Full Papers

  • Pavol Bokes, Michal Hojcka and Abhyudai Singh. Buffering gene expression noise by microRNA based feedforward regulation
  • Cameron Chalk, Niels Kornerup, Wyatt Reeves and David Soloveichik. Composable Rate-Independent Computation in Continuous Chemical Reaction Networks
  • Keenan Breik, Cameron Chalk, David Doty, David Haley and David Soloveichik. Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks
  • Hillel Kugler, Sara-Jane Dunn and Boyan Yordanov. Formal Analysis of Network Motifs
  • Emine Güven, Michael J Wester, Bridget S Wilson, Jeremy S Edwards and Ádám M Halász. Characterization of the Experimentally Observed Clustering of VEGF Receptors
  • Jeremy Revell and Paolo Zuliani. Stochastic Rate Parameter Inference using the Cross-Entropy Method
  • Carolyn Talcott, Akos Vertes, Mark-Oliver Stehr, Brian Davis, Et. Al. Inferring Mechanism of Action of an Unknown Compound from Time Series Omics Data
  • Samuel M.D. Oliveira, Mohamed N.M. Bahrudeen, Sofia Startceva, Vinodh Kandavalli and Andre S. Ribeiro. Modeling and engineering promoters with pre-defined RNA production dynamics in Escherichia coli
  • Jonathan Laurent, Hector F Medina-Abarca, Pierre Boutillier, Jean Yang and Walter Fontana. A Trace Query Language for Rule-based Models
  • Misbah Razzaq, Roland Kaminiski, Javier Romero, Torsten Schaub, Jeremie Bourdon and Carito Guziolowski. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data
  • Timothy Self, David Gilbert and Monika Heiner. Derivation of a biomass proxy for dynamic analysis of whole genome metabolic models
  • Taisa Kushner, Sriram Sankaranarayanan and Souradeep Dutta. Robust Data-Driven Control of Artificial Pancreas Systems using Neural Networks
  • Luca Laurenti, Alessandro Abate, Luca Cardelli, Marta Kwiatkowska and Boyan Yordanov. Experimental Biological Protocols with Formal Semantics
  • Ashutosh Gupta, Ankit Shukla and Somya Mani. Synthesis for Vesicle Traffic Systems
  • Luca Bortolussi and Luca Palmieri. Deep Abstractions of Chemical Reaction Networks

Tool Papers

  • Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jerome Feret, Nathalie Theret, Kim Quyen Ly and Pierre Vignet. KaSa: a Static Analyzer for Kappa
  • Justin Feigelman, Daniel Weindl, Fabian J Theis, Carsten Marr and Jan Hasenauer. LNA++: Linear Noise Approximation with First and Second Order Sensitivities
  • François Fages and Sylvain Soliman. On Robustness Computation and Optimization in BIOCHAM-4
  • Andrzej Mizera, Jun Pang, Hongyang Qu and Qixia Yuan. ASSA-PBN 3.0: Analysing Context-sensitive Probabilistic Boolean Networks

Posters with Abstracts in LNCS (incl. flash presentation)

  • Sally Radwan and Dr Hugh Shanahan. Systems Metagenomics: applying systems biology thinking to human microbiome analysis
  • Martin Modrák. Genexpi-Stan: Fully Bayesian Model of Gene Regulation
  • Soumya Paul, Jun Pang and Cui Su. On the Full Control of Boolean Networks

Posters with flash oral presentation

  • Thomas Wright and Ian Stark. Modelling Patterns of Gene Regulation in the Bond Calculus
  • Carolin Loos, Katharina Moeller, Fabian Fröhlich, Tim Hucho and Jan Hasenauer. Mechanistic hierarchical population model predicts latent causes of cell-to-cell variability
  • Jonathan Laurent, Jean Yang and Walter Fontana. Counterfactual Resimulation for Causal Analysis of Rule-Based Models
  • David Gilbert, Monika Heiner and Leila Ghanbar. Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking
  • Matej Troják, David Šafránek, Jakub Hrabec, Jakub Šalagovič, Jan Červený, Matej Hajnal, Lukrécia Mertová, Katarína Palubová and Marek Havlík.  E-cyanobacterium.org: A Web-based Platform for Systems Biology of Cyanobacteria.
  • Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro Monteiro, Claudine Chaouiya, Thomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry and Loïc Paulevé. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
  • Thomas Chatain, Stefan Haar and Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity
  • Pia Wilsdorf, Andreas Ruscheinski and Adelinde M. Uhrmacher. Synergies of Simulation Model Documentation and Simulation Experiment Generation
  • Leonard Schmiester, Yannik Schälte, Fabian Fröhlich, Jan Hasenauer and Daniel Weindl. Efficient parameterization of large-scale dynamic models using relative protein, phospho-protein and proliferation measurements

Regular posters

  • Elife Bagci, Buket Ozahioglu, Muzaffer Erdogan, Tanju Gurel and Serbulent Yildirim. Pore Opening in Mitochondrial Cristae through Interaction of Cytochrome c with Cardiolipin: Insights from a Mass-Action Kinetics Model
  • Anna Poskrobko and Antoni Leon Dawidowicz. On mathematical model of the bats population’s development under the assumption of variable capacity of the habitats
  • Nikola Beneš, Luboš Brim, Martin Demko and Samuel Pastva. Attractor Analysis in Pithya
  • Veronika Hajnová and Lenka Přibylová. Biological and physiological phenomena in view of applied bifurcation theory
  • František Muzika, Lenka Schreiberová and Igor Schreiber. Chemical computing by spatiotemporal patterns in a ring of coupled cells
  • Andrej Blejec, Maja Zagorščak and Kristina Gruden. Being FAIR with pISA-tree
  • Cameron Chalk, Niels Kornerup, Wyatt Reeves and David Soloveichik. Converging Rate-Independent Computation in Continuous Chemical Reaction Networks

Oral presentations of recently published work

  • Christoph Flamm, Jakob Lykke Andersen, Daniel Merkle and Peter Florian Stadler. Discovering Reaction Patterns in Chemical Reaction Networks
  • Igor Schreiber, Vuk Radojkovic, František Muzika, Radovan Jurašek, Lenka Schreiberová and Jan Červený. Reaction network theory as a tool for finding network motifs for oscillatory dynamics and kinetic parameter estimation in complex biochemical mechanisms
  • Jan H. van Schuppen, Jana Němcová and Kaihua Xi. System identification of a continuous-time polynomial system by a subalgebraic procedure

Late posters

  • Marcin Choiński, Urszula Foryś, Mariusz Bodzioch. Criss-cross model of tuberculosis for homeless and non-homeless subpopulations
  • Jiří Jablonský. Multi-level kinetic modeling: a tool for analysis of local and global properties of isozymes
  • G. Pinto, P. Kokkonen, J. Filipovic, O. Vavra, A. Jurcik, B. Kozlikova, D. Bednar, J. Damborsky. Analysis of Protein Tunnels and Screening the Binding Trajectories of Inhibitors using Novel Software Caver Analyst 2.0 and CaverDock 1.0
  • Emine Güven, Michael J. Wester, Jeremy Edwards and Ádám M. Halász. Toward A Predictive Model of Spontaneous Clustering of VEGF Receptors