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Snoopy's bibliography - External Papers

latest update: May 01, 2021, at 08:53 AM

Please use the following reference to give credits to Snoopy:
M Heiner, M Herajy, F Liu, C Rohr and M Schwarick:
Snoopy – a unifying Petri net tool;
In Proc. PETRI NETS 2012, Hamburg, Springer, LNCS, volume 7347, 398–407, June 2012

This list contains literature references (papers, Master theses, PhD theses, etc.) where Snoopy has been used by authors who are not members of Snoopy's development team. Please let us know if we missed your paper.

147 entries

2021 - 2020 - 2019 - 2018 - 2017 - 2016 - 2015 - 2014 - 2013 - 2012 - 2011 - 2010 - 2009 - 2008 - 2007

2021

• [GFK21]
  Sakshi Gupta, Zeeshan Fatima and Sunita Kumawat:
  Study of the bioenergetics to identify the novel pathways as a drug target against Mycobacterium tuberculosis using Petri net;
  Biosystems, 209:104509, 2021. [ url ] [ doi ] [ BibTeX ]
• [Somekh2021]
  Somekh, Judith:
  Model-based pathway enrichment analysis applied to the TGF-beta regulation of autophagy in autism;
  Journal of Biomedical Informatics, 118:103781, 2021. [ doi ] [ BibTeX ]

2020

• [AAI+20]
  Azim, N, Ahmad, J, Iqbal, N, Siddiqa, A, Majid, A, Ashraf, J and Jalil, F:
  Petri Net modelling approach for analysing the behaviour of Wnt/$eta$-catenin and Wnt/Ca2+ signalling pathways in arrhythmogenic right ventricular cardiomyopathy;
  IET Systems Biology, 14(6):350–367, 2020. [ doi ] [ BibTeX ]
• [NSD20]
  Nadal, M, Schierle, GSK and Dikicioglu, D:
  Formal model of Parkinson's disease neurons unveils possible causality links in the pathophysiology of the disease;
  bioRxiv, 2020. [ doi ] [ BibTeX ]
• [MKA+20]
  Malik, S, Khalid, S, Ali, H, Khan, M, Mehwish, F, Javed, A, Akbar, F, Hanif, R and Suleman, M:
  In-silico modeling and analysis of the therapeutic potential of miRNA-7 on EGFR associated signaling network involved in breast cancer;
  Gene Reports, 2020. [ doi ] [ BibTeX ]
• [Connolly20]
  Connolly, Shannon Faye:
  Developing a Pandemic Model of Europe using Coloured Continuous Petri Nets with Validation against the COVID-19 Pandemic;
  Master thesis, Brunel University London, Department of Computer Science, MSc Data Science & Analytics, 2020. [ BibTeX ]
• [FRR+20]
  Formanowicz, D, Rybarczyk, A, Radom, M, Tanas, K and Formanowicz, P:
  A Stochastic Petri Net-Based Model of the Involvement of Interleukin 18 in Atherosclerosis;
  International Journal of Molecular Sciences, 21(22):8574, 2020. [ doi ] [ BibTeX ]
• [GFF20]
  Gutowska, K, Formanowicz, D and Formanowicz, P:
  Systems Approach Based on Petri Nets as a Method for Modeling and Analysis of Complex Biological Systems Presented on the Example of Atherosclerosis Development Process;
  In Advanced, Contemporary Control, AISC, volume 1196, Springer International Publishing, pages 579–586, 2020. [ doi ] [ BibTeX ]
• [RWH+20]
  V Rätzel, B Werthmann, M Haas, J Strube and W Marwan:
  Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets;
  Biosystems, 189:1040929, 2020. [ url ] [ doi ] [ BibTeX ]

2019

• [AAU19]
  Ashraf, J, Ahmad, J and Ul-Haq, Z:
  Deciphering the Role of PKC in Calpain-CAST System Through Formal Modeling Approach;
  In International Work-Conference on Bioinformatics and Biomedical Engineering, Springer, LNBI 11465, pages 60–71, 2019. [ doi ] [ BibTeX ]
• [Conway19]
  Darren Conway:
  Integrating In-Silico Models with In-Vitro Data to Generate Novel Insights into Biological Systems;
  PhD thesis, Liverpool John Moores University, 2019. [ pdf ] [ BibTeX ]
• [AAHA19]
  H Ashraf, J Ahmad, A Hassan and A Ali:
  Computational Modeling and Analysis of the Impacts of Sleep Deprivation on Glucose Stimulated Insulin Secretion;
  Biosystems, 2019. [ doi ] [ BibTeX ]
• [DSKV19]
  SN Danial, J Smith, F Khan and B Veitch:
  Human-Like Sequential Learning of Escape Routes for Virtual Reality Agents;
  Fire Technology, 2019. [ doi ] [ BibTeX ]
• [EL19]
  I Edhlund and C Lee:
  A Petri Net Approach to Physiologically Based Toxicokinetic (PBTK) Modeling;
  Environmental toxicology and chemistry, 2019. [ doi ] [ BibTeX ]
• [RMMP19]
  S Rova, F Müller, P Meire and F Pranovi:
  Sustainability perspectives and spatial patterns of multiple ecosystem services in the Venice lagoon: Possible roles in the implementation of the EU Water Framework Directive;
  Ecological Indicators, 98:556-567, 2019. [ doi ] [ BibTeX ]
• [WR19]
  Walton, R and De Roure, D:
  Modelling web based socio-technical systems through formalising possible sequences of human experience;
  In Proceedings of the 10th ACM Conference on Web Science (WebSci '19), ACM Digital Library, pages 301–310, 2019. [ url ] [ doi ] [ BibTeX ]

2018

• [GFF18]
  K Gutowska, D Formanowicz and P Formanowicz:
  Selected Aspects of Tobacco-Induced Prothrombotic State, Inflammation and Oxidative Stress: Modeled and Analyzed Using Petri Nets;
  Interdiscip Sci Comput Life Sci, 2018. [ doi ] [ BibTeX ]
• [RMM+18]
  S Rova, P Meire, F Müller, M Simeoni and F Pranovi:
  A Petri net modeling approach to explore the temporal dynamics of the provision of multiple ecosystem services;
  Science of The Total Environment, 655:1047-1061, 2018 (10 March 2019). [ doi ] [ BibTeX ]
• [RON+18]
  S Rehman, A Obaid, A Naz, A Ali, S Kanwal and J Ahmad:
  Model-based in silico analysis of the PI3K/Akt pathway: the elucidation of cross-talk between diabetes and breast cancer;
  PeerJ, 6:e5917, 2018. [ doi ] [ BibTeX ]
• [FGF18]
  D Formanowicz, K Gutowska and P Formanowicz:
  Theoretical Studies on the Engagement of Interleukin 18 in the Immuno-Inflammatory Processes Underlying Atherosclerosis;
  International Journal of Molecular Sciences, 19(11):3476, 2018. [ url ] [ doi ] [ BibTeX ]
• [MFM+18]
  EM Maldonado , CP Fisher, DJ Mazzatti, AL Barber, MJ Tindall, NJ Plant, AM Kierzek and JB Moore:
  Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease;
  npj Systems Biology and Applications, 4(1):33, 2018. [ url ] [ doi ] [ BibTeX ]
• [WPB+18]
  M Weyder, M Prudhomme, M Berge, P Polard and G Fichant:
  Dynamic Modeling of Streptococcus pneumoniae Competence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation;
  Frontiers in Microbiology, 9:1637, 2018. [ doi ] [ BibTeX ]
• [ONTA+18]
  A Obaid, A Naz, S Tariq Ashraf, FM Awan, A Ikram, M Tariq Saeed, A Raza, J Ahmad and A Ali:
  Formal modeling of the key determinants of Hepatitis C Virus (HCV) induced adaptive immune response network: An integrative approach to map the cellular and cytokine-mediated host immune regulations;
  PeerJ Preprints, 6:e26456v1, 2018. [ doi ] [ BibTeX ]
• [CVC18]
  RV Carvalho, FJ Verbeek and CJ Coelho:
  Bio-modeling Using Petri Nets: A Computational Approach;
  In Theoretical and Applied Aspects of Systems Biology, Springer, pages 3–26, 2018. [ doi ] [ BibTeX ]
• [ONI+18]
  A Obaid, A Naz, A Ikram, FM Awan, A Raza, J Ahmad and A Ali:
  Model of the adaptive immune response system against HCV infection reveals potential immunomodulatory agents for combination therapy;
  Scientific Reports, 8(1):8874, 2018. [ doi ] [ BibTeX ]
• [KHJ+18]
  S Khalid, R Hanif, I Jabeen, Q Mansoor and M Ismail:
  Pharmacophore modeling for identification of anti-IGF-1R drugs and in-vitro validation of fulvestrant as a potential inhibitor;
  PloS one, 13(5):e0196312, 2018. [ doi ] [ BibTeX ]
• [AAAU18]
  J Ashraf, J Ahmad, A Ali and Z Ul-Haq:
  Analyzing the behavior of neuronal pathways in Alzheimer's using Petri net modeling approach;
  Frontiers in Neuroinformatics, 12:26, 2018. [ doi ] [ BibTeX ]
• [KFF2018]
  A Kozak, D Formanowicz and P Formanowicz:
  Structural analysis of a Petri net model of oxidative stress in atherosclerosis;
  IET Systems Biology, 12(3):108-117, 2018. [ doi ] [ BibTeX ]
• [FH18]
  MP Fortina nd SV Hardy:
  A Hybrid Petri Net Model of the Akt-Wnt-mTOR-p70S6K Signalling Network in Neurons;
  Fundamenta Informaticae, 160(1-2):1-25, 2018. [ doi ] [ BibTeX ]
• [BMZM18]
  J Bordon, M Moškon, N Zimic and M Mraz:
  Semi-quantitative Modelling of Gene Regulatory Processes with Unknown Parameter Values Using Fuzzy Logic and Petri Nets;
  Fundamenta Informaticae, 160(1-2):81-100, 2018. [ doi ] [ BibTeX ]
• [DGG+18]
  F Delaplace, C Di Giusto, JL Giavitto, H Klaudel and A Spicher:
  Activity Networks with Delays an Application to Toxicity Analysis;
  Fundamenta Informaticae, 160(1-2):119-142, 2018. [ doi ] [ BibTeX ]
• [FRF18]
  D Formanowicz, A Rybarczyk and P Formanowicz:
  Factors Influencing Essential Hypertension and Cardiovascular Disease Modeled and Analyzed using Stochastic Petri Nets;
  Fundamenta Informaticae, 160(1-2):143-165, 2018. [ doi ] [ BibTeX ]
• [BA18]
  R Bashirov and NI Akçay:
  Stochastic Simulation-based Prediction of the Behavior of the p16-mediated Signaling Pathway;
  Fundamenta Informaticae, 160(1-2):167-179, 2018. [ doi ] [ BibTeX ]
• [GBSK18]
  M Grabowski, Marek, G Bokota, J Sroka and A Kierzek:
  Verification of Dynamic Behaviour in Qualitative Molecular Networks Describing Gene Regulation, Signalling and Whole-cell Metabolism;
  Fundamenta Informaticae, 160(1-2):199-219, 2018. [ doi ] [ BibTeX ]

2017

• [M17]
  M Mehraei:
  Mood States Prediction By Stochastic Petri Nets;
  In International Psychological Applications Conference and Trends (InPACT), Budapest, Hungary, World Institute for Advanced Research and Science, pages 258–262, 2017. [ BibTeX ]
• [DBS17]
  R Duranay, R Bashirov and A Seytanoglu:
  Simulation-based identification of optimal combination of drug candidates for spinal muscular atrophy;
  Procedia Computer Science, 120:253–259, 2017. [ doi ] [ BibTeX ]
• [GD17]
  D Ghosh and RK De:
  In Silico Modeling of Crabtree Effect;
  Endocrine, Metabolic & Immune Disorders-Drug Targets (Formerly Current Drug Targets-Immune, Endocrine & Metabolic Disorders), 17(3):182–188, 2017. [ doi ] [ BibTeX ]
• [KPSK17]
  K Kedzia, W Ptak, J Sroka and AM Kierzek:
  Simulation of multicellular populations with Petri nets and genome scale intracellular networks;
  Science of Computer Programming, 2017. [ doi ] [ BibTeX ]
• [SL17]
  K Selvakumar and K Latha:
  An approach of disease-drug interaction model with Stochastic Petri Net;
  In Trends in Industrial Measurement and Automation (TIMA), 2017, IEEE, pages 1–4, 2017. [ doi ] [ BibTeX ]
• [WM17]
  B Werthmann and W Marwan:
  Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape;
  Journal of Physics D: Applied Physics, 50(46):464003, 2017. [ doi ] [ BibTeX ]
• [NOA+17]
  A Naz, A Obaid, FM Awan, A Ikram, J Ahmad and A Ali:
  Petri Net-based model of Helicobacter pylori mediated disruption of tight junction proteins in stomach lining during gastric carcinoma;
  Frontiers in Microbiology, 8, 2017. [ doi ] [ BibTeX ]
• [ANO+17]
  FM Awan, A Naz, A Obaid, A Ikram, A Ali, J Ahmad, AK Naveed and HA Janjua:
  MicroRNA pharmacogenomics based integrated model of miR-17-92 cluster in sorafenib resistant HCC cells reveals a strategy to forestall drug resistance;
  Scientific Reports, 2017. [ doi ] [ BibTeX ]
• [BAPS17]
  Z Bibi, J Ahmad, RZ Paracha and A Siddiqa:
  Modeling and analysis of the signaling crosstalk of PI3K, AMPK and MAPK with Timed Hybrid Petri Nets approach;
  In Computational Science and Its Applications (ICCSA), 2017 17th International Conference on, IEEE, pages 1–7, July 2017. [ doi ] [ BibTeX ]
• [CFF17]
  K Chmielewska, D Formanowicz and P Formanowicz:
  The effect of cigarette smoking on endothelial damage and atherosclerosis development–modeled and analyzed using Petri nets;
  Archives of Control Sciences, 27(2):211–228, 2017. [ doi ] [ BibTeX ]
• [Blaetke17]
  Mary-Ann Blätke:
  BIOMODELKIT – a framework for modular biomodel engineering;
  PhD thesis, Otto-von-Guericke University Magdeburg, Faculty for Natural Sciences, April 2017. [ pdf ] [ BibTeX ]
• [FRZF17]
  D Formanowicz, M Radom, P Zawierucha and P Formanowicz:
  Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis;
  PloS one, 12(3):e0173020, 2017. [ doi ] [ BibTeX ]

2016

• [KHT+16]
  S Khalid, R Hanif, SHK Tareen, A Siddiqa, Z Bibi and J Ahmad:
  Formal modeling and analysis of ER-$lpha$ associated Biological Regulatory Network in breast cancer;
  PeerJ, 4:e2542, 2016. [ doi ] [ BibTeX ]
• [S16]
  IA Sheikh, J Ahmad and MT Saeed:
  Modelling and Simulation of Biological Regulatory Networks by Stochastic Petri Nets;
  In Proceedings of the World Congress on Engineering and Computer Science (WCECS 2016), volume 2, 2016. [ url ] [ BibTeX ]
• [B16]
  R Bronis:
  Data transfer in HBB-Next architecture;
  Information Sciences & Technologies: Bulletin of the ACM Slovakia, 8(1):7-13, 2016. [ url ] [ BibTeX ]
• [GG16]
  DE Gratie and C Gratie:
  Composition colored Petri nets for the refinement of reaction-based models;
  Electronic Notes in Theoretical Computer Science, 326:51–72, 2016. [ doi ] [ BibTeX ]
• [Gratie16]
  Diana-Elena Gratie:
  Refinement of Biomodels Using Petri Nets;
  PhD thesis, Abo Akademi University, Faculty of Science and Engineering, October 2016. [ url ] [ pdf ] [ BibTeX ]
• [Louro16]
  Louro, Marco António Dias:
  A stochastic model of centriole assembly;
  Master thesis, Universidade de Lisboa, Faculdade de Ciências, Bioinformática e Biologia Computacional (Biologia Computacional), 2016. [ pdf ] [ BibTeX ]
• [PCMP16]
  Pennisi, M, Cavalieri, S, Motta, S and Pappalardo, F:
  A methodological approach for using high-level Petri nets to model the immune system response;
  BMC Bioinformatics, 17(19):91, 2016. [ doi ] [ BibTeX ]
• [BRS16]
  B Behinaein, K Rudie and W Sangrar:
  Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer;
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99), 2016. [ doi ] [ BibTeX ]
• [Behinaein16]
  Behnam Behinaein Hamgini:
  Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways;
  PhD thesis, Queen's University Kingston, Ontario, Canada, September 2016. [ pdf ] [ BibTeX ]
• [PKS16]
  W Ptak, AM Kierzek and J Sroka:
  AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks;
  In International Conference on Applications and Theory of Petri Nets and Concurrency, Springer, Lecture Notes in Computer Science, volume 9698, pages 113–122, 2016. [ doi ] [ BibTeX ]
• [HGM+16]
  Z Heidary, J Ghaisari, S Moein, M Naderi and Y Gheisari:
  Stochastic Petri net modeling of hypoxia pathway predicts a novel incoherent feed-forward loop controlling sdf-1 expression in acute kidney injury;
  IEEE transactions on nanobioscience, 15(1):19–26, 2016. [ doi ] [ BibTeX ]
• [Shirt-Ediss16]
  Benjamin John Shirt-Ediss:
  Modelling Early Transitions Toward Autonomous Protocells;
  PhD thesis, Universitat Pompeu Fabra Barcelona, 2016. [ pdf ] [ BibTeX ]

2015

• [NGGM15]
  N Nickaeen, J Ghaisari, Y Gheisari and S Moein:
  Modeling and controlling TGF-$eta$ pathway using standard Petri Nets;
  In 23rd Iranian Conference on Electrical Engineering (ICEE), IEEE, pages 38–43, 2015. [ doi ] [ BibTeX ]
• [MVRR+15]
  Morales Varela, Alberto, Rojas Ramírez, Jorge Armando, Hernndez Gómez, Luis Héctor, Morales González, Ángel and Jiménez Reyes, María Yanet:
  Modelo de un sistema de produccion esbelto con redes de Petri para apoyar la toma de decisiones;
  Ingeniare. Revista chilena de ingeniería, 23(2):182–195, 2015. [ doi ] [ BibTeX ]
• [Carvalho15]
  Viana de Carvalho, Rafael:
  Computational modeling of mycobacterium infection and innate immune reponse in zebrafish;
  PhD thesis, Leiden Institute of Advanced Computer Science (LIACS), Faculty of Science, Leiden University, January 2015. [ url ] [ BibTeX ]
• [BBB+15]
  P Baldan, M Bocci, D Brigolin, N Cocco and M Simeoni:
  Petri nets for modelling and analysing trophic networks;
  In Proc. of the 6rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2015, CEUR-WS.org, CEUR Workshop Proceedings, volume 1373, pages 21–36, June 2015. [ url ] [ pdf ] [ BibTeX ]
• [CHK+15]
  RV Carvalho, J van den Heuvel , J Kleijn and FJ Verbeek:
  Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response;
  Computation, 3(2):150–176, 2015. [ pdf ] [ doi ] [ BibTeX ]
• [TA15]
  SHK Tareen and J Ahmad:
  Modelling and Analysis of the Feeding Regimen Induced Entrainment of Hepatocyte Circadian Oscillators Using Petri Nets;
  PloS one, 10(3):e0117519, 2015. [ doi ] [ BibTeX ]
• [WPC15]
  Wu, Zujian, Pang, Wei and Coghill, George M:
  An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing;
  Cognitive Computation, 2015. [ BibTeX ]

2014

• [Kozak14]
  Adam Kozak:
  Grafy etykietowalne i sieci Petriego w analizie procesów biochemicznych i biologicznych;
  PhD thesis, Politechnika Poznańska, 2014 (Wydzial Informatyki Instytut Informatyki). [ url ] [ BibTeX ]
• [FRF14]
  D Formanowicz, M Radom and P Formanowicz:
  Modelowanie udziau zelaza w powstawaniu miazdzycy-podejscie systemowe;
  Kosmos, 3(63):331–344, 2014 (journal ISSN 0023-4249). [ url ] [ BibTeX ]
• [BM14]
  Boysen, Jakob Jakobsen and Laursen, Sune Mlgaard:
  A modelling framework for Synthetic Biology;
  Master thesis, Technical University of Denmark, 2014 (M.Sc. in Computer Science and Engineering). [ pdf ] [ BibTeX ]
• [WGG14]
  B Behinaein, K Rudie and W Sangrar:
  Structural Analysis of Petri Nets for Modeling and Analyzing Signaling Pathways;
  In Canadian Conference on Electrical and Computer Engineering (CCECCE 2014), IEEE, pages 522-526, 2014. [ url ] [ doi ] [ BibTeX ]
• [AIK+14]
  IR Akberdin, NV Ivanisenko, FV Kazantsev, EA Oschepkova, NA Omelyanchuk, YG Matushkin and DA Afonnikov:
  Modeling of Regulatory Mechanisms for mESC Self-Renewal: Kinetic and Stochastic Approaches;
  Mathematical Biology and Bioinformatics, 9(2):504-517, 2014. [ url ] [ pdf ] [ BibTeX ]
• [KPV14]
  Kuttippurathu, L, Parrish, A and Vadigepalli, R:
  Integrated Computational Model of Intracellular Signaling and microRNA Regulation Predicts the Network Balances and Timing Constraints Critical to the Hepatic Stellate Cell Activation Process;
  Processes, 2(4):773–794, 2014. [ url ] [ doi ] [ BibTeX ]
• [MSDH14]
  Majumdar, A, Scott, SD, Deogun, JS and Harris, S:
  Yeast pheromone pathway modeling using Petri nets;
  BMC Bioinformatics, 15(Suppl 7):S13, 2014. [ url ] [ BibTeX ]
• [Castaldi14]
  Castaldi, Davide Fabio:
  Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation;
  PhD thesis, Università degli Studi di Milano-Bicocca, 2014. [ pdf ] [ BibTeX ]
• [MPG+14]
  G Minervini, E Panizzoni, M Giollo, A Masiero, C Ferrari and SCE Tosatto:
  Design and Analysis of a Petri Net Model of the Von Hippel-Lindau (VHL) Tumor Suppressor Interaction Network;
  PloS one, 9(6):e96986, 2014. [ doi ] [ BibTeX ]
• [CKV14]
  RV Carvalho, J Kleijn and F Verbeek:
  A multi-scale extensive Petri net model of the bacterial-macrophage interaction;
  In Proc. of the 5rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of PETRI NETS 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 15–29, June 2014. [ url ] [ pdf ] [ BibTeX ]
• [WGG14]
  Z Wu, C Grosan and D Gilbert:
  Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling;
  In Nature Inspired Cooperative Strategies for Optimization (NICSO 2013), Springer International Publishing, Studies in Computational Intelligence, volume 512, pages 245-260, 2014. [ doi ] [ BibTeX ]

2013

• [FKG+13]
  Formanowicz, D, Kozak, A, Gowacki, T, Radom, M and Formanowicz, P:
  Hemojuvelin–hepcidin axis modeled and analyzed using Petri nets;
  Journal of biomedical Informatics, 46(6):1030–1043, 2013. [ pdf ] [ doi ] [ BibTeX ]
• [GP13]
  DE Gratie and I Petre:
  Quantitative Petri Nets Models for the Heat Shock Response;
  Technical report 1068, 2013. [ pdf ] [ BibTeX ]
• [ATBK13]
  L Albergante, J Timmis, L Beattie and PM Kaye:
  A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection;
  PLoS Comput Biol, 9(11):e1003334, 2013. [ doi ] [ BibTeX ]
• [LY13]
  F Liu and M Yang:
  Colored Stochastic Petri Nets for Modeling Complex Biological Systems;
  International Journal of Hybrid Information Technology, 6(5):11-24, 2013. [ url ] [ doi ] [ BibTeX ]
• [FPMK13]
  CP Fisher, NJ Plant, JB Moore and AM Kierzek:
  QSSPN: Dynamic Simulation of Molecular Interaction Networks Describing Gene Regulation, Signalling and Whole-Cell Metabolism in Human Cells;
  Bioinformatics, 2013. [ url ] [ BibTeX ]
• [Gao13]
  Q Gao:
  A Systems Biology Approach to Multi-Scale Modelling and Analysis Of Planar Cell Polarity In Drosophila Melanogaster Wing;
  PhD thesis, Brunel University, London/Uxbridge, February 2013. [ url ] [ BibTeX ]
• [CMMA13]
  D Castaldi, D Maccagnola, D Mari and F Archetti:
  Mining for Variability in the Coagulation Pathway: A Systems Biology Approach;
  In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Springer Berlin Heidelberg, Lecture Notes in Computer Science, volume 7833, pages 153-164, 2013. [ url ] [ doi ] [ BibTeX ]

2012

• [Majumdar12]
  A Majumdar:
  Modeling of Yeast Pheromone Pathway using Petri Nets;
  Master thesis, University of Nebraska, Lincoln, Computer Science and Engineering Dep., December 2012. [ url ] [ BibTeX ]
• [Wu2012]
  Z Wu:
  A generic approach to behaviour-driven biochemical model construction;
  PhD thesis, Brunel University, London/Uxbridge, October 2012. [ url ] [ BibTeX ]
• [CKMV12]
  R.V. Carvalho, J. Kleijn, A.H. Meijer and F.J. Verbeek:
  Modeling Innate Immune Response to Early Mycobacterium Infection;
  Computational and Mathematical Methods in Medicine, 2012:12, 2012. [ doi ] [ BibTeX ]
• [Bertens12]
  Bertens, LMF:
  Computerised modelling for developmental biology: an exploration with case studies;
  PhD thesis, Leiden University, 2012. [ url ] [ BibTeX ]
• [Donaldson12]
  R Donaldson:
  Modelling and Analysis of Structure in Cellular Signalling Systems;
  PhD thesis, University of Glasgow, 2012. [ url ] [ BibTeX ]
• [BFSK12]
  Behre, J, de Figueiredo, LF, Schuster, S and Kaleta, C:
  Detecting structural invariants in biological reaction networks;
  Methods in molecular biology (Clifton, NJ), 804:377, 2012. [ pdf ] [ BibTeX ]
• [BGC12]
  Barros, JP, Gomes, L and Costa, A:
  On the verification of non-autonomous Petri net models using autonomous Petri net tools;
  In IECON 2012 - 38th Annual Conference on IEEE Industrial Electronics Society, pages 6138-6143, oct. 2012. [ doi ] [ BibTeX ]
• [CMNV12]
  R. S. Costa, D. Machado, A. R. Neves and S. Vinga:
  Multi-level dynamic Modeling in Biological Systems - Application of Hybrid Petri Nets to Network Simulation;
  In Proceedings of BIOINFORMATICS 2012 - International Conference on Bioinformatics Models, Methods and Algorithms, pages 317-321, 2012. [ pdf ] [ doi ] [ BibTeX ]
• [GN12]
  Gogolinska, A and Nowak, W:
  Petri Nets Approach to Modeling of Immune System and Autism;
  In Artificial Immune Systems, Springer Berlin / Heidelberg, Lecture Notes in Computer Science, volume 7597, pages 86-99, 2012. [ url ] [ doi ] [ BibTeX ]
• [Kno12]
  S Knowlton:
  Petri Net Modeling and Analysis of Biological Processes Implicated in Amyotrophic Lateral Sclerosis;
  Technical report, 2012. [ pdf ] [ BibTeX ]
• [MB12]
  Marwan, W and Blätke, MA:
  A module-based approach to biomodel engineering with Petri nets;
  In Proceedings of the Winter Simulation Conference, Berlin, Germany, Winter Simulation Conference, WSC '12, pages 297:1–297:12, 2012. [ url ] [ BibTeX ]

2011

• [BMM11]
  MA Blätke, S Meyer and W Marwan:
  Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform;
  In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 117–134, June 2011. [ pdf ] [ BibTeX ]
• [DWM11]
  Durzinsky, M., Wagler, A. and Marwan, W.:
  Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks;
  BMC systems biology, 5(1):113, 2011. [ url ] [ BibTeX ]
• [FCG2011]
  Ferreira, R., Costa, A. and Gomes, L.:
  Intra-and inter-circuit network for Petri nets based components;
  In Industrial Electronics (ISIE), 2011 IEEE International Symposium on, IEEE, pages 1529–1534, 2011. [ url ] [ BibTeX ]
• [FSK+11]
  Formanowicz, D., Sackmann, A., Kozak, A., Bazewicz, J. and Formanowicz, P.:
  Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach;
  Bioprocess and biosystems engineering, 2011. [ url ] [ BibTeX ]
• [Fongwa11]
  Fongwa, EA:
  A business modelling approach using Petri nets to preserve ecosystem services by community-based financial participation;
  PhD thesis, Brandenburg University of Technology Cottbus, 2011. [ url ] [ BibTeX ]
• [HBG+11]
  Hinkelmann, F., Brandon, M., Guang, B., McNeill, R., Blekherman, G., Veliz-Cuba, A. and Laubenbacher, R.:
  ADAM: Analysis of discrete models of biological systems using computer algebra;
  BMC bioinformatics, 12(1):295, 2011. [ url ] [ BibTeX ]
• [HI11]
  Hardy, S. and Iyengar, R.:
  Analysis of Dynamical Models of Signaling Networks with Petri Nets and Dynamic Graphs;
  Modeling in Systems Biology, 2011. [ url ] [ BibTeX ]
• [KT11]
  D Kafura and D Tatar:
  Initial experience with a computational thinking course for computer science students;
  In Proceedings of the 42nd ACM technical symposium on Computer science education, Dallas, TX, USA, ACM, SIGCSE '11, pages 251–256, 2011. [ url ] [ doi ] [ BibTeX ]
• [P11]
  Pagnoni, A.:
  Error-correcting Petri nets;
  Natural Computing, 10(2):711–725, 2011. [ url ] [ BibTeX ]
• [Petre11]
  I Petre (ed.):
  Introduction to Computational and Systems Biology, Collection of Modelling Reports;
  , Abo Akademi, Department of IT, 2011. [ url ] [ BibTeX ]
• [PGM11]
  Pereira, F., Gomes, L. and Moutinho, F.:
  Automatic Generation of Run-Time Monitoring Capabilities to Petri Nets Based Controllers with Graphical User Interfaces;
  Technological Innovation for Sustainability, 2011. [ BibTeX ]
• [PZ11]
  Popova-Zeugmann, L.:
  Quantitative evaluation of time-dependent Petri nets and applications to biochemical networks;
  Natural Computing, 10(3):1017–1043, 2011. [ url ] [ BibTeX ]
• [PZP11]
  L Popova-Zeugmann and E Pelz:
  Studying Steady States in Biochemical Reaction Systems by Time Petri Nets;
  In Proc. of the International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR-WS.org, CEUR Workshop Proceedings, volume 724, pages 71–86, June 2011. [ pdf ] [ BibTeX ]
• [RCG11]
  Reis, M., Campos-Rebelo, R. and Gomes, L.:
  Introducing model-based development within the reengineering of a Smart House controllers system;
  In Industrial Informatics (INDIN), 2011 9th IEEE International Conference on, IEEE, pages 753–758, 2011. [ url ] [ BibTeX ]
• [RRR+11]
  Rodriguez, E.M., Rudy, A., del Rosario, R.C.H., Vollmar, A.M. and Mendoza, E.R.:
  A discrete Petri net model for cephalostatin-induced apoptosis in leukemic cells;
  Natural Computing, 10(3):993–1015, 2011. [ url ] [ BibTeX ]
• [S11]
  Sackmann, A.:
  Discrete Modeling;
  Modeling in Systems Biology, 2011. [ url ] [ BibTeX ]
• [Yang11]
  Yang, Y.:
  Investigation of the Regulatory Roles of Micrornas by Systems Biology Approaches;
  PhD thesis, National University of Singapore, Electrical & Computer Engineering, 2011. [ url ] [ BibTeX ]

2010

• [Albergante10]
  Albergante, L.:
  A Petri Net Model of Liver Response to Visceral Leishmaniasis: Self-Regulation and Complex Interplay in the Vertebrate Immune System;
  PhD thesis, Università degli Studi di Milano, 2010. [ url ] [ BibTeX ]
• [BMSM10]
  MA Blätke, S Meyer, C Stein and W Marwan:
  Petri Net Modeling via a Modular and Hierarchical Approach Applied to Nociception;
  In Proc. International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, ISBN: 978-972-8692-53-7, pages 131–143, June 2010. [ pdf ] [ BibTeX ]
• [BSK10]
  Bortfeldt, RH, Schuster, S. and Koch, I.:
  Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.;
  In Silico Biology, 10, 0007, 2010. [ url ] [ BibTeX ]
• [DTKC10]
  Donaldson, R., Talcott, C., Knapp, M. and Calder, M.:
  Understanding signalling networks as collections of signal transduction pathways;
  In Proceedings of the 8th International Conference on Computational Methods in Systems Biology, ACM, pages 86–95, 2010. [ url ] [ BibTeX ]
• [GL10]
  Gomes, L. and Lourenco, J.:
  Rapid Prototyping of Graphical User Interfaces for Petri-Net-Based Controllers;
  Industrial Electronics, IEEE Transactions on, 57(5):1806–1813, 2010. [ url ] [ BibTeX ]
• [GTR+10]
  Gu, X., Trybio, M., Ramsay, S., Jensen, M., Fulton, R., Rosser, S. and Gilbert, D.:
  Engineering a novel self-powering electrochemical biosensor;
  Systems and synthetic biology, 2010. [ url ] [ BibTeX ]
• [M10]
  ER Mendoza:
  From Communicational to Computational: Systems Modeling Approaches for Psychiatric Research;
  In Systems Biology in Psychiatric Research, Wiley Online Library, pages 231–242, 2010. [ url ] [ doi ] [ BibTeX ]
• [MCR+10]
  Machado, D., Costa, R.S., Rocha, M., Rocha, I., Tidor, B. and Ferreira, E.C.:
  Model transformation of metabolic networks using a Petri net based framework;
  In Proc. International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, ISBN: 978-972-8692-53-7, pages 101–115, June 2010. [ pdf ] [ BibTeX ]
• [MGVV10]
  Macia, H., Gonzalez-Sanchez, M.I., Valero, V. and Valero, E.:
  Applying Petri nets for the analysis of the GSH-ASC cycle in chloroplasts;
  In Proc. International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2010, ISBN: 978-972-8692-53-7, pages 116–130, June 2010. [ pdf ] [ BibTeX ]
• [WGG10]
  Wu, Zujian, Gao, Qian and Gilbert, David:
  Target driven biochemical network reconstruction based on petri nets and simulated annealing;
  In Proceedings of the 8th International Conference on Computational Methods in Systems Biology, Trento, Italy, ACM, CMSB '10, pages 33–42, 2010. [ url ] [ doi ] [ BibTeX ]

2009

• [BFF+09]
  Blazewicz, J., Formanowicz, D., Formanowicz, P., Sackmann, A. and Sajkowski, M.:
  Modeling the process of human body iron homeostasis using a variant of timed Petri nets;
  Discrete Applied Mathematics, 157(10):2221–2231, 2009. [ url ] [ BibTeX ]
• [D09]
  Ding, Z.:
  Static analysis of concurrent programs using ordinary differential equations;
  Theoretical Aspects of Computing-ICTAC 2009, 2009. [ url ] [ BibTeX ]
• [GB09]
  Gomes, L. and Barros, J.P.:
  PNML based composition in non-autonomous Petri net models;
  In Industrial Electronics, 2009. IECON'09. 35th Annual Conference of IEEE, IEEE, pages 4377–4382, 2009. [ url ] [ BibTeX ]
• [Grunwald09]
  Grunwald, S.:
  Identification and characterisation of muscular dystrophy Duchenne modifying genes and signal transduction pathways;
  PhD thesis, Humboldt University, 2009. [ url ] [ BibTeX ]
• [KBSK09]
  Kielbassa, J., Bortfeldt, R., Schuster, S. and Koch, I.:
  Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets;
  Computational biology and chemistry, 33(1):46–61, 2009. [ url ] [ BibTeX ]
• [LYL09]
  Low, I.W.J., Yang, Y. and Lin, H.:
  Validation of Petri net apoptosis models using P-invariant analysis;
  In Control and Automation, 2009. ICCA 2009. IEEE International Conference on, IEEE, pages 416–421, 2009. [ url ] [ BibTeX ]
• [MG09]
  Moutinho, F. and Gomes, L.:
  From models to controllers integrating graphical animation in FPGA through automatic code generation;
  In Industrial Electronics, 2009. ISIE 2009. IEEE International Symposium on, IEEE, pages 712–717, 2009. [ url ] [ BibTeX ]
• [MGVV09]
  H Macià, MI Gonzalez-Sanchez, V Valero and E Valero:
  Analyzing the Glutathione Ascorbate Redox cycle using Petri Nets;
  In Computational Methods in Systems Biology, Abstract of the Posters, CMCB 2009, Bologna, Università di Pisa, Dipartimento di Informatica, pages 13–17, 2009. [ pdf ] [ BibTeX ]
• [PG2009]
  Patricio, G. and Gomes, L.:
  Smart house monitoring and actuating system development using automatic code generation;
  In Industrial Informatics, 2009. INDIN 2009. 7th IEEE International Conference on, IEEE, pages 256–261, 2009. [ url ] [ BibTeX ]
• [RMO09]
  del Rosario, RCH, Mendoza, E. and Oesterhelt, D.:
  Modelling the Bioenergetics of Halobacterium Salinarum with Petri Nets;
  Journal of Computational and Theoretical Nanoscience, 6(8):1965–1976, 2009. [ url ] [ BibTeX ]
• [SFFB09]
  Sackmann, A., Formanowicz, D., Formanowicz, P. and Blazewicz, J.:
  New insights into the human body iron metabolism analyzed by a Petri net based approach;
  Biosystems, 96(1):104–113, 2009. [ url ] [ BibTeX ]

2008

• [Rodriguez2008]
  Eva M. Rodriguez:
  A Mathematical Model For Cephalostatin 1-Induced Apoptosis In Leukemic Cells;
  PhD thesis, University of the Philippines, College of Science,Institute of Mathematics, Diliman, Quezon City, 2008. [ BibTeX ]
• [Weiss08]
  RP Weiß:
  Modelling the Intracellular Life-Cycle of Enteroviruses Using Petri Nets;
  Diploma thesis, Friedrich Schiller University Jena, Faculty for Mathematics and Informatics, Chair BioSystem Analysis, July 2008. [ BibTeX ]
• [DZ08]
  Ding, Z. and Zhang, K.:
  Performance analysis of concurrent programs using ordinary differential equations;
  In Computer Software and Applications, 2008. COMPSAC'08. 32nd Annual IEEE International, IEEE, pages 841–846, 2008. [ url ] [ BibTeX ]
• [DXH08]
  Ding, Z., Xiao, L. and Hu, J.:
  Performance analysis of service composition using ordinary differential equations;
  In Future Trends of Distributed Computing Systems, 2008. FTDCS'08. 12th IEEE International Workshop on, IEEE, pages 30–36, 2008. [ url ] [ BibTeX ]
• [GL08]
  Gomes, L. and Lourenco, J.:
  Petri nets-based automatic generation GUI tools for embedded systems;
  In Human System Interactions, 2008 Conference on, IEEE, pages 269–274, 2008. [ url ] [ BibTeX ]
• [GSAK08]
  Grunwald, S., Speer, A., Ackermann, J. and Koch, I.:
  Petri net modelling of gene regulation of the Duchenne muscular dystrophy;
  Biosystems, 92(2):189–205, 2008. [ url ] [ BibTeX ]
• [LG08]
  Lourenco, J. and Gomes, L.:
  Animated Graphical User Interface Generator Framework for Input-Output Place-Transition Petri Net Models;
  Applications and Theory of Petri Nets, 2008. [ url ] [ BibTeX ]
• [MHN+08]
  Mao, L., Hartl, D., Nolden, T., Koppelstätter, A., Klose, J., Himmelbauer, H. and Zabel, C.:
  Pronounced alterations of cellular metabolism and structure due to hyper-or hypo-osmosis;
  Journal of proteome research, 7(9):3968–3983, 2008. [ url ] [ BibTeX ]
• [Sackmann08]
  A Sackmann:
  Network algorithms and bioinformatics problems;
  PhD thesis, Poznan University Of Technology, Institute of Computing Science, May 2008. [ BibTeX ]

2007

• [CG07]
  Costa, A. and Gomes, L.:
  Module Composition within Petri Nets Model-based Development;
  In Industrial Embedded Systems, 2007. SIES'07. International Symposium on, IEEE, pages 316–319, 2007. [ url ] [ BibTeX ]
• [GBCN07]
  Gomes, L., Barros, J.P., Costa, A. and Nunes, R.:
  The Input-Output Place-Transition Petri Net Class and Associated Tools;
  In Industrial Informatics, 2007 5th IEEE International Conference on, IEEE, volume 1, pages 509–514, 2007. [ url ] [ BibTeX ]
• [GCBL07]
  Gomes, L., Costa, A., Barros, J.P. and Lima, P.:
  From Petri net models to VHDL implementation of digital controllers;
  In Industrial Electronics Society, 2007. IECON 2007. 33rd Annual Conference of the IEEE, IEEE, pages 94–99, 2007. [ url ] [ BibTeX ]
• [FSFB07]
  Formanowicz, D., Sackmann, A., Formanowicz, P. and Blazewicz, J.:
  Petri net based model of the body iron homeostasis;
  Journal of Biomedical Informatics, 40(5):476–485, 2007. [ url ] [ BibTeX ]
• [NGB07]
  Nunes, R., Gomes, L. and Barros, J.P.:
  A graphical editor for the input-output place-transition Petri net class;
  In Emerging Technologies and Factory Automation, 2007. ETFA. IEEE Conference on, IEEE, pages 788–791, 2007. [ url ] [ BibTeX ]
• [SFF+07]
  Sackmann, A., Formanowicz, D., Formanowicz, P., Koch, I. and Blazewicz, J.:
  An analysis of the Petri net based model of the human body iron homeostasis process;
  Computational Biology and Chemistry, 31(1):1–10, 2007. [ url ] [ BibTeX ]