Publikationen
2021
Begutachteter Zeitschriftenartikel
Quantifying 35 transcripts in a single tube - model-based calibration of the GeXP multiplex RT-PCR assay
In: BMC biotechnology - London: BioMed Central, 2001, Bd. 21 (2021), insges. 15 S.
Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells
In: Frontiers in genetics - Lausanne: Frontiers Media, Bd. 11 (2021), insges. 17 S.
2020
Begutachteter Zeitschriftenartikel
Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets
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
In: bioRxiv beta - Cold Spring Harbor: Cold Spring Harbor Laboratory, NY, 2013 . - 2019, S. 38
Dissertation
Biologische Variabilität bei der Musterbildung von 'Dictyostelium discoideum'
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010, X, 168 S., Ill., graph. Darst., 30 cm
2017
Begutachteter Zeitschriftenartikel
Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks
In: Scientific reports - [London]: Macmillan Publishers Limited, part of Springer Nature, Vol. 7.2017, Art. 12304, insgesamt 12 S.
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
In: Journal of physics / D - Bristol: IOP Publ, Vol. 50.2017, 46, Art. 464003, insgesamt 18 S.
Dissertation
Biomodelkit - a framework for modular biomodel-engineering
In: Magdeburg, 2017, 190 Seiten, Illustrationen ; [Literaturverzeichnis: Seite [177]-188]
Bestimmung von Signalflüssen zwischen Faktoren der zellulären Differenzierungskontrolle - zeitabhängige Veränderung von Expressionsprofilen auf Einzelzellebene
In: Magdeburg, 2017, VIII, 147 Blätter, Illustrationen ; [Literaturverzeichnis: Blatt 140-146]
2016
Begutachteter Zeitschriftenartikel
The physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling
In: Genome biology and evolution: GBE - Oxford: Oxford Univ. Press, Bd. 8.2016, 1, S. 109-125
2015
Begutachteter Zeitschriftenartikel
Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation
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
Buchbeitrag
BioModel engineering with Petri nets
In: Algebraic and discrete mathematical methods for modern biology - London, UK: Academic Press, S. 141-192, 2015
Dissertation
Infection dynamics and virus-induced apoptosis in influenza virus A infected adherent and suspension MDCK cells
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)
Dynamische Fließgleichgewichte und ihre Übergänge in Reaktionsnetzwerken - experimenteller Nachweis der Quasi-potential-Landschaft der zellulären Reprogrammierung
In: Magdeburg, 2015, 146 Blätter, Illustrationen, 30 cm ; [Literaturverzeichnis: Seite 132-136]
2014
Begutachteter Zeitschriftenartikel
EXACT2 - the semantics of biomedical protocols
In: BMC bioinformatics - London: BioMed Central, 2000, Vol. 15.2014, Suppl. 14, S. S5
Buchbeitrag
A Petri-net-based framework for biomodel engineering
In: Large-Scale Networks in Engineering and Life Sciences - Cham: Birkhäuser, 2014 . - 2014, S. 317-366
Integrating prior knowledge in automatic network reconstruction
In: CEUR workshop proceedings - Aachen, Germany: RWTH Aachen, 1995, Bd. 1159.2014, S. 45-59
Dissertation
The transcriptomic networks controlling the sporulation in Physarum polycephalum
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
In: Molecular BioSystems - Cambridge: Royal Society of Chemistry, 2005, Bd. 9.2013, S. 1290-1307
Dissertation
Zellheterogenität am Beispiel der Expression des Escherichia coli lac Operons
In: Magdeburg Univ., Fak. für Naturwiss., Diss., 2013, X, 126 S., Ill., graph. Darst., 30 cm
Untersuchungen zum biotechnologischen Potenzial des fakultativ photosynthetischen Bakteriums Rhodospirillum rubrum und dessen Zentralstoffwechsel
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2013, XV, 233 S., graph. Darst.
2012
Abstract
A database-supported modular modelling platform for systems and synthetic biology
In: Biological processes & Petri Nets, S. 18-19, 2012 - (CEUR workshop proceedings; 852)
Begutachteter Zeitschriftenartikel
JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems- and synthetic biology
In: De.arxiv.org. - [S.l.] : Arxiv.org, insges. 54 S., 2012
Reconstruction of extended Petri nets from time-series data by using logical control functions
In: Journal of mathematical biology. - Berlin : Springer, insges. 21 S., 2012
Buchbeitrag
JAK-STAT signalling as example for a database-supported modular modelling concept
In: Gilbert, David: : Computational Methods in Systems Biology. - Berlin : Springer, S. 362-365, 2012 - (Lecture Notes in Bioinformatics; 7605)
Predicting phenotype from genotype through automatically composed Petri nets
In: Gilbert, David: : Computational Methods in Systems Biology. - Berlin : Springer, S. 87-106, 2012 - (Lecture Notes in Bioinformatics; 7605)
Dissertation
Untersuchungen zur Redoxregulation der Photosynthesemembranexpression in dem fakultativ phototrophen Bakterium Rhodospirillum rubrum
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2012, III, 134 S., graph. Darst.
Nicht begutachteter Zeitschriftenartikel
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level
In: Gene regulation and systems biology. - Auckland, NZ : Libertas Academica, 6, S. 127-137, 2012
Originalartikel in begutachteter internationaler Zeitschrift
Futile attempts to differentiate provide molecular evidence for individual differences within a population of cells during cellular reprogramming
In: FEMS microbiology letters. - Malden, Mass : Wiley-Blackwell, Bd. 329.2012, 1, S. 78-86
2011
Dissertation
Understanding phototaxis of Halobacterium salinarum - a systems biology approach
In: Zugl.: Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik., Diss., 2011: Aachen: Shaker, XIX, 165 S., Ill., graph. Darst., 21 cm - (Contributions in systems theory and automatic control; 1)
Originalartikel in begutachteter internationaler Zeitschrift
Automatic network reconstruction using ASP
In: Theory and practice of logic programming: TPLP - Cambridge: Cambridge Univ. Press, Bd. 11.2011, 4/5, S. 749-766
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks
In: BMC systems biology - London: BioMed Central, Bd. 5.2011, 113, insges. 17 S.
Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks
In: Natural computing: an international journal - Dordrecht [u.a.]: Kluwer Academic Press, Bd. 10.2011, 2, S. 639-654
The circuits of live
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
In: Bacterial molecular networks . - New York, NY [u.a.] : Humana Press, ISBN 978-1-617-79361-5, S. 409-437
2010
Originalartikel in begutachteter internationaler Zeitschrift
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum
In: BMC genomics . - London : BioMed Central, Abstract unter URL: http://dx.doi.org/10.1186/1471-2164-11-115, 2010
Amoeba-inspired network design
In: Science . - Washington, DC : American Assoc. for the Advancement of Science, Bd. 327.2010, 5964, S. 419-420
Snoopy: a unifying Petri net framework to investigate biomolecular networks
In: Bioinformatics . - Oxford : Oxford Univ. Press, Bd. 26.2010, 7, S. 974-975
A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis
In: BMC systems biology . - London : BioMed Central, Bd. 4.2010, 27, insges. 18 S.
Originalartikel in begutachteter zeitschriftenartiger Reihe
Modular and hierarchical modelling concept for large biological Petri nets applied to nociception
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
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
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
Automatic reconstruction of molecular and genetic networks from discrete time series data
In: Biosystems . - Amsterdam : North-Holland Publ. Co., Bd. 93.2008, 3, S. 181-190
A first glimpse at the transcriptome of physarum polycephalum
In: BMC genomics . - London : BioMed Central, Bd. 9.2008, insges. 11 S.
A mathematical approach to solve the network reconstruction problem
In: Mathematical methods of operations research . - Berlin : Springer, Bd. 67.2008, 1, S. 117-132
Flagellar rotation in the archaeon halobacterium salinarum depends on ATP
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
In: Journal of theoretical biology - Amsterdam: Elsevier Ltd., 1961, Bd. 236.2005, 4, S. 349-365