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

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

Biologische Variabilität bei der Musterbildung von 'Dictyostelium discoideum'
In: Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010, X, 168 S., Ill., graph. Darst., 30 cm

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.

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]

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

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

BioModel engineering with Petri nets
In: Algebraic and discrete mathematical methods for modern biology - London, UK: Academic Press, S. 141-192, 2015

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]

EXACT2 - the semantics of biomedical protocols
In: BMC bioinformatics - London: BioMed Central, 2000, Vol. 15.2014, Suppl. 14, S. S5

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

The transcriptomic networks controlling the sporulation in Physarum polycephalum
In: Magdeburg Univ., Fak. für Naturwiss., Diss., 2015, 2014, XVI, 227 S., graph. Darst.

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

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.

A database-supported modular modelling platform for systems and synthetic biology
In: Biological processes & Petri Nets, S. 18-19, 2012 - (CEUR workshop proceedings; 852)

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

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)

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.

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

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

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)

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

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

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.

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.

Quantitative analysis of signal transduction in motile and phototactic cells by computerized light stimulation and model based tracking
In: Review of scientific instruments . - Melville, NY : AIP, Bd. 80.2009, 2, insges. 8 S.

Extended stochastic Petri nets for model-based design of wetlab experiments
In: Berlin [u.a.] : Springer, ISBN 3-642-04185-X, S. 138-163; Lecture notes in computer science; 5750, 2009 ; [Transactions on computational systems biology ; 11.2009]

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

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