Wednesday     Thursday     Friday

Wednesday, 12th September

8:45 – 9:15 Registration
9:15 – 9:30 Welcome Session (including practical information)
9:30 – 10:30 Invited talk: Andrew Phillips
Programming Languages for Molecular and Genetic Devices
10:30 – 11:00 coffee break
11:00 – 12:30 Session I – Modelling and Engineering

Keenan Breik, Cameron Chalk, David Doty, David Haley and David Soloveichik. Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks
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
Luca Laurenti, Alessandro Abate, Luca Cardelli, Marta Kwiatkowska and Boyan Yordanov. Experimental Biological Protocols with Formal Semantics
12:30 – 14:00 lunch
14:00 – 15:10 Session II.A (Flash Poster Presentations)
5 minutes per each presentation
15:10 – 15:40 Session II.B (Oral Presentation)

Christoph Flamm, Jakob Lykke Andersen, Daniel Merkle and Peter Florian Stadler. Discovering Reaction Patterns in Chemical Reaction Networks
15:40 – 16:00 coffee break
16:00 – 17:00 transfer to Mendel Museum (by trolley 25,26 or by tram 6 or by foot)
17:15 – 18:15 Invited talk: Ilka Axmann
What Time Is It?
18:30 – 22:30 Welcome Drink & Raut at Mendel museum

Thursday, 13th September

9:00 – 10:00 Invited talk: Mustafa Khammash
Biomolecular Control Systems
10:00 – 10:30 coffee break
10:30 – 12:30 Session III – Learning From Data

Carolyn Talcott, Akos Vertes, Mark-Oliver Stehr, Brian Davis, et al. Inferring Mechanism of Action of an Unknown Compound from Time Series Omics Data
Misbah Razzaq, Roland Kaminiski, Javier Romero, Torsten Schaub, Jeremie Bourdon and Carito Guziolowski. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data
Taisa Kushner, Sriram Sankaranarayanan and Souradeep Dutta. Robust Data-Driven Control of Artificial Pancreas Systems using Neural Networks
Emine Güven, Michael J Wester, Bridget S Wilson, Jeremy S Edwards and Ádám M Halász. Characterization of the Experimentally Observed Clustering of VEGF Receptors
12:30 – 14:00 lunch
14:00 – 15:00 Invited talk: Andrew Turberfield
Modelling Biomimetic Structures and Machinery Using DNA
15:00 – 15:30 coffee break
15:30 – 17:10 Session IV – Stochastic Analysis of Biochemical Systems

Luca Bortolussi and Luca Palmieri. Deep Abstractions of Chemical Reaction Networks
Pavol Bokes, Michal Hojcka and Abhyudai Singh. Buffering Gene Expression Noise by MicroRNA Based Feedforward Regulation
(Tool) Justin Feigelman, Daniel Weindl, Fabian J Theis, Carsten Marr and Jan Hasenauer. LNA++: Linear Noise Approximation with First and Second Order Sensitivities
(Tool) Andrzej Mizera, Jun Pang, Hongyang Qu and Qixia Yuan. ASSA-PBN 3.0: Analysing Context-sensitive Probabilistic Boolean Networks
17:10 – 18:10 business meeting
19:30 – 22:30 Conference Dinner including Best Paper Award

Friday, 14th September

9:00 – 10:00 Invited talk: Chris J. Myers
A Standard-Enabled Workflow for Synthetic Biology
10:00 – 10:30 coffee break
10:30 – 12:20 Session V – Analysis of Biochemical Systems

Timothy Self, David Gilbert and Monika Heiner. Derivation of a Biomass Proxy for Dynamic Analysis of Whole Genome Metabolic Models
Cameron Chalk, Niels Kornerup, Wyatt Reeves and David Soloveichik. Composable Rate-Independent Computation in Continuous Chemical Reaction Networks
Jonathan Laurent, Hector F Medina-Abarca, Pierre Boutillier, Jean Yang and Walter Fontana. A Trace Query Language for Rule-based Models
(Tool) Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jerome Feret, Nathalie Theret, Kim Quyen Ly and Pierre Vignet. KaSa: a Static Analyzer for Kappa
12:20 – 13:30 lunch
13:30 – 15:20 Session VI – Synthesis and Inference

Jeremy Revell and Paolo Zuliani. Stochastic Rate Parameter Inference using the Cross-Entropy Method
Ashutosh Gupta, Ankit Shukla and Somya Mani. Synthesis for Vesicle Traffic Systems
Hillel Kugler, Sara-Jane Dunn and Boyan Yordanov. Formal Analysis of Network Motifs
(Tool) François Fages and Sylvain Soliman. On Robustness Computation and Optimization in BIOCHAM-4
15:20 – 15:45 coffee break
15:45 – 16:45 Session VII (Oral Presentations) – System Identification

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 and Jana Nemcova. System Identification of a Continuous-Time Polynomial System by a Subalgebraic Procedure
16:45 Conference Closing