@misc{BlaetkeDittrichRohretal., author = {Bl{\"a}tke, Mary-Ann and Dittrich, Anna and Rohr, Christian and Heiner, Monika and Schaper, Fred and Marwan, Wolfgang}, title = {JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology}, series = {Molecular BioSystems}, volume = {9}, journal = {Molecular BioSystems}, number = {6}, issn = {1742-2051}, doi = {10.1039/C3MB25593J}, pages = {1290 -- 1307}, language = {en} } @incollection{HeinerLehrackGilbertetal., author = {Heiner, Monika and Lehrack, Sebastian and Gilbert, David and Marwan, Wolfgang}, title = {Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments}, series = {Transactions on Computational Systems Biology XI}, booktitle = {Transactions on Computational Systems Biology XI}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-04185-3}, pages = {138 -- 163}, language = {en} } @misc{RohrMarwanHeiner, author = {Rohr, Christian and Marwan, Wolfgang and Heiner, Monika}, title = {Snoopy - a unifying Petri net framework to investigate biomolecular networks}, series = {Bioinformatics}, volume = {26}, journal = {Bioinformatics}, number = {7}, issn = {1460-2059}, pages = {974 -- 975}, language = {en} } @incollection{BlaetkeHeinerMarwan, author = {Bl{\"a}tke, Mary-Ann and Heiner, Monika and Marwan, Wolfgang}, title = {BioModel Engineering with Petri Nets}, series = {Algebraic and Discrete Mathematical Methods for Modern Biology}, booktitle = {Algebraic and Discrete Mathematical Methods for Modern Biology}, editor = {Robeva, Raina S.}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, isbn = {978-0-12-801213-0}, pages = {141 -- 193}, language = {en} } @incollection{BlaetkeRohrHeineretal., author = {Bl{\"a}tke, Mary-Ann and Rohr, Christian and Heiner, Monika and Marwan, Wolfgang}, title = {A Petri Net based Framework for Biomodel Engineering}, series = {Large-Scale Networks in Engineering and Life Sciences}, booktitle = {Large-Scale Networks in Engineering and Life Sciences}, editor = {Benner, Peter}, publisher = {Springer}, address = {Heidelberg}, isbn = {978-3-319-08436-7}, doi = {10.1007/978-3-319-08437-4_6}, pages = {317 -- 366}, language = {en} } @misc{PretschnerPabelHaasetal., author = {Pretschner, Anna and Pabel, Sophie and Haas, Markus and Heiner, Monika and Marwan, Wolfgang}, title = {Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells}, series = {Frontiers in Genetics}, journal = {Frontiers in Genetics}, number = {11}, issn = {1664-8021}, doi = {10.3389/fgene.2020.612256}, pages = {17}, abstract = {Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields unidirectional, eventually branching Markov chains with a single source node. In an alternative approach, we used multi-nucleate cells to follow gene expression taking true time series. Assembling state machines, each made from single-cell trajectories, gives a network of highly structured Markov chains of states with different source and sink nodes including cycles, revealing essential information on the dynamics of regulatory events. We argue that the obtained networks depict aspects of the Waddington landscape of cell differentiation and characterize them as reachability graphs that provide the basis for the reconstruction of the underlying gene regulatory network.}, language = {en} }