@misc{HeinerYangLiu, author = {Heiner, Monika and Yang, Ming and Liu, Fei}, title = {Modeling and analyzing biological systems using colored hierarchical Petri nets illustrated by C. elegans vulval development}, series = {Journal of Biological Systems}, volume = {22}, journal = {Journal of Biological Systems}, number = {3}, issn = {1793-6470}, doi = {10.1142/S0218339014500181}, pages = {463 -- 493}, language = {en} } @misc{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Representing Network Reconstruction Solutions with Colored Petri Nets}, series = {Neurocomputing}, volume = {174}, journal = {Neurocomputing}, number = {A}, issn = {0925-2312}, doi = {10.1016/j.neucom.2015.04.112}, pages = {483 -- 493}, language = {en} } @misc{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Fuzzy stochastic Petri nets for modeling biological systems with uncertain kinetic parameters}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {2}, issn = {1932-6203}, doi = {10.1371/journal.pone.0149674}, pages = {0149674}, language = {en} } @misc{LiuBlaetkeHeineretal., author = {Liu, Fei and Bl{\"a}tke, Mary-Ann and Heiner, Monika and Yang, Ming}, title = {Modelling and simulating reaction-diffusion systems using coloured Petri nets}, series = {Computers in Biology and Medicine}, volume = {53}, journal = {Computers in Biology and Medicine}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2014.07.004}, pages = {297 -- 308}, language = {en} } @inproceedings{LiuHeinerYang, author = {Liu, Fei and Heiner, Monika and Yang, Ming}, title = {Colored Petri Nets for Multiscale Systems Biology - Current Modeling and Analysis Capabilities in Snoopy}, series = {7th International Conference on Systems Biology (ISB), 2013, 23 - 25 Aug. 2013, Huangshan, China}, booktitle = {7th International Conference on Systems Biology (ISB), 2013, 23 - 25 Aug. 2013, Huangshan, China}, publisher = {IEEE}, address = {Piscataway, NJ}, isbn = {978-1-4799-1387-9}, doi = {10.1109/ISB.2013.6623788}, pages = {24 -- 30}, language = {en} } @misc{WangXiaLiangetal., author = {Wang, Pu and Xia, Ming and Liang, Owen and Sun, Ke and Cipriano, Aaron F. and Schr{\"o}der, Thomas and Liu, Huinan and Xie, Ya-Hong}, title = {Label-free Neurotransmitter SERS Detection by Graphene-Gold Nanopyramid Heterostructure}, series = {Analytical Chemistry}, volume = {87}, journal = {Analytical Chemistry}, number = {20}, issn = {0003-2700}, doi = {10.1021/acs.analchem.5b01560}, pages = {10255 -- 10261}, language = {en} } @misc{LiuAssafChenetal., author = {Liu, Fei and Assaf, George and Chen, Ming and Heiner, Monika}, title = {A Petri nets-based framework for whole-cell modeling}, series = {Biosystems}, volume = {210}, journal = {Biosystems}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2021.104533}, abstract = {Whole-cell modeling aims to incorporate all main genes and processes, and their interactions of a cell in one model. Whole-cell modeling has been regarded as the central aim of systems biology but also as a grand challenge, which plays essential roles in current and future systems biology. In this paper, we analyze whole-cell modeling challenges and requirements and classify them into three aspects (or dimensions): heterogeneous biochemical networks, uncertainties in components, and representation of cell structure. We then explore how to use different Petri net classes to address different aspects of whole-cell modeling requirements. Based on these analyses, we present a Petri nets-based framework for whole-cell modeling, which not only addresses many whole-cell modeling requirements, but also offers a graphical, modular, and hierarchical modeling tool. We think this framework can offer a feasible modeling approach for whole-cell model construction.}, language = {en} }