ICSB2016 >

Systems biology of transcription regulation

Workshop details

Date: Thursday 15 September 2016
Time: 9:00 – 19:30
Venue: UPF lecture halls

Dr. Aiguader building of the Mar Campus of the Universitat Pompeu Fabra, located at

Carrer Dr. Aiguader 80

08003 Barcelona

Campus map

right next to the Parc de Recerca Biomedica de Barcelona.

Registration fee:

Standard 100 Euro

Student 70 Euro

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

Please transfer the money to : Genexplain GmbH

Bank: Bankhaus C.L. Seeliger

IBAN: DE79270325000000001575


Reason for payment: Workshop SBTR

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

Registration and submission of abstracts

Submission deadline: 22 August 2016 Extended deadline: 27 August

Registration here:

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). Please note that the abstract should be in plain text format without special characters.

Please note in the comments whether you would like to present a poster or a talk. If you are not going to present anything please write in the comments "no presentation".

Fields marked with an asterisk (*) are required.

The confirmation of registration will be sent to you per email.


Scope and Call for abstracts

Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches.

Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks.

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). For abstract details, click here

Keynote speakers

Dr. Mattia Pelizzola



Ekaterina Shelest Hans-Knoell-Institute, Jena, Germany

Welcome and opening


Mattia Pelizzola Center for Genomic Science of IIT@SEMM, Milan, Italy

Interplay of RNAPII dynamics and the regulation of pre-mRNA synthesis and processing rates upon Myc activation


Saúl Ares Grupo Interdisciplinar de Sistemas Complejos / Universidad Carlos III de Madrid, Spain

Formation and maintenance of nitrogen fixing cell patterns in filamentous cyanobacteria


Arnau Montagud Institute Curie, Paris, France

Independent component analysis undercovers clinical traits that cause cancer stratification

11.00-11.30 Coffee break

Alexander Kel geneXplain GmbH, Wolfenbuettel, Germany

Walking pathways of transcription regulation


Joerg Linde Hans-Knoell-Institute, Jena, Germany

Using dual-RNASeq to predict molecular host-pathogen interaction networks


Loredana MartignettiInstitut Curie / INSERM U900 / Mines ParisTech, Paris, France

ROMA: Representation and Quantification of Module Activity from Target Expression Data

13.00-14.00 Lunch

Melanie Boerries, Hauke Busch Institute for Molecular Medicine and Cell Research, Albert-Ludwigs-University of Freiburg /German Cancer Consortium (DKTK, Freiburg) /German Cancer Research Center (DKFZ), Heidelberg, Germany

Boolean modeling reveals the necessity of transcriptional regulation for cellular decisions


Lisa Davis Department of Mathematical Sciences, Montana State University, USA

Mathematical Models of Transcription and the Data Driving Them


Ross Thorne Weatherall Institute of Molecular Medicine, University of Oxford, UK

Using systems theory to analyse the transcription network of MLL-AF4 leukaemias


Martin Haubrock Institute of Bioinformatics, University Medical Center, Goettingen, Germany

Linking distal regulatory elements to their target genes: The enhancer-promoter interaction model encoded by the transcription factors AP-1 and NF-Y


Silvia Gerber Hans-Knoell-Institute, Jena, Germany

Genome-wide gene regulatory network inference in the opportunistic human pathogenic fungi Aspergillus fumigatus

15.45-16.15 Coffee break
16.15-18.00 Round table on the main problems, challenges, and perspectives of systems biology of transcription regulation.
18.00-19.30 Poster session, networking, discussions.

If you have any further questions please do not hesitate to contact us ekaterina.shelest@leibniz-hki.de

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