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Selected References - Journal Papers

61 entries

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2024 - 2023 - 2022 - 2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2006 - 2005 - 2004 - 2003 - 1994

2024

• [HLH24]
  M Herajy, F Liu and M Heiner:
  Design Patterns for the Construction of Computational Biological Models;
  Briefings in Bioinformatics, 25, 2024 (accepted: 10 June 2024). [ doi ] [ BibTeX ]

2023

• [LHG23]
  F Liu, M Heiner and D Gilbert:
  Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets;
  STAR Protocols, 4(4):102651, 2023 (accepted: September 2023). [ doi ] [ BibTeX ]
• [SAH23]
  NH Sweilam, S Ahmed and M Heiner:
  Two different parallel approaches for a hybrid fractional order Coronavirus model;
  Egyptian Informatics Journal, 24(4):100408, December 2023 (accepted: 28 September 2023, available online 12 October 2023). [ doi ] [ BibTeX ]

2022

• [CGH22]
  S Connolly, D Gilbert and M Heiner:
  From Epidemic to Pandemic Modelling;
  Frontiers in Systems Biology, March 2022 (accepted: 14 March 2022, published: 14 July 2022). [ url ] [ doi ] [ BibTeX ]
• [FHG22]
  F Liu, M Heiner and D Gilbert:
  Hybrid modelling of biological systems: current progress and future prospects;
  Briefings in Bioinformatics, 2022 (accepted: 16 February 2022, published: 30 March 2022). [ doi ] [ BibTeX ]
• [AHL22]
  G Assaf, M Heiner and F Liu:
  Coloured fuzzy Petri nets for modelling and analysing membrane systems;
  Biosystems, 2022. [ url ] [ doi ] [ BibTeX ]

2021

• [LAC+21]
  F Liu, G Assaf, M Chen and M Heiner:
  A Petri nets-based framework for whole-cell modeling;
  BioSystems, 210:104533, 2021 (accepted: 06 September 2021). [ url ] [ doi ] [ BibTeX ]
• [AHL21]
  G Assaf, M Heiner and F Liu:
  Colouring Fuzziness for Systems Biology;
  Theoretical Computer Science, 875(0304-3975):52-64, 2021 (accepted: 11 April 2021, online: 19 April 2021). [ url ] [ doi ] [ BibTeX ]
• [PPH+21]
  A Pretschner, S Pabel, M Haas, M Heiner and W Marwan:
  Regulatory dynamics of cell differentiation revealed by true time series from multinucleate single cells;
  Frontiers in Genetics, section Systems Biology, 2021 (accepted: 07 December 2020; published: 08 January 2021). [ url ] [ doi ] [ BibTeX ]

2020

• [IHAH20]
  A Ismail, M Herajy, ES Atlam and M Heiner:
  A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-models via Coloured Hybrid Petri Nets;
  Modelling and Simulation in Engineering, 2020, 2020 (Article ID 4715172, 14 pages). [ doi ] [ BibTeX ]
• [LHG20]
  F Liu, M Heiner and D Gilbert:
  Fuzzy Petri nets for modelling of uncertain biological systems;
  Briefings in Bioinformatics, 21(1):198-210, 2020 (accepted: November 16, 2018; published: December 27, 2018). [ url ] [ doi ] [ BibTeX ]

2019

• [NGH+19]
  N Nickaeen, J Ghaisari, M Heiner, S Moein and Y Gheisari:
  Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution;
  Scientific Reports, 9:Article number: 12764, 2019 (accepted: August 14, 2019, published: September 04, 2019). [ doi ] [ BibTeX ]
• [LSHG19]
  F Liu, W Sun, M Heiner and D Gilbert:
  Hybrid modelling of biological systems using fuzzy continuous Petri nets;
  Briefings in Bioinformatics, 12 2019. [ url ] [ doi ] [ BibTeX ]
• [GHGC19]
  D Gilbert, M Heiner, L Ghanbar and J Chodak:
  Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking;
  BMC Bioinformatics, 20(supplement 4), 2019 (accepted: July, 26 2018; published: April 2019). [ doi ] [ BibTeX ]
• [LHG19]
  F Liu, M Heiner and D Gilbert:
  Coloured Petri nets for multilevel, multiscale, and multidimensional modelling of biological systems;
  Briefings in Bioinformatics, 20(3):877-886, 2019 (Published: November 03, 2017). [ doi ] [ BibTeX ]

2018

• [HLRH18]
  M Herajy, F Liu, C Rohr and M Heiner:
  Coloured Hybrid Petri Nets: an Adaptable Modelling Approach for Multi-scale Biological Networks;
  Computational Biology and Chemistry, 76:87-100, 2018. [ doi ] [ BibTeX ]
• [CDG+18]
  R Colombo, C Damiani, D Gilbert, M Heiner, G Mauri and D Pescini:
  Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes;
  BMC Bioinformatics, 19(Suppl 7):251, 2018 (accepted: February 19, 2018). [ doi ] [ BibTeX ]
• [LCHS18]
  F Liu, S Chen, M Heiner and H Song:
  Modeling Biological Systems with Uncertain Kinetic Data Using Fuzzy Continuous Petri Nets;
  BMC Systems Biology, 12(Suppl 4):42, 2018 (accepted: January 2018). [ doi ] [ BibTeX ]
• [GHR18]
  D Gilbert, M Heiner and Christian Rohr:
  Petri-net-based 2D Design of DNA Walker Circuits;
  Natural Computing, 17(1):161–182, 2018 (accepted: November 20, 2017; online February 28, 2018). [ doi ] [ BibTeX ]
• [XCP+18]
  H Xu, TY Curtis, SJ Powers, S Raffan, R Gao, J Huang, M Heiner, DR Gilbert and NG Halford:
  Genomic, biochemical and modelling analyses of asparagine synthetases from wheat;
  Frontiers in Plant Science, section Plant Physiology, 2018 (accepted: December 20, 2017). [ doi ] [ BibTeX ]
• [HLH17]
  M Herajy, F Liu and M Heiner:
  Efficient Modelling of Yeast Cell Cycles Based on Multisite Phosphorylation Using Coloured Hybrid Petri Nets with Marking-dependent Arc Weights;
  J. Nonlinear Analysis: Hybrid Systems, 27(February):191-212, 2018 (online: October 10, 2017). [ doi ] [ BibTeX ]
• [BBB+17]
  Baldan, P, Bocci, M, Brigolin, D, Cocco, N , Heiner, M and Simeoni, M:
  Petri Nets for modelling and analysing Trophic Networks;
  Fundamenta Informaticae, 160(1-2):27-52, 2018 (accepted: May 18, 2017). [ doi ] [ BibTeX ]
• [HH17]
  Herajy, M and Heiner, M:
  Adaptive and Bio-semantics of Continuous Petri Nets: Choosing the Appropriate Interpretation;
  Fundamenta Informaticae, 160(1-2):53-80, 2018 (accepted: May 18, 2017). [ doi ] [ BibTeX ]
• [BR17]
  MA Blätke and Rohr, C:
  BioModelKit: Spatial Modelling of Complex Multiscale Molecular Biosystems based on Modular Models;
  Fundamenta Informaticae, 160(1-2):221-254, 2018 (accepted: May 16, 2017). [ doi ] [ BibTeX ]
• [R17]
  Rohr, C:
  Discrete-Time Leap Method For Stochastic Simulation;
  Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted: May 16, 2017). [ doi ] [ BibTeX ]

2017

• [GHJR17]
  D Gilbert, M Heiner, Y Jayaweera and C Rohr:
  Towards dynamic genome scale models;
  Briefings in Bioinformatics, 2017 (online: October 13, 2017). [ doi ] [ BibTeX ]
• [HLRH17]
  M Herajy, F Liu, C Rohr and M Heiner:
  Snoopy's Hybrid Simulator: a Tool to Construct and Simulate Hybrid Biological Models;
  BMC Systems Biology, 2017 (published: July 28, 2017). [ url ] [ doi ] [ BibTeX ]

2016

• [SPE+16]
  J Somekh, M Peleg, A Eran, I Koren, A Feiglin, A Demishtein, R Shiloh, M Heiner, SW Kong, Z Elazar and I Kohane:
  A Model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease;
  Biomedical Informatics, 63(366-378), 2016 (accepted: August 08, 2016). [ doi ] [ BibTeX ]
• [HRST16]
  M Heiner, C Rohr, M Schwarick and A Tovchigrechko:
  MARCIE’s secrets of efficient model checking;
  Transactions on Petri Nets and Other Models of Concurrency (ToPNoC) XI, LNCS 9930, 2016 (accepted: March 11, 2016). [ url ] [ doi ] [ BibTeX ]
• [LHY16b]
  F Liu, M Heiner and M Yang:
  Fuzzy stochastic Petri nets for modeling biological systems with uncertain kinetic parameters;
  PLoS ONE, 11(2):e0149674, 2016 (accepted: February 09, 2016). [ url ] [ doi ] [ BibTeX ]
• [LHY16a]
  F Liu, M Heiner and M Yang:
  Representing Network Reconstruction Solutions with Colored Petri Nets;
  Neurocomputing, 174, Part A:483–493, January 2016 (accepted: April 2015). [ url ] [ doi ] [ BibTeX ]
• [BKH+16]
  LMF Bertens, J Kleijn, SC Hille, M Heiner, M Koutny and FJ Verbeek:
  Modeling biological gradient formation: combining partial differential equations and Petri nets;
  Natural Computing, 15(4):665-675, 2016 (First online: October 31, 2015). [ url ] [ doi ] [ BibTeX ]

2015

• [BHHP15]
  B Barbot, S Haddad, M Heiner and C Picaronny:
  A Rare Event Method Applied to Signalling Cascades;
  International Journal on Advances in Systems and Measurements, 8(1-2):69-79, 2015 (improved version of [BHHP14]). [ pdf ] [ BibTeX ]
• [HH15]
  Herajy, M and Heiner, M:
  Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets;
  Frontiers in Environmental Science, 3(53), 2015 (accepted: July 13, 2015). [ url ] [ doi ] [ BibTeX ]
• [PGH+15]
  O Pârvu, D Gilbert, M Heiner, F Liu, N Saunders and S Shaw:
  Spatial-temporal modelling and analysis of bacterial colonies with phase variable genes;
  ACM Transactions on Modeling and Computer Simulation (TOMACS), 25(2):25p., May 2015. [ url ] [ doi ] [ BibTeX ]

2014

• [LBHY14]
  F Liu, MA Blätke, M Heiner and M Yang:
  Modelling and simulating reaction–diffusion systems using coloured Petri nets;
  Computers in Biology and Medicine, 53:297–308, October 2014 (online July 2014). [ url ] [ doi ] [ BibTeX ]
• [LHY14]
  F Liu, M Heiner and M Yang:
  Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development;
  WSPC Journal of Biological Systems, 22(3):463–493, online May 2014. [ doi ] [ BibTeX ]
• [HH14a]
  M Herajy and M Heiner:
  Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks;
  Fundamenta Informaticae, 129(1-2):49-67, 2014. [ url ] [ doi ] [ BibTeX ]

2013

• [Rohr13]
  C Rohr:
  Simulative Model Checking of Steady-State and Time-Unbounded Temporal Operators;
  ToPNoC VIII, LNCS 8100, 2013. [ doi ] [ BibTeX ]
• [HSH13]
  M Herajy, M Schwarick and M Heiner:
  Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle;
  ToPNoC VIII, LNCS 8100, 2013. [ pdf ] [ doi ] [ BibTeX ]
• [LH13b]
  F Liu and M Heiner:
  Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets;
  IET Systems Biology, 7(4):106 - 113, August 2013. [ doi ] [ BibTeX ]
• [LH13a]
  F Liu and M Heiner:
  Modeling membrane systems using colored stochastic Petri nets;
  Nat. Computing, 12(4):617 - 629, 2013. [ url ] [ doi ] [ BibTeX ]
• [BDR+13]
  MA Blätke, A Dittrich, C Rohr, M Heiner, F Schaper and W Marwan:
  JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology;
  Molecular BioSystems, 9(6):1290-1307, 2013. [ url ] [ doi ] [ BibTeX ]
• [HG13]
  M Heiner and D Gilbert:
  BioModel Engineering for Multiscale Systems Biology;
  Progress in Biophysics and Molecular Biology, 111(2-3):119–128, April 2013 (online: October 12, 2012). [ url ] [ doi ] [ BibTeX ]
• [GGH+13]
  Q Gao, D Gilbert, M Heiner, F Liu, D Maccagnola and D Tree:
  Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing;
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(2):337-351, 2013 (online: August 01, 2012). [ doi ] [ BibTeX ]

2012

• [HH12]
  M Herajy and M Heiner:
  Hybrid Representation and Simulation of Stiff Biochemical Networks;
  J. Nonlinear Analysis: Hybrid Systems, 6(4):942–959, November 2012. [ url ] [ doi ] [ BibTeX ]

2011

• [ST11]
  M Schwarick and A Tovchigrechko:
  IDD-based model validation of biochemical networks;
  Theoretical Computer Science, 412(26):2884–2908, 2011 (online: July 2010). [ pdf ] [ doi ] [ BibTeX ]

2010

• [BDGH10]
  R Breitling, RA Donaldson, DR Gilbert and M Heiner:
  Biomodel Engineering - From Structure to Behavior (position paper);
  Transactions on Computational Systems Biology XII, Special Issue on Modeling Methodologies, 5945:1–12, 2010. [ pdf ] [ doi ] [ BibTeX ]
• [HS10]
  M Heiner and K Sriram:
  Structural Analysis to Determine the Core of Hypoxia Response Network;
  PLoS ONE, 5(1):e8600, 2010. [ doi ] [ BibTeX ]
• [RMH10]
  C Rohr, W Marwan and M Heiner:
  Snoopy - a unifying Petri net framework to investigate biomolecular networks;
  Bioinformatics, 26(7):974–975, 2010 ((Advanced Access: February 7, 2010)). [ url ] [ doi ] [ BibTeX ]
• [SH10b]
  S Soliman and M Heiner:
  A Unique Transformation from Ordinary Differential Equations to Reaction Networks;
  PLoS ONE, 5(12):e14284, 2010. [ doi ] [ BibTeX ]

2009

• [HLGM09]
  M Heiner, S Lehrack, D Gilbert and W Marwan:
  Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments;
  Transactions on Computational Systems Biology XI, 5750:138–163, 2009. [ url ] [ pdf ] [ doi ] [ BibTeX ]

2008

• [BGHO08]
  R Breitling, D Gilbert, M Heiner and R Orton:
  A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
  Briefings in Bioinformatics, 9(5):404–421, September 2008. [ doi ] [ BibTeX ]
• [GSH+08]
  E Grafahrend-Belau, F Schreiber, M Heiner, A Sackmann, BH Junker, S Grunwald, A Speer, K Winder and I Koch:
  Modularization of biochemical networks based on classification of Petri net T-invariants;
  BMC Bioinformatics, 9:90, 2008. [ doi ] [ BibTeX ]

2006

• [SHK06]
  A Sackmann, M Heiner and I Koch:
  Application of Petri net based analysis techniques to signal transduction pathways;
  BMC Bioinformatics 2006, 7:482, 2006. [ url ] [ doi ] [ BibTeX ]

2005

• [KJH05]
  I Koch, BH Junker and M Heiner:
  Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber;
  Bioinformatics, April 2005, 21:1219 - 1226, 2005. [ doi ] [ BibTeX ]
• [PHK05]
  L Popova-Zeugmann, M Heiner and I Koch:
  Time Petri Nets for Modelling and Analysis of Biochemical Networks);
  Fundamenta Informaticae, 67:149–162, 2005. [ url ] [ pdf ] [ BibTeX ]

2004

• [HKW04]
  M Heiner, I Koch and J Will:
  Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis;
  BioSystems, 75/1-3:15-28, 2004. [ pdf ] [ doi ] [ BibTeX ]
• [KSH04]
  I Koch, M Schüler and M Heiner:
  STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks;
  In Silico Biology, 5, 2004. [ url ] [ BibTeX ]

2003

• [VHK03]
  K Voss, M Heiner and I Koch:
  Steady State Analysis of Metabolic Pathways Using Petri Nets;
  In Silico Biology, 3:367–387, 2003. [ url ] [ pdf ] [ BibTeX ]

1994

• [HVW94]
  M Heiner, G Ventre and D Wikarski:
  A Petri Net Based Methodology to Integrate Qaulitative and Quantitative Analysis;
  Information and Software Technology, 7(36):435–441, 1994. [ url ] [ pdf ] [ BibTeX ]