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data structures and software dependability

computer science department

brandenburg university of technology cottbus - senftenberg

Selected References - Journal Papers

49 entries


2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2006 - 2005 - 2004 - 2003 - 1994

2019

  • [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 for publication: 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: 03 November 2017). [ doi ] [ BibTeX ]

2018

  • [LHG18]
    F Liu, M Heiner and D Gilbert:
    Fuzzy Petri nets for modelling of uncertain biological systems;
    Briefings in Bioinformatics, 2018 (accepted for publication:16 November 2018, published: 27 December 2018). [ url ] [ doi ] [ BibTeX ]
  • [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 for publication: 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 for publication: 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 for publication: 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 for publication: 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 for publication: 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 for publication: 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 for publication: May, 16 2017). [ doi ] [ BibTeX ]
  • [R17]
    Rohr, C:
    Discrete-Time Leap Method For Stochastic Simulation;
    Fundamenta Informaticae, 160(1-2):181-198, 2018 (accepted for publication: 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 for publication: 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 for publication: 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 for publication: 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 for publication: 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: 31 October 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 for publication: 13 July 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 available 12-OCT-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 01 August 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 published 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 ]

… the end …

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