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  <doc>
    <id>6996</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1</pageFirst>
    <pageLast>16</pageLast>
    <pageNumber>16</pageNumber>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-08-10</completedDate>
    <publishedDate>2018-08-10</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computing Personalised Treatments through In Silico Clinical Trials. A Case Study on Downregulation in Assisted Reproduction</title>
    <abstract language="eng">In Silico Clinical Trials (ISCT), i.e., clinical experimental campaigns carried out by means of computer simulations, hold the promise to decrease time and cost for the safety and efficacy assessment of pharmacological treatments, reduce the need for animal and human testing, and enable precision medicine.&#13;
&#13;
In this paper we present a case study aiming at quantifying, by means of a multi-arm ISCT supervised by intelligent search, the potential impact of precision medicine approaches on a real pharmacological treatment, namely the downregulation phase of a complex clinical protocol for assisted reproduction.</abstract>
    <parentTitle language="eng">Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion, Workshop of the Federated Logic Conference 2018 (FLoC 2018), Oxford</parentTitle>
    <identifier type="doi">10.29007/g864</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Toni Mancini</author>
    <submitter>Rainald Ehrig</submitter>
    <author>Federico Mari</author>
    <author>Annalisa Massini</author>
    <author>Igor Melatti</author>
    <author>Ivano Salvo</author>
    <author>Stefano Sinisi</author>
    <author>Enrico Tronci</author>
    <author>Rainald Ehrig</author>
    <author>Susanna Röblitz</author>
    <author>Brigitte Leeners</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="ehrig">Ehrig, Rainald</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="PAEON">PAEON</collection>
  </doc>
  <doc>
    <id>6092</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-07-14</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Follicular maturation in cows: mathematical models and data</title>
    <parentTitle language="eng">10. European Conference on Mathematical and Theoretical Biology</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Alexander Lange</author>
    <submitter>Alexander Lange</submitter>
    <author>Julia Plöntzke</author>
    <author>Stefan Schäfer</author>
    <author>Susanna Röblitz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="BovSys">BovSys</collection>
  </doc>
  <doc>
    <id>5979</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Mathematical Modelling of Follicular Maturation in Cows and Women</title>
    <parentTitle language="deu">49. Jahrestagung der Physiologie und Pathologie der Fortpflanzung und gleichzeitig 41. Veterinär-Humanmedizinische Gemeinschaftstagung 2016, Leipzig.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SubmissionStatus">epub ahead of print</enrichment>
    <author>Stefan Schäfer</author>
    <submitter>Bodo Erdmann</submitter>
    <author>Julia Plöntzke</author>
    <author>Susanna Röblitz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="BovSys">BovSys</collection>
    <collection role="projects" number="PAEON">PAEON</collection>
  </doc>
  <doc>
    <id>6034</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC</title>
    <abstract language="eng">Multivalent sugar/protein interactions are well-known to proceed through different binding modes 1-5 which in turn can be described by their binding kinetics 3-5. This study provides additional insight into the association and dissociation reaction rates of complex multivalent sugar/protein interactions. Binding kinetics of recently introduced multivalent precision glycomacromolecules 6-8 to Concanavalin A (Con A) were studied by " kinetic Isothermal Titration Calorimetry " (kinITC) 9-11. The effect of multivalency is evaluated by comparing rate constants of glycomacromolecules obtaining the same and different valency of mannose ligands and by variation of the overall backbone properties, such as hydrophilic/ hydrophoboc. In addition, binding kinetics were studied using different conformations of Con A (homodimer vs.-tetramer) and thus a different protein valency. Our results show that precision glycomacromolecule/Con A binding proceeds non-cooperatively. Further, association and dissociation rates are mainly described by intermolecular complex formation. Together with the so-called functional valency, we can discriminate between " bound " and " unbound " states for macroscopic on-and off-rates, even for such complex glycooligomer/protein systems. By comparing e.g. a mono-to a divalent glycomacromolecule for their binding to dimeric Con A, we see a lower dissociation rate for the latter. As both bind monovalently to Con A, this is a strong indication for a statistical rebinding event. Further, there is a strong dependence of multivalent binding kinetics on the ligand density of glycomacromolecules as well as the Con A conformation and thus the overall on-and off-rates.</abstract>
    <parentTitle language="eng">Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015</parentTitle>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Sinaida Igde</author>
    <submitter>Regine Kossick</submitter>
    <author>Hendrik Wölk</author>
    <author>Susanna Röblitz</author>
    <author>Marco Reidelbach</author>
    <author>Marcus Weber</author>
    <author>Laura Hartmann</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="SFB765-C2">SFB765-C2</collection>
  </doc>
  <doc>
    <id>5584</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">An integrative approach for model driven computation of treatments in reproductive medicine</title>
    <parentTitle language="eng">BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, Rorkee, India</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-57103</enrichment>
    <author>Rainald Ehrig</author>
    <submitter>Mascha Berg</submitter>
    <author>Thomas Dierkes</author>
    <author>Stefan Schäfer</author>
    <author>Susanna Röblitz</author>
    <author>Enrico Tronci</author>
    <author>Toni Mancini</author>
    <author>Ivano Salvo</author>
    <author>Vadim Alimguzhin</author>
    <author>Federico Mari</author>
    <author>Igor Melatti</author>
    <author>Annalisa Massini</author>
    <author>Tillmann H. C. Krüger</author>
    <author>Marcel Egli</author>
    <author>Fabian Ille</author>
    <author>Brigitte Leeners</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="ehrig">Ehrig, Rainald</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="PAEON">PAEON</collection>
  </doc>
  <doc>
    <id>5585</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model</title>
    <parentTitle language="eng">15th International Symposium on Mathematical and Computational Biology, Rorkee, India</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-56453</enrichment>
    <author>Julia Plöntzke</author>
    <submitter>Mascha Berg</submitter>
    <author>Mascha Berg</author>
    <author>Claudia Stötzel</author>
    <author>Susanna Röblitz</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="BovSys">BovSys</collection>
  </doc>
  <doc>
    <id>5163</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>207</pageFirst>
    <pageLast>214</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Patient-Specific Models from Inter-Patient Biological Models and Clinical Records</title>
    <parentTitle language="eng">Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design (FMCAD 2014)</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Toni Mancini</author>
    <submitter> Stötzel</submitter>
    <author>Ivano Salvo</author>
    <author>Federico Mari</author>
    <author>Igor Melatti</author>
    <author>Annalisa Massini</author>
    <author>Stefano Sinisi</author>
    <author>Enrico Tronci</author>
    <author>Francesco Davi</author>
    <author>Thomas Dierkes</author>
    <author>Rainald Ehrig</author>
    <author>Susanna Röblitz</author>
    <author>Brigitte Leeners</author>
    <author>Tillmann H. C. Krüger</author>
    <author>Marcel Egli</author>
    <author>Fabian Ille</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="ehrig">Ehrig, Rainald</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="projects" number="PAEON">PAEON</collection>
  </doc>
  <doc>
    <id>5816</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Modeling of the BMP mediated co-regulation of the Smad and Non-Smad pathways in the context of cell density</title>
    <parentTitle language="eng">10th International BMP conference, 2014, Berlin, Germany</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Pooja Gupta</author>
    <submitter> lange</submitter>
    <author>Carola Krause</author>
    <author>Paul Rikeit</author>
    <author>Susanna Röblitz</author>
    <author>Petra Knaus</author>
    <author>Christof Schütte</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="gupta">Gupta, Pooja</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="schuette">Schütte, Christof</collection>
    <collection role="projects" number="BMPsys">BMPsys</collection>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
  </doc>
  <doc>
    <id>10043</id>
    <completedYear/>
    <publishedYear>2026</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>126</pageFirst>
    <pageLast>149</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>15959</volume>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2025-08-19</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Exploring Metastable Dynamics of Gene Regulatory Networks with ISOKANN</title>
    <abstract language="eng">Stochastic dynamical systems like gene regulatory networks (GRNs) often exhibit behavior characterized by metastable sets (representing cellular phenotypes), in which trajectories remain for long times, whereas switches between these sets in the phase space are rare events. One way to capture these rare events is to infer the system’s long-term behavior from the spectral characteristics (eigenvalues and eigenvectors) of its Koopman operator. For GRNs, the Koopman operator is based on the chemical master equation (CME), which provides a precise mathematical modeling framework for stochastic GRNs. Since the CME is typically analytically intractable, methods based on discretizing the CME operator have been developed. However, determining the number and location of metastable sets in the phase space as well as the transition rates between them remains computationally challenging, especially for large GRNs with many genes and interactions. A promising alternative method, called ISOKANN (invariant subspaces of Koopman operators with artificial neural networks) has been developed in the context of molecular dynamics. ISOKANN uses a combination of the power iteration and neural networks to learn the basis functions of an invariant subspace of the Koopman operator. In this paper, we extend the application of ISOKANN to the&#13;
CME operator and apply it to two small GRNs: a genetic toggle switch model and a model for macrophage polarization. Our work opens a new field of application for the ISOKANN algorithm and demonstrates the potential of this algorithm for studying large GRNs.</abstract>
    <parentTitle language="eng">Computational Methods in Systems Biology. CMSB 2025</parentTitle>
    <identifier type="doi">10.1007/978-3-032-01436-8_8</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2025-06-09</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="Series">Lecture Notes in Computer Science</enrichment>
    <author>Maryam Yousefian</author>
    <submitter>Alexander Sikorski</submitter>
    <author>Luca Donati</author>
    <author>Alexander Sikorski</author>
    <author>Marcus Weber</author>
    <author>Susanna Röblitz</author>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="persons" number="sikorski">Sikorski, Alexander</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="persons" number="donati">Donati, Luca</collection>
  </doc>
</export-example>
