Program

  • Saturday, October 27, 2018

    09:00 am - 06:00 pm

    Workshops / satellite meetings / tutorials

    More information by clicking here 

  • Sunday, October 28, 2018

    08:30 am - 10:00 am
    Welcome - Coffee break
    10:00 am - 10:50 am Opening ceremony
    10:50 am - 11:50 am

    Chair: Olivier GANDRILLON, Lyon, France
    Julie THERIOT, Seattle, USA
    The fast and the furious: dissecting the mechanics and dynamics of rapid cell locomotion

    11:50 am - 12:30 pm Chair: Olivier GANDRILLON, Lyon, France
    Andrew OATES, Lausanne, Switzerland
    Clocks and timers in development
    12:30 pm - 02:00 pm Lunch
    02:00 pm - 03:30 pm Poster session
    03:30 pm - 04:00 pm Coffee break
    04:00 pm - 05:40 pm Three parallel sessions

    Multiscale Systems Biology

    Chair: Marija CVIJOVIC, Gothenburg, Sweden


    Matteo BARBERIS, Amsterdam, Netherlands  
    04:00 pm - 04:20 pm
    Deciphering yeast physiology by a multi‐scale framework integrating cell cycle and metabolism

    David HENRIQUES, Vigo, Spain
    04:20 pm - 04:40 pm 
    Enabling the comparison of conventional and non-conventional winemaking Saccharomyces species with genome-scale models

    Xiaoqiang SUN, Guangzhou, China
    04:40 pm - 05:00 pm          
    Multi-scale modeling reveals angiogenesis-induced drug resistance in brain tumor and predicts a synergistic drug combination targeting EGFR and VEGFR

    Annabelle BALLESTA, Villejuif, France
    05:00 pm - 05:20 pm
    A multi-scale systems pharmacology approach for personalizing cancer chronotherapy

    Frederique CLEMENT, Palaiseau, France 
    05:20 pm - 05:40 pm               
    A multiscale mathematical model of neural progenitor dynamics during the development of the cerebral cortex in mice

    Developmental Systems Biology A

    Chair: Benjamin AUDIT, Lyon, France


    Erika TSINGOS, Heidelberg, Germany
    04:00 pm - 04:20 pm
    Coordination of different stem cell niches during homeostatic growth of the adult fish eye

    Elias FRIMAN, Lausanne, Switzerland
    04:20 pm - 04:40 pm
    OCT4 is required at the M-G1 transition to reestablish chromatin accessibility at enhancers in pluripotent stem cells

    Mahé RACCAUD, Lausanne, Switzerland   
    04:40 pm - 05:00 pm        
    Mitotic chromosome binding predicts transcription factor dynamics, target site occupancy and ability to modify chromatin accessibility

    Didier GONZE, Bruxelles, Belgium
    05:00 pm - 05:20 pm   
    Modeling cell fate specification during early embryonic development in mouse

    Honda NAOKI, Kyoto, Japan
    05:20 pm - 05:40 pm
    Noise-resistant developmental reproducibility in vertebrate somite formation

    Systems Neurosciences

    Melanie STEFAN, Edinburgh, United Kingdom
    04:00 pm - 04:20 pm
    Modelling hyperpolarisation-gated synaptic plasticity in motor learning

    Uiryong KANG, Daejeon, South Korea
    04:20 pm - 04:40 pm
    Robustness of controllability in structural brain networks

    Marti JETT, Washington, United States
    04:40 pm - 05:00 pm
    Systems biology applied to post-traumatic stress disorder to stratify into subtypes

    Dennis VITKUP, New York, United States
    05:00 pm - 05:20 pm
    Gene networks, neuron types, and brain circuits underlying common psychiatric disorders

    Maria SERBAN, Copenhagen, Denmark
    05:20 pm - 05:40 pm
    Hierarchical modularity in neural networks

    05:50 pm - 06:30 pm

    Chair: David SUTER, Lausanne, Switzerland
    James FERRELL, Stanford, USA
    Trigger waves in cellular regulation

    From 06:30 pm Welcome cocktail
  • Monday, October 29, 2018

    08:30 am - 09:00 am Welcome
    09:00 am - 09:40 am

    Chair: Jan TRAAS, Lyon, France
    Takashi HIIRAGI, Heidelberg, Germany
    Self-organisation in mouse development

    09:40 am - 10:20 am Chair: Jan TRAAS, Lyon, France
    Ottoline LEYSER, Cambridge, UK
    Auxin and the self-organisation of plant form
    10:20 am - 10:50 am Coffee break
    10:50 am - 12:30 pm Three parallel sessions

    Methodological developments for Systems Biology A

    Chair: Frédérique CLEMENT, Palaiseau, France


    Hugo DOURADO, Düsseldorf, Germany
    10:50 am - 11:10 pm
    Enzyme and substrate concentrations in cellular reaction networks at maximal growth rate

    Romain YVINEC, Nouzilly, France
    11:10 am - 11:30 am
    Using dynamical reaction network to infer drugs selectivity in pharmacology

    Corinna SCHMALOHR, Cologne, Germany
    11:30 am - 11:50 am
    Detecting epistasis using random forest

    Elif OZKIRIMLI, Istanbul, Turkey
    11:50 am - 12:10 pm
    SMILES-based prediction of drug-target interaction binding affinity

    Min Kyoung ROH, Bellevue, United States 
    12:10 pm - 12:30 pm         
    Automated stochastic parameter estimation for events

    Systems Medicine A

    Chair: Matteo BARBERIS, Amsterdam, Netherlands

    Eyal SIMONOVSKY, Beer Sheva, Israel
    10:50 am - 11:10 am
    Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety

    Xin LAI, Erlangen, Germany
    11:10 am - 11:30 am
    Mathematical modelling of E2F1 repression by cooperative microRNA pairs in the context of anticancer chemotherapy resistance

    Juan MARTINEZ, Mexico City, Mexico  
    11:30 am - 11:50 am
    Controllability analysis of the core gene regulatory network underlying epithelial-to-mesenchymal transition in the context of epithelial cancer

    Dirk FEY, Dublin, Ireland 
    11:50 am - 12:10 pm               
    Patient-specific modelling of the network dynamics induced by chemotherapeutic drugs in primary and relapsed tumours

    Lan NGUYEN, Melbourne, Australia
    12:10 pm - 12:30 pm 
    Optimizing drug combinations for cancer treatment using integrative network modelling

    Modelling Networks and Circuits A

    Chair: Daniel JOST, La Tronche, France


    Om PATANGE, Cambridge, United Kingdom
    10:50 am - 11:10 am
    E. coli can survive stress by noisy growth modulation

    Johannes BORGQVIST, Gothenburg, Sweden
    11:10 am - 11:30 am
    The triangle of ageing: a model of the accumulation of damaged proteins in Saccharomyces cerevisiae shows how retention enables replicative ageing

    Mona TONN, London, United Kingdom
    11:30 am - 11:50 am
    Emergence of non-genetic heterogeneity in metabolic reactions

    Christian EULER , Toronto, Canada
    11:50 am - 12:10 pm
    Functional topology of the E. coli small molecule regulatory network

    Purushottam DIXIT, New York, United States
    12:10 pm - 12:30 pm
    A probabilistic framework to explore thermodynamically consistent metabolic flux distributions in mammalian cells

    12:30 pm - 02:00 pm Lunch
    02:00 pm - 03:30 pm Poster session
    02:30 pm - 03:30 pm BIOASTER Session: Systems Biology for Infectious Diseases and Microbiology
    03:30 pm - 04:00 pm Coffee break
    04:00 pm - 05:40 pm Three parallel sessions

    Developmental Systems Biology B

    Chair: Didier GONZE, Brussels, Belgium


    Lidia YAMAMOTO, Leuven, Belgium
    04:00 pm - 04:20 pm
    Simulating cellular movements in early C. elegans embryogenesis

    Sophie PANTALACCI, Lyon, France
    04:20 pm - 04:40 pm
    Making and erasing patterns in the tooth field: lessons from Edar dynamics and mathematical modeling

    Olivier ALI, Lyon, France
    04:40 pm - 05:00 pm
    3D mechanical stress patterning during flower morphogenesis

    Edgar HERRERA DELGADO, London United Kingdom
    05:00 pm - 05:20 pm      
    Enhancer function underpins essential properties of gene regulatory networks for patterning precision

    Lutz BRUSCH, Dresden, Germany
    05:20 pm - 05:40 pm 
    Wet-tip versus dry-tip regimes of osmotically driven bile flow in the liver

    Multi-omics

    Chair: Pedro MENDES, Farmington, United States


    Chris PLAISIER, Tempe, United States  
    04:00 pm - 04:20 pm  
    Causal and mechanistic pan-cancer immune regulatory network deciphered using systems genetics network analysis (SYGNAL)

    Katsuyuki YUGI, Yokohama, Japan
    04:20 pm - 04:40 pm        
    Dynamic metabolomics and phosphoproteomics reveal that insulin primes the adipocyte for glucose metabolism

    Jean-Michel ARBONA, Lyon, France
    04:40 pm - 05:00 pm       
    Emergence of the spatio-temporal replication program: role of origin distribution heterogeneity and 3D chromatin structure

    Magali RICHARD, La Tronche, France
    05:00 pm - 05:20 pm  
    PenDA, a rank-based method for personalized differential analysis: application to lung cancer

    Pascale CRÉPIEUX, Nouzilly, France
    05:20 pm - 05:40 pm         
    A hormone-regulated translatome in primary cells highlights a positive feedback loop of signaling components operating at the level of translation

    Evolutionary and Ecological Systems Biology

    Chair: Ellen DECAESTECKER, Kortrijk, Belgium

    Dennis VITKUP, New York, United States
    04:00 pm - 04:20 pm
    Quantifying spatiotemporal dynamics and noise in microbiome studies using replicate sampling

    Juan POYATOS, Madrid, Spain 
    04:20 pm - 04:40 pm
    High-order interactions and the predictability of function in microbial consortia

    German PLATA, New York, United States 
    04:40 pm - 05:00 pm           
    The percolation of metabolism and bacterial lifestyle and evolvability

    Marco GALARDINI, Cambridge, United Kingdom 
    05:00 pm - 05:20 pm               
    Systematic evaluation of conditional gene essentiality changes across genetic backgrounds in Saccharomyces cerevisiae

    Gabriel CARVALHO, Villeurbanne, France
    05:20 pm - 05:40 pm
    Natural transformation: acquisition and removal of mobile genetic elements in stochastic environments

    05:50 pm - 06:30 pm Chair: Fabien CRAUSTE, Lyon, France
    Mariko OKADA, Osaka, Japan
    Quantitative transcription control mediated by signaling network

  • Tuesday, October 30, 2018

    08:30 am - 09:00 am Welcome
    09:00 am - 09:40 am Chair: Sophie PANTALACCI, Lyon, France
    James SHARPE, Barcelona, Spain
    Limb development, Turing patterns, and computer modelling
    09:40 am - 10:20 am Chair: Sophie PANTALACCI, Lyon, France
    Marie-Anne FELIX, Paris, France
    Variational properties in a developmental system with six precursor cells
    10:20 am - 10:50 am Coffee break
    10:50 am - 12:30 pm Three parallel sessions

    Single-cell Systems Biology

    Chair: Nathalie BALABAN, Jerusalem, Israel


    Rinat ARBEL-GOREN, Rehovot, Israel 
    10:50 am - 11:10 am
    Noise and correlated gene expression in a one-dimensional organism

    Nacho MOLINA, Strasbourg, France 
    11:10 am - 11:30 am 
    Experimental and theoretical study of nuclear diffusion dynamics of transcription factors

    Marie GUILBERT, Villeneuve d'Ascq, France
    11:30 am - 11:50 am          
    Cell-to-cell variability in the activation of the heat shock response

    Aneta KOSESKA , Dortmund, Germany
    11:50 am - 12:10 pm
    Spatially distributed network between EGFR and phosphatases optimizes growth factor sensing at criticality

    Lorenz RIPKA, Mainz, Germany
    12:10 pm - 12:30 pm  
    Integration of GDF11 and TGF-β on the SMAD-signaling pathway - modelling population average and variability based on single cell data

    Quantitative Systems Physiology

    Chair: Delphine ROPERS, Montbonnot, France


    Vakil TAKHAVEEV, Groningen, Netherlands 
    10:50 am - 11:10 am
    What causes metabolic oscillations in the eukaryotic cell?

    Andrea WEISSE, London, United Kingdom
    11:10 am - 11:30 am
    Stochasticity of cellular growth: sources, propagation and consequences

    Shiny MARTIS B., Lyon, France 
    11:30 am - 11:50 am
    Interplay of local and global regulators in pectin catabolism during plant infection by Dickeya dadantii.

    Bruno MARTINS, Cambridge, United Kingdom
    11:50 am - 12:10 pm  
    Circadian regulation of cell size, division timing and growth in cyanobacteria

    Dipali SINGH, Dusseldorf, Germany
    12:10 pm - 12:30 pm
    Network reduction for genome scale metabolic models

    Systems Biology for Synthetic Biology

    Chair: Igor GORYANIN, Okinawa, Japan


    Qiong YANG, Ann Arbor, United States 
    10:50 am - 11:10 am
    An artificial cell-cycle system: how network structures modulate the clock functions

    Carlos TOSCANO OCHOA, Barcelona, Spain
    11:10 am - 11:30 am      
    On the feasibility of complex synthetic biological circuits

    Britte BOUCHAUT, Delft, Netherlands 
    11:30 am - 11:50 am     
    Perceptions of inherent safety: a comparison study from the bioengineering field

    Dvir SCHIRMAN, Revadim, Israel
    11:50 am - 12:10 pm            
    Optimization of gene expression through cost-effective promoter architectures

    Claude LORMEAU, Zurich, Switzerland
    12:10 pm - 12:30 pm    
    Model-based design of robust synthetic biological circuits

    12:30 pm - 02:00 pm Lunch
    02:00 pm - 08:00 pm Cultural program
    From 08:00 pm Gala reception at The Selcius
  • Wednesday, October 31, 2018

    08:30 am - 09:00 am Welcome
    09:00 am - 09:40 am Chair: Daniel KAHN, Lyon, France
    Ines THIELE, Esch-sur-Alzette, Luxembourg
    Personalized whole-body models integrate metabolism, physiology, and the gut microbiome
    09:40 am - 10:20 am Chair: Daniel KAHN, Lyon, France
    Uwe SAUER, Zurich, Switzerland
    Metabolic coordination through metabolite-protein interactions
    10:20 am - 10:50 am Coffee break
    10:50 am - 12:30 pm Three parallel sessions

    Methodological developments for Systems Biology B

    Chair: Mustafa KHAMMASH, Basel, Switzerland


    Satya SAMAL, Aachen, Germany 
    10:50 am - 11:10 am
    Sensitive parameters and tipping points of biochemical networks with potential applications in precision medicine

    Anne POUPON, Nouzilly, France 
    11:10 am - 11:30 am      
    Parameter estimation in dynamical models for systems biology – the delicate balance between identifiability and predictivity

    Ozgur AKMAN, Exeter, United Kingdom
    11:30 am - 11:50 am    
    The parameter explosion problem: extending the scope of GRN modelling by combining reduced models with evolutionary computation

    Martial GUILLAUD, Vancouver, Canada
    11:50 am - 12:10 pm
    Hyperspectral cell sociology analysis of histological specimens

    Serge PELET, Lausanne, Switzerland
    12:10 pm - 12:30 pm
    Dynamic single cell analysis of a cell fate decision system

    Systems Medicine B

    Chair: Jacqueline MARVEL, Lyon, France


    Teresa LEHNERT, Jena, Germany 
    10:50 am - 11:10 am
    Characterization of different sepsis phases by virtual infection modeling of the innate immune response in human whole blood

    Anna MEDYUKHINA, Jena, Germany
    11:10 am - 11:30 am  
    Automated image analysis of mast cell - dendritic cell interactions reveals weapon transfer in immune system

    Chloe AUDEBERT, Villeurbanne, France
    11:30 am - 11:50 am 
    Non-linear mixed effects models to study inter-individual variability in CD8 T cell immune responses in mice.

    Chen-Hsiang YEANG, Taipei, Taiwan 
    11:50 am - 12:10 pm       
    Modelling bistable tumour population dynamics to design effective treatment strategies

    Marcel SCHILLING, Heidelberg, Germany
    12:10 pm - 12:30 pm             
    The complex life of Smad isoforms determines gene expression in hepatocellular carcinoma

    Modelling Networks and Circuits B

    Chair: Ina KOCH, Frankfurt, Germany


    Jonas BÉAL, Paris, France
    10:50 am - 11:10 am        
    Instantiation of patient-specific logical models with multi-omics data allows clinical stratification of patients

    Oleksii RUKHLENKO, Dublin, Ireland
    11:10 am - 11:30 am        
    Structure-based kinetic modelling reveals kinase inhibitor combinations to overcome oncogenic RAS signalling

    Yaroslav NIKOLAEV, Zurich, Switzerland
    11:30 am - 11:50 am 
    Systems NMR: simultaneous quantitative monitoring of RNA, protein, and metabolite dynamics for biomolecular network analysis

    Daniel JOST, La Tronche, France
    11:50 am - 12:10 pm             
    Assigning function to natural allelic variation via dynamic modeling of gene network induction

    Ulysse HERBACH, Lyon, France 
    12:10 pm - 12:30 pm   
    Inferring gene regulatory networks using single-cell data: from mechanistic modelling to statistics

    12:30 pm - 02:00 pm Lunch
    02:00 pm - 03:30 pm Poster session
    03:30 pm - 04:00 pm Coffee break
    04:00 pm - 05:40 pm Three parallel sessions

    Methodological developments for Systems Biology C

    Chair: Anne POUPON, Nouzilly, France


    Laurent GUYON, Grenoble, France
    04:00 pm - 04:20 pm       
    miRNA selection using miRNA network a priori showed improved reliability and identify functionally related miRNAs

    Andras GYORGY, Abu Dhabi, United Arab Emirates
    04:20 pm - 04:40 pm
    Optimal part characterization with shared cellular resources

    Arthur GOLDBERG, New York, United States
    04:40 pm - 05:00 pm       
    A multialgorithmic simulator for whole-cell biochemical models

    Silas Boye NISSEN, Copenhagen, Danmark
    05:00 pm - 05:20 pm
    Four simple rules that are sufficient to generate the mammalian blastocyst 

    Jörn STARRUSS, Dresden, Germany 
    05:20 pm - 05:40 pm      
    Morpheus: a user-friendly and extensible simulation framework for declarative modelling in multiscale and multicellular systems biology

    Systems Medicine C

    Chair: Maria Manuela NOGUEIRA, Lyon, France


    Fortunato BIANCONI, Perugia, Italy
    04:00 pm - 04:20 pm     
    Machine learning pipeline for pathways analysis with reverse phase microarray data of non-small cell lung cancer cell lines and different drugs

    Michiel ADRIAENS, Maastricht, Netherlands
    04:20 pm - 04:40 pm 
    Putting the squeeze on RNA-seq data: mapping individualized genetic and epigenetic regulation in complex diseases

    Avijit PODDER, New Delhi, India
    04:40 pm - 05:00 pm                     
    Therapeutic understanding of human dopaminergic system in neurological diseases - a systems biology approach

    Pedro MENDES, Farmington, United States
    05:00 pm - 05:20 pm
    Transforming physiological models from mice to humans - the case of iron homeostasis.

    Dominik LUTTER, Neuherberg, Germany
    05:20 pm - 05:40 pm
    A circadian metabolomics atlas of the body under chronic nutrient stress

    Modelling Networks and Circuits C

    Chair: Ralf STEUER, Berlin, Germany


    Congxin LI, Heidelberg, Germany
    04:00 pm - 04:20 pm
    Transcriptional regulation out of equilibrium: theory and experiment

    Niklas KORSBO, Cambridge, United Kingdom
    04:20 pm - 04:40 pm  
    Precise adaptation in stem cell control

    Martin  ZAUSER, Heidelberg, Germany 
    04:40 pm - 05:00 pm  
    Automated image analysis and modeling of calcium waves in plant roots

    Jian-Geng CHIOU, Durham, United States
    05:00 pm - 05:20 pm           
    Principles that govern competition or co-existence in Rho-GTPase driven polarization in the budding yeast

    Atsushi MOCHIZUKI, Kyoto, Japan
    05:20 pm - 05:40 pm            
    Controlling cell fate specification system based on network structure

    05:50 pm - 06:30 pm Chair: Annamaria CARUSI, Sheffield, UK
    Barbara PRAINSACK, Vienna, Austria
    Is precision medicine “open”?
  • Thursday, November 1, 2018

    08:30 am - 09:00 am  Welcome
    09:00 am - 09:40 am  Chair: Andrea WEISSE, London, UK
    Mustafa KHAMMASH, Basel, Switzerland
    Rationally-Designed Biomolecular Control Systems
    09:40 am - 10:20 am Chair: Andrea WEISSE, London, UK
    Nathalie BALABAN, Jerusalem, Israel
    To grow or not to grow: phenotypic variability of growth in single cells
    10:20 am - 10:50 am Coffee break
    10:50 am - 11:50 am

    Chair: Jan TRAAS, Lyon, France
    Johan ELF, Uppsala, Sweden
    Adventures with single molecules in bacterial cells 

    11:50 am - 12:30 pm  Closing ceremony
    12:30 pm - 02:00 pm  Lunch