List of works by Monika Heiner

A Case Study in Model-driven Synthetic Biology

scholarly article published in International Federation for Information Processing

A Petri net based methodology to integrate qualitative and quantitative analysis

A Petri nets-based framework for whole-cell modeling

scientific article published in 2021

A Petri-Net-Based Framework for Biomodel Engineering

A Steering Server for Collaborative Simulation of Quantitative Petri Nets

A comparative study of stochastic analysis techniques

A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease

scientific article published on 10 August 2016

A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured Petri nets

scholarly article published 2011

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

scientific article published on 23 June 2008

A unique transformation from ordinary differential equations to reaction networks

scientific article

Accelerated Simulation of Hybrid Biological Models with Quasi-Disjoint Deterministic and Stochastic Subnets

Advances in Computational Methods in Systems Biology

Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution

scientific article published on 04 September 2019

An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways

article

An efficient method for unfolding colored Petri nets

Application of Petri net based analysis techniques to signal transduction pathways

scientific article

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber

scientific article published on 16 November 2004

Auto- and cross-regulation of the hnRNP L proteins by alternative splicing.

scientific article published on 5 January 2009

BioModel engineering for multiscale Systems Biology

scientific article published on 12 October 2012

Biomodel Engineering – From Structure to Behavior

CSL Model Checking of Biochemical Networks with Interval Decision Diagrams

Charlie – An Extensible Petri Net Analysis Tool

Colored Petri nets for multiscale systems biology - Current modeling and analysis capabilities in snoopy

Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks

scientific article published on 28 May 2018

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

scientific article published on 3 November 2017

Coloured fuzzy Petri nets for modelling and analysing membrane systems

scientific article published in 2022

Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology

article by David Gilbert et al published 2013 in Lecture Notes in Computer Science

Comparison of methods for quantification of subtle splice variants

scientific article published in November 2009

Computational modelling of kinase signalling cascades.

scientific article published in January 2010

DSSZ-MC – A Tool for Symbolic Analysis of Extended Petri Nets

Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis

scientific article published on 11 December 2007

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes

scientific article published on 09 July 2018

Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments

Foundations of formal reconstruction of biochemical networks

From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis

Fuzzy Petri nets for modelling of uncertain biological systems

scientific article published on 27 December 2018

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

scientific article

Generation of a variety of stable Influenza A reporter viruses by genetic engineering of the NS gene segment

scientific article published on 12 June 2015

Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat.

scientific article published in January 2017

HnRNP L-mediated regulation of mammalian alternative splicing by interference with splice site recognition

scientific article published on 21 January 2010

How Might Petri Nets Enhance Your Systems Biology Toolkit

Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle

Hybrid representation and simulation of stiff biochemical networks

Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing

scientific article

JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept

JAK/STAT signalling--an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology.

scientific article published on 26 February 2013

MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly

article

MARCIE – Model Checking and Reachability Analysis Done Efficiently

MARCIE’s Secrets of Efficient Model Checking

Mediator complex regulates alternative mRNA processing via the MED23 subunit.

scientific article published on 19 January 2012

Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis

Model validation of biological pathways using Petri nets—demonstrated for apoptosis

scientific article published on 01 July 2004

Modeling and simulation of multi-scale environmental systems with Generalized Hybrid Petri Nets

scientific article published in 2015

Modeling biological gradient formation: combining partial differential equations and Petri nets.

scientific article published on 31 October 2015

Modeling biological systems with uncertain kinetic data using fuzzy continuous Petri nets.

scientific article

Modeling membrane systems using colored stochastic Petri nets

Modelling and simulating reaction-diffusion systems using coloured Petri nets

scientific article published on 15 July 2014

Modularization of biochemical networks based on classification of Petri net t-invariants

scientific article

Multiscale modeling and analysis of planar cell polarity in the Drosophila wing

scientific article published in March 2013

Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets

scientific article

Petri Nets

scholarly article

Petri Nets for Modeling and Analyzing Biochemical Reaction Networks

Petri Nets for Systems and Synthetic Biology

scholarly article

Petri nets for steady state analysis of metabolic systems.

scientific article

Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks

scientific article published in January 2012

Petri-net-based 2D design of DNA walker circuits.

scientific article

Predicting Phenotype from Genotype through Automatically Composed Petri Nets

Preface: Petri nets for Systems and Synthetic Biology

scholarly article by Monika Heiner published 19 April 2011 in Natural Computing

Preface: Petri nets for Systems and Synthetic Biology

scholarly article by Monika Heiner published 14 July 2011 in Natural Computing

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

scientific article

Representing network reconstruction solutions with colored Petri nets

STEPP - Search Tool for Exploration of Petri net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks.

scientific article published in January 2011

STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks

scientific article published in January 2005

Snoopy – A Unifying Petri Net Tool

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

scientific article

Snoopy--a unifying Petri net framework to investigate biomolecular networks

scientific article published on 07 February 2010

Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking

article by David Gilbert et al published 18 April 2019 in BMC Bioinformatics

Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes

article

Steady state analysis of metabolic pathways using Petri nets

scientific article

Structural analysis to determine the core of hypoxia response network

scientific article

The RNA-binding protein QKI suppresses cancer-associated aberrant splicing

scientific article published on 10 April 2014

Towards dynamic genome-scale models.

scientific article

Understanding Network Behavior by Structured Representations of Transition Invariants

YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

scientific article

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