasiertes Metabolic Engineering zur Optimierung der Itaconatproduktion in Escherichia coli
Harder, Björn-Johannes; Marwan, Wolfgang
In: Aachen: Shaker Verlag, 2018, [1. Auflage], IX, 130 Seiten, Illustrationen, Diagramme, 21 cm, 203 g - (Forschungsberichte aus dem Max-Planck-Institut für Dynamik Komplexer Technischer Systeme; Band 52)
2017
Begutachteter Zeitschriftenartikel
Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks
Glöckner, Gernot; Marwan, Wolfgang
In: Scientific reports - [London] : Macmillan Publishers Limited, part of Springer Nature, Vol. 7.2017, Art. 12304, insgesamt 12 S.
Begutachteter Zeitschriftenartikel
Developmental switching in Physarum polycephalum - Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape
Werthmann, Britta; Marwan, Wolfgang
In: Journal of physics / D - Bristol: IOP Publ, Vol. 50.2017, 46, Art. 464003, insgesamt 18 S.
Dissertation
Bestimmung von Signalflüssen zwischen Faktoren der zellulären Differenzierungskontrolle - zeitabhängige Veränderung von Expressionsprofilen auf Einzelzellebene
Werthmann, Britta; Marwan, Wolfgang
In: Magdeburg, 2017, VIII, 147 Blätter, Illustrationen[Literaturverzeichnis: Blatt 140-146]
Dissertation
Biomodelkit - a framework for modular biomodel-engineering
Blätke, Mary-Ann; Marwan, Wolfgang
In: Magdeburg, Dissertation Otto-von-Guericke-Universität Magdeburg, Fakultät für Naturwissenschaften 2017, 190 Seiten, Illustrationen [Literaturverzeichnis: Seite [177]-188]
2016
Begutachteter Zeitschriftenartikel
The physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling
Schaap, Pauline; Barrantes, Israel; Minx, Pat; Sasaki, Narie; Anderson, Roger W.; Bénard, Marianne; Biggar, Kyle K.; Buchler, Nicolas E.; Bundschuh, Ralf; Chen, Xiao; Fronick, Catrina; Fulton, Lucinda; Golderer, Georg; Jahn, Niels; Knoop, Volker; Landweber, Laura F.; Maric, Chrystelle; Miller, Dennis; Noegel, Angelika A.; Peace, Rob; Pierron, Gérard; Sasaki, Taeko; Schallenberg-Rüdinger, Mareike; Schleicher, Michael; Singh, Reema; Spaller, Thomas; Storey, Kenneth B.; Suzuki, Takamasa; Tomlinson, Chad; Tyson, John J.; Warren, Wesley C.; Werner, Ernst R.; Werner-Felmayer, Gabriele; Wilson, Richard K.; Winckler, Thomas; Gott, Jonatha M.; Glöckner, Gernot; Marwan, Wolfgang
In: Genome biology and evolution: GBE - Oxford: Oxford Univ. Press, Bd. 8.2016, 1, S. 109-125
2015
Buchbeitrag
BioModel engineering with Petri nets
Blätke, Mary Ann; Heiner, Monika; Marwan, Wolfgang
In: Algebraic and discrete mathematical methods for modern biology - London, UK: Academic Press, S. 141-192, 2015
Begutachteter Zeitschriftenartikel
Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation
Rätzel, Viktoria; Marwan, Wolfgang
In: Development, growth & differentiation: official journal of the Japanese Society of Developmental Biologists - Oxford [u.a.]: Wiley-Blackwell, Bd. 57.2015, 5, S. 408-420
Dissertation
Dynamische Fließgleichgewichte und ihre Übergänge in Reaktionsnetzwerken - experimenteller Nachweis der Quasi-potential-Landschaft der zellulären Reprogrammierung
Rätzel, Viktoria; Marwan, Wolfgang
In: Magdeburg, 2015, 146 Blätter, Illustrationen, 30 cm[Literaturverzeichnis: Seite 132-136]
Dissertation
Infection dynamics and virus-induced apoptosis in influenza virus A infected adherent and suspension MDCK cells
Peschel, Britta; Reichl, Udo; Marwan, Wolfgang
In: Zugl.: Magdeburg, Univ., Fak. für Verfahrens- und Systemtechnik, Diss., 2015: Aachen: Shaker, VI, 180 S., Ill., graph. Darst., 21 cm, 291 g - (Forschungsberichte aus dem Max-Planck-Institut für Dynamik komplexer technischer Systeme; 44)
2014
Buchbeitrag
Integrating prior knowledge in automatic network reconstruction
Favre, Marie C. F.; Marwan, Wolfgang; Wagler, Annegret K.
In: CEUR workshop proceedings - Aachen, Germany: RWTH Aachen, 1995, Bd. 1159.2014, S. 45-59Kongress: International Workshop on Biological Processes & Petri Nets 5 (Tunis, Tunisia : 2014.06.23)
Buchbeitrag
A Petri-net-based framework for biomodel engineering
Blätke, Mary Ann; Rohr, Christian; Heiner, Monika; Marwan, Wolfgang
In: Large-Scale Networks in Engineering and Life Sciences - Cham : Birkhäuser , 2014, S. 317-366
Begutachteter Zeitschriftenartikel
EXACT2 - the semantics of biomedical protocols
Soldatova, Larisa N.; Nadis, Daniel; King, Ross D.; Basu, Piyali S.; Haddi, Emma; Baumlé, Véronique; Saunders, Nigel J.; Marwan, Wolfgang; Rudkin, Brian B.
In: BMC bioinformatics - London: BioMed Central, 2000, Vol. 15.2014, Suppl. 14, S. S5
Dissertation
The transcriptomic networks controlling the sporulation in Physarum polycephalum
Barrantes Bustinza, Walter Israel; Marwan, Wolfgang
In: Magdeburg Univ., Fak. für Naturwiss., Diss., 2015, 2014, XVI, 227 S., graph. Darst.
2013
Begutachteter Zeitschriftenartikel
JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology
Blätke, Mary Ann; Dittrich, Anna; Rohr, Christian; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang
In: Molecular BioSystems - Cambridge: Royal Society of Chemistry, 2005, Bd. 9.2013, S. 1290-1307
Dissertation
Untersuchungen zum biotechnologischen Potenzial des fakultativ photosynthetischen Bakteriums Rhodospirillum rubrum und dessen Zentralstoffwechsel
Rudolf, Christiane; Marwan, Wolfgang
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2013, XV, 233 S., graph. Darst.
Dissertation
Zellheterogenität am Beispiel der Expression des Escherichia coli lac Operons
Marbach, Anja; Marwan, Wolfgang
In: Magdeburg Univ., Fak. für Naturwiss., Diss., 2013, X, 126 S., Ill., graph. Darst., 30 cm
2012
Abstract
A database-supported modular modelling platform for systems and synthetic biology
Blätke, Mary Ann; Marwan, Wolfgang
In: Biological processes & Petri Nets, S. 18-19, 2012 - (CEUR workshop proceedings; 852)Kongress: International Workshop on Biological Processes & Petri Nets; 3 (Hamburg) : 2012.06.25
Buchbeitrag
JAK-STAT signalling as example for a database-supported modular modelling concept
Blätke, Mary Ann; Dittrich, Anna; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang
In: Computational Methods in Systems Biology / Gilbert , David - Berlin, Heidelberg : Springer ; Gilbert, David . - 2012, S. 362-365 - (Lecture Notes in Bioinformatics; 7605) Kongress: CMSB 2012 10 London, UK 2012.10.03-05
Buchbeitrag
Predicting phenotype from genotype through automatically composed Petri nets
Blätke, Mary Ann; Heiner, Monika; Marwan, Wolfgang
In: Computational Methods in Systems Biology / Gilbert , David - Berlin, Heidelberg : Springer ; Gilbert, David . - 2012, S. 87-106 - (Lecture Notes in Bioinformatics; 7605) Kongress: CMSB 2012 10 London, UK 2012.10.03-05
Begutachteter Zeitschriftenartikel
JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems- and synthetic biology
Blätke, Mary Ann; Dittrich, Anna; Rohr, Christian; Heiner, Monika; Schaper, Fred; Marwan, Wolfgang
In: De.arxiv.org. - [S.l.] : Arxiv.org, insges. 54 S., 2012
Begutachteter Zeitschriftenartikel
Reconstruction of extended Petri nets from time-series data by using logical control functions
Durzinsky, Markus; Marwan, Wolfgang; Wagler, Annegret
In: Journal of mathematical biology. - Berlin : Springer, insges. 21 S., 2012
Dissertation
Untersuchungen zur Redoxregulation der Photosynthesemembranexpression in dem fakultativ phototrophen Bakterium Rhodospirillum rubrum
Carius, Anke Berit; Marwan, Wolfgang
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2012, III, 134 S., graph. Darst.
Originalartikel in begutachteter internationaler Zeitschrift
Futile attempts to differentiate provide molecular evidence for individual differences within a population of cells during cellular reprogramming
Hoffmann, Xenia-Katharina; Tesmer, Jens; Souquet, Manfred; Marwan, Wolfgang
In: FEMS microbiology letters. - Malden, Mass : Wiley-Blackwell, Bd. 329.2012, 1, S. 78-86
Nicht begutachteter Zeitschriftenartikel
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level
Barrantes, Israel; Leipzig, Jeremy; Marwan, Wolfgang
In: Gene regulation and systems biology. - Auckland, NZ : Libertas Academica, 6, S. 127-137, 2012
2011
Dissertation
Understanding phototaxis of Halobacterium salinarum - a systems biology approach
Streif, Stefan; Findeisen, Rolf; Marwan, Wolfgang
In: Aachen: Shaker, Zugl.: Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik., Diss., 2011, XIX, 165 S., Ill., graph. Darst., 21 cm - (Contributions in systems theory and automatic control; 1)
Originalartikel in begutachteter internationaler Zeitschrift
Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks
Marwan, Wolfgang; Wagler, Annegret; Weismantel, Robert
In: Natural computing: an international journal - Dordrecht [u.a.]: Kluwer Academic Press, Bd. 10.2011, 2, S. 639-654
Originalartikel in begutachteter internationaler Zeitschrift
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks
Durzinsky, Markus; Wagler, Annegret; Marwan, Wolfgang
In: BMC systems biology - London: BioMed Central, Bd. 5.2011, 113, insges. 17 S.
Originalartikel in begutachteter internationaler Zeitschrift
Automatic network reconstruction using ASP
Durzinsky, Markus; Marwan, Wolfgang; Ostrowski, Max; Schaub, Torsten; Wagler, Annegret
In: Theory and practice of logic programming: TPLP - Cambridge: Cambridge Univ. Press, Bd. 11.2011, 4/5, S. 749-766[Special issue: 27th International Conference on Logic Programming, 2011]
Originalartikel in begutachteter internationaler Zeitschrift
The circuits of live
Marwan, Wolfgang
In: Public service review / Science and technology - Newcastle-under-Lyme: PSCA International, insges. 1 S., 2011
Originalartikel in begutachteter zeitschriftenartiger Reihe
Petri nets in Snoopy - a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks in Methods in Molecular Biology
Marwan, Wolfgang; Rohr, Christian; Heiner, Monika
In: Bacterial molecular networks . - New York, NY [u.a.] : Humana Press, ISBN 978-1-617-79361-5, S. 409-437; Abstract
2010
Originalartikel in begutachteter internationaler Zeitschrift
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis
Streif, Stefan; Oesterhelt, Dieter; Marwan, Wolfgang
In: BMC systems biology . - London : BioMed Central, Bd. 4.2010, 27, insges. 18 S.; Abstract
Originalartikel in begutachteter internationaler Zeitschrift
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum
Barrantes, Israel; Glöckner, Gernot; Meyer, Sonja; Marwan, Wolfgang
In: BMC genomics . - London : BioMed Central, Abstract
Originalartikel in begutachteter internationaler Zeitschrift
Amoeba-inspired network design
Marwan, Wolfgang
In: Science . - Washington, DC : American Assoc. for the Advancement of Science, Bd. 327.2010, 5964, S. 419-420
Originalartikel in begutachteter internationaler Zeitschrift
Snoopy: a unifying Petri net framework to investigate biomolecular networks
Rohr, Christian; Marwan, Wolfgang; Heiner, Monika
In: Bioinformatics . - Oxford : Oxford Univ. Press, Bd. 26.2010, 7, S. 974-975
Originalartikel in begutachteter zeitschriftenartiger Reihe
Modular and hierarchical modelling concept for large biological Petri nets applied to nociception
Blätke, Mary Ann; Marwan, Wolfgang
In: Algorithmen und Werkzeuge: Proceedings of the 17th German Workshop on on Algorithms and Tools for Petri Nets, Cottbus, Germany, October 07-08, 2010 - Proceedings of the 17th German Workshop on on Algorithms and Tools for Petri Nets, Cottbus, Germany, October 07-08, 2010 , 2010 . - 2010, insges. 9 S.
2009
Originalartikel in begutachteter internationaler Zeitschrift
Quantitative analysis of signal transduction in motile and phototactic cells by computerized light stimulation and model based tracking
Streif, Stefan; Staudinger, Wilfried Franz; Oesterhelt, Dieter; Marwan, Wolfgang
In: Review of scientific instruments: RSI / publ. by the American Institute of Physics: RSI - Melville, NY: AIP, 80.2009, 2, Art. 023709, insges. 8 S.
Originalartikel in begutachteter zeitschriftenartiger Reihe
Extended stochastic Petri nets for model-based design of wetlab experiments
Heiner, Monika; Lehrack, Sebastian; Gilbert, David; Marwan, Wolfgang
In: Transactions on computational systems biology ; 11.2009 - Berlin [u.a.]: Springer, 2009 . - 2009, S. 138-163 - (Lecture notes in computer science; 5750; Lecture notes in bioinformatics; Journal subline)
2008
Originalartikel in begutachteter internationaler Zeitschrift
A first glimpse at the transcriptome of physarum polycephalum
Glöckner, Gernot; Golderer, Georg; Werner-Felmayer, Gabriele; Meyer, Sonja; Marwan, Wolfgang
In: BMC genomics . - London : BioMed Central, Bd. 9.2008, insges. 11 S.; Abstract
Originalartikel in begutachteter internationaler Zeitschrift
A mathematical approach to solve the network reconstruction problem
Marwan, Wolfgang; Wagler, Annegret; Weismantel, Robert
In: Mathematical methods of operations research . - Berlin : Springer, Bd. 67.2008, 1, S. 117-132
Originalartikel in begutachteter internationaler Zeitschrift
Automatic reconstruction of molecular and genetic networks from discrete time series data
Durzinsky, Markus; Wagler, Annegret; Weismantel, Robert; Marwan, Wolfgang
In: Biosystems . - Amsterdam : North-Holland Publ. Co., Bd. 93.2008, 3, S. 181-190
Originalartikel in begutachteter internationaler Zeitschrift
Flagellar rotation in the archaeon halobacterium salinarum depends on ATP
Streif, Stefan; Staudinger, Wilfried Franz; Marwan, Wolfgang; Oesterhelt, Dieter
In: Journal of molecular biology . - Amsterdam [u.a.] : Elsevier, Bd. 384.2008, 1, S. 1-8
2005
Begutachteter Zeitschriftenartikel
Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation
Marwan, Wolfgang; Sujatha, Arumugam; Starostzik, Christine
In: Journal of theoretical biology - Amsterdam: Elsevier Ltd., 1961, Bd. 236.2005, 4, S. 349-365