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Systems biology of transcription regulation @ ICSB 2018

Workshop details

Date: Saturday 27th October 2018
Time: 9:00 – 18:30
Venue: Ecole Normale Supérieure (ENS), Campus Monod 46, allée d’Italie 69007 Lyon, FRANCE
Biology Amphitheater (within the main ENS building)

Campus map

Registration fee:

Standard 100 Euro

Student 70 Euro

The fee includes attandance to the workshop, poster session and coffee breaks.

Please transfer the money to : Genexplain GmbH

Bank: Bankhaus C.L. Seeliger

IBAN: DE79270325000000001575


Reason for payment: Workshop SBTR2 (your Last Name, First Name)

For payment by invoce: please, contact the organizers sending your institution billing address and VAT

Please note that this is a non-profit event, the role of geneXplain is to just kindly handling the fees.

The organisers are grateful to geneXplain GmbH for sponsorship and organizational help.

Registration and submission of abstracts (closed)


The complex nature of transcription regulation can be investigated with various methods and under different angles. Systems Biology approaches allow us to get a holistic and systemic view on regulation of gene expression by bringing together and combining various perspectives, from signal transduction to transcription factors (TFs)- and chromatin-mediated gene regulation, to network inference.

This meeting aims at bringing together researchers representing the views on the process of transcription regulation from different perspectives, from the regulation of expression through transcription factors (TFs) to the field of chromatin structure, remodeling and its involvement in the regulation. We will welcome stories of success, discussions of actual problems and of methodology development, which is an actual issue in this field.

The first edition of this satellite workshop was held during the 17th edition of the International Conference on Systems Biology in Barcelona (Spain) on 2016, achieving a very good public success with an excellent panel of speakers, interactive discussions at both the talks and poster sessions, and a highly appreciated round table.

For this second edition, we would like to structure the workshop in two sessions: the first one would be dedicated to all variety of Systems Biology approaches to transcription regulation, for instance, but not limited to, data deconvolution, dynamical modeling, network inference, etc. The second session would focus on the impact of chromatin structure and histone modifications on gene expression and how this layer of regulation is incorporated in Systems Biology approaches. Additionally, we plan to end the workshop with a round table for discussion on how to address most actual problems, from methodology use to data analyses.

In the Workshop Systems Biology of Transcription Regulation we therefore welcome efforts related to:

We will appreciate abstracts representing the views on the process of transcription regulation from different perspectives and different angles, preferably combining the abovementioned issues.

Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems will be a subject of discussion in the Round Table (see Agenda).

Registration and submission are closed.

You are invited to submit a one-page abstract that will be reviewed and selected for a 20-minute talk, short talk (10 min) or poster. The abstract should include all authors' names with affiliations (please mark the presenting author with an asterisk).
Confirmation receipt will be sent on request.

Keynote speakers

  • María Rodríguez Martínez, IBM Zurich Research Laboratory, Zurich, Switzerland
    Keynote Talk: Systems approaches to unravel cancer molecular mechanisms

  • Carl Herrmann, DFKZ German Cancer Research Center, Heidelberg, Germany
    Keynote Talk: Multi-omics data integration for single-cell

  • Jasmin Fisher, Microsoft Research & University of Cambridge, UK
    Keynote Talk: Executable Biology: From Mechanistic Insights to New Avenues in Cancer Therapy



Ekaterina Shelest German Centre for Integrative Biodiversity Research (iDiv), Leipzig

Welcome and opening


María Rodríguez Martínez IBM Zurich Research Laboratory, Zurich, Switzerland

Systems approaches to unravel cancer molecular mechanisms

10.30-11.00 Coffee break (poster viewing)

Arnaud Bonnafoux, ENS Lyon, France - WASABI: a dynamic iterative framework for gene regulatory network inference


Ovidiu Radulescu, University of Montpellier, France - Mathematical models of transcriptional memory in eukaryotic transcription


Matteo Barberis, University of Amsterdam, The Netherlands - The Multplex Phase Interlocker: A Novel and Robust Molecular Design Synchronizing Transcripton and Cell Cycle Oscillators


Jasmin Fisher Microsoft Research & University of Cambridge, UK

Executable Biology: From Mechanistic Insights to New Avenues in Cancer Therapy

12.50-14.00 Lunch break

Carl Herrmann DFKZ German Cancer Research Center, Heidelberg, Germany

Multi-omics data integration for single-cell


Hauke Busch, University of Lübeck, Germany - Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles


Harukazu Suzuki, RIKEN IMS, Japan - TF-mediated site-specific DNA demethylation in cellular differentiation


Jérôme Eeckhoute, University of Lille, France - Organizing combinatorial transcription factor recruitment at cis-regulatory modules

16.00-16.30 Coffee break (poster viewing)

Nacho Molina, IGBMC Strasbourg, France - Transcription reactivation kinetics after mitosis


Laurent Trilling, University of Grenoble, France - Constraint ASP Based Inference of Delay Parameters for Discrete Genetic Networks. Application to the Mammalian Circadian Clock


Samuel Miravet-Verde, CRG Barcelona, Spain - Comprehensive modeling of transcription in a minimal cell

17.15-18.00 Round table on the main problems, challenges, and perspectives of systems biology of transcription regulation.
18.00-18.30 Poster session, networking, discussions.


If you have any further questions please do not hesitate to contact us ekaterina.shelest@idiv.de, loredana.martignetti@curie.fr

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