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  <doc>
    <id>1318</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2011-06-22</completedDate>
    <publishedDate>2011-06-22</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Soft Versus Hard Metastable Conformations in Molecular Simulations</title>
    <abstract language="eng">Particle methods have become indispensible in conformation dynamics to&#13;
compute transition rates in protein folding, binding processes and&#13;
molecular design, to mention a few.&#13;
Conformation dynamics requires at a decomposition of a molecule's position&#13;
space into metastable conformations.   &#13;
 In this paper, we show how this decomposition&#13;
can be obtained via the design of either  ``soft'' or ``hard''&#13;
molecular conformations.&#13;
We show, that the soft approach results in a larger metastabilitiy of&#13;
the decomposition and is thus more advantegous. This is illustrated&#13;
by a simulation of Alanine Dipeptide.</abstract>
    <identifier type="serial">11-27</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-13189</identifier>
    <submitter>Konstantin Fackeldey</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>Olga Scharkoi</author>
    <author>Marcus Weber</author>
    <series>
      <title>ZIB-Report</title>
      <number>11-27</number>
    </series>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Proteins, Conformation Space, Meshfree Methods</value>
    </subject>
    <collection role="ccs" number="G.">Mathematics of Computing</collection>
    <collection role="pacs" number="30.00.00">ATOMIC AND MOLECULAR PHYSICS</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1318/ZR-11-27.pdf</file>
  </doc>
  <doc>
    <id>2207</id>
    <completedYear>2010</completedYear>
    <publishedYear>2010</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1585</pageFirst>
    <pageLast>1588</pageLast>
    <pageNumber/>
    <edition/>
    <issue>1</issue>
    <volume>1281</volume>
    <type>article</type>
    <publisherName>AIP</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Adaptive Spectral Clustering for Conformation Analysis</title>
    <parentTitle language="eng">AIP Conference Proceedings</parentTitle>
    <identifier type="doi">10.1063/1.3498116</identifier>
    <identifier type="url">http://link.aip.org/link/?APC/1281/1585/1</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Fiete Haack</author>
    <author>Susanna Röblitz</author>
    <author>Olga Scharkoi</author>
    <author>Burkhard Schmidt</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>4614</id>
    <completedYear/>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>73</pageFirst>
    <pageLast>79</pageLast>
    <pageNumber/>
    <edition/>
    <issue>WIAS Report No. 26</issue>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Fuzzy Spectral Clustering by PCCA+</title>
    <parentTitle language="eng">Classification and Clustering: Models, Software and Applications</parentTitle>
    <identifier type="url">http://www.wias-berlin.de/publications/wias-publ/run.jsp?template=abstract&amp;type=Report&amp;year=2009&amp;number=26</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Susanna Röblitz</author>
    <submitter> Stötzel</submitter>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>4583</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>147</pageFirst>
    <pageLast>179</pageLast>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification</title>
    <parentTitle language="eng">Advances in Data Analysis and Classification</parentTitle>
    <identifier type="doi">10.1007/s11634-013-0134-6</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Susanna Röblitz</author>
    <submitter> Stötzel</submitter>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
  </doc>
  <doc>
    <id>4640</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>110</pageFirst>
    <pageLast>194</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>139</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Adaptive spectral clustering with application to tripeptide conformation analysis</title>
    <parentTitle language="eng">The Journal of Chemical Physics</parentTitle>
    <identifier type="doi">10.1063/1.4830409</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Fiete Haack</author>
    <submitter>Adam Nielsen</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>Olga Scharkoi</author>
    <author>Marcus Weber</author>
    <author>Burkhard Schmidt</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="institutes" number="compsys">Computational Systems Biology</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="BMS-Nielsen">BMS-Nielsen</collection>
    <collection role="projects" number="EyeTracking">EyeTracking</collection>
    <collection role="projects" number="Matheon-A19">Matheon-A19</collection>
    <collection role="projects" number="NAMPAR">NAMPAR</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>6922</id>
    <completedYear>2018</completedYear>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>3579</pageFirst>
    <pageLast>3594</pageLast>
    <pageNumber/>
    <edition/>
    <issue>7</issue>
    <volume>14</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-05-29</completedDate>
    <publishedDate>2018-07-10</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field</title>
    <abstract language="eng">Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very&#13;
well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a&#13;
detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with&#13;
general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems.&#13;
To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid β (1−40) peptide, periodically driven by an oscillating electric field.</abstract>
    <parentTitle language="eng">Journal of Chemical Theory and Computation</parentTitle>
    <identifier type="doi">10.1021/acs.jctc.8b00079</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">29.05.2018</enrichment>
    <author>Bernhard Reuter</author>
    <submitter>Bernhard Reuter</submitter>
    <author>Marcus Weber</author>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>Martin E. Garcia</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="fackeldey">Fackeldey, Konstantin</collection>
    <collection role="persons" number="susanna.roeblitz">Röblitz, Susanna</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="projects" number="NonequiMSM">NonequiMSM</collection>
  </doc>
  <doc>
    <id>7563</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>46</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>7</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC</title>
    <abstract language="eng">In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies.</abstract>
    <parentTitle language="eng">Computation</parentTitle>
    <identifier type="doi">10.3390/computation7030046</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2019-08-16</enrichment>
    <author>Franziska Erlekam</author>
    <submitter>Marcus Weber</submitter>
    <author>Sinaida Igde</author>
    <author>Susanna Röblitz</author>
    <author>Laura Hartmann</author>
    <author>Marcus Weber</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>4653</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst>899</pageFirst>
    <pageLast>909</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Soft Versus Hard Metastable Conformations in Molecular Simulations</title>
    <parentTitle language="eng">Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.)</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-13189</enrichment>
    <submitter>Adam Nielsen</submitter>
    <author>Konstantin Fackeldey</author>
    <author>Susanna Röblitz</author>
    <author>O. Scharkoi</author>
    <author>Marcus Weber</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="compmol">Computational Molecular Design</collection>
    <collection role="persons" number="weber">Weber, Marcus</collection>
  </doc>
  <doc>
    <id>6646</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1700198</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>12</issue>
    <volume>17</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH</title>
    <parentTitle language="eng">Marcomolecular Bioscience</parentTitle>
    <identifier type="doi">10.1002/mabi.201700198</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Sinaida Igde</author>
    <submitter>Marcus Weber</submitter>
    <author>Susanna Röblitz</author>
    <author>Anne Müller</author>
    <author>Katharina Kolbe</author>
    <author>Sophia Boden</author>
    <author>Claudia Fessele</author>
    <author>Thisbe Lindhorst</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="institutes" number="compsys">Computational Systems Biology</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>10042</id>
    <completedYear/>
    <publishedYear>2025</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>147</issue>
    <volume>26</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2025-06-02</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition</title>
    <abstract language="eng">The dynamics of many gene regulatory networks (GRNs) is characterized by the occurrence of metastable phenotypes and stochastic phenotype switches. The chemical master equation (CME) is the most accurate description to model such stochastic dynamics, whereby the long-time dynamics of the system is encoded in the spectral properties of the CME operator. Markov State Models (MSMs) provide a general framework for analyzing and visualizing stochastic multistability and state transitions based on these spectral properties. Until now, however, this approach is either limited to low-dimensional systems or requires the use of high-performance computing facilities, thus limiting its usability.</abstract>
    <parentTitle language="eng">BMC Bioinformatics</parentTitle>
    <identifier type="doi">10.1186/s12859-025-06174-5</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="opus.doi.autoCreate">false</enrichment>
    <enrichment key="opus.urn.autoCreate">true</enrichment>
    <author>Maryam Yousefian</author>
    <submitter>Marcus Weber</submitter>
    <author>Anne-Simone Frank</author>
    <author>Marcus Weber</author>
    <author>Susanna Röblitz</author>
    <collection role="persons" number="weber">Weber, Marcus</collection>
    <collection role="institutes" number="MSoCP">Modeling and Simulation of Complex Processes</collection>
    <collection role="projects" number="MathPlusAA1-15">MathPlusAA1-15</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>
