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BioNetVisA workshop

From biological network reconstruction to data visualization and analysis in molecular biology and medicine


During the ECCB’14 in Strasbourg, France, on September 7-10, 2014


Program and abstracts booklet 2014             Presentations 2014

BioNetVisA workshop brings together different actors of network biology from database providers, networks creators, computational biologists, biotech companies involved in data analysis and modeling to experimental biologists, clinicians that use systems biology approaches. The participants are exposed to the different paradigms of network biology and the latest achievements in the field.



The goal of BioNetVisA workshop is to build a discussion around various approaches for biological knowledge formalisation, data integration and analysis; compatibility between different methods and biological networks resources available the field; applicability for concrete research and clinical projects depending on scientific question and type of high-throughput data.


The BioNetVisA workshop aims at identifying bottlenecks and proposing short- and long-term objectives for the community as discussing questions about accessibility of available tools for wide range of user in every-day standalone application in biological and clinical labs. In addition, the possibilities for collective efforts by academic researchers, clinicians, biotech companies and future development directions in the field will be discussed during the round table panel.




Graphical representation of biological knowledge

Molecular interaction and pathway databases

Comprehensive signalling networks

Networks annotation and curation

High-throughput data visualisation, analysis and interpretation in the context of networks

Network modelling

Basic research and clinical application of networks



Development, curation and maintenance of biological network databases

Data models from interaction to pathway and network, available tools for the integration of new discoveries into existing signalling diagrams. Discussion of curation models from map manager-oriented to community-based update using web-tools and forums.


Cell signalling knowledge representation paradigms

From interaction to single pathways representation to comprehensive signalling networks: discussion of modes of biological processes representation; granularity, coverage, sources of information, annotation modes, cross-citations between different signalling networks resources, etc. Standard data formats, graphical representation standards.


Visualization of data through networks

Paradigms of visualization of different types of high-throughput data on a network map. Data integration with a map. Methods compatibility with different paradigms of signalling networks reconstruction in various databases and resources.


Analytical tools for network biology

Tools for network analysis and manipulation, network modeling, network-based statistics. Studying network activation and inhibition, feedbacks and compensations, synthetic interactions, clinical treatment response and resistance.




9.00-9.40 Keynote talk

                    Network visualization and analysis of gene expression data

                              Tom Freeman (University of Edinburgh, Edinburgh, UK) Slides


Session1 (part 1)

Development, curation and maintenance of biological network databases

Chair: Emmanuel Barillot (Institut Curie, Paris, France)

9.40-10.00    Reactome: Linking Biological Pathways and Networks to Disease

                    Robin Haw (Ontario Institute for Cancer Research, Toronto, Canada) Slides


10.10-10.20  IntAct - High Resolution Disease-centric Networks

                    Henning Hermjakob (European Bioinformatics Institute, Hinxton, UK) Slides


10.20-10.40  Coffee break and posters

Session1 (part 2)

Development, curation and maintenance of biological network databases

Chair: Emmanuel Barillot (Institut Curie, Paris, France)

10.40-11.00  Visualization and analysis of data using Atlas of Cancer Signalling Networks (ACSN) and NaviCell tools for integrative systems biology of cancer

                    Inna Kuperstein (Institut Curie, Paris, France) Slides


11.00-11.20  Graphical data representation

Pauline Gloaguen (cea- CEA, Grenoble, France) Slides


11.20-12.00  Keynote talk

                    Garuda- The way biology connects

Samik Ghosh (Systems Biology Institute, Tokyo, Japan) Slides


12.00-12.20  Posters flash presentations (5 posters x 3 minutes)


Poster10: Global Analysis of coregulation for the identification of functional modules

Rim Zaag (Plant Genomics Research, Evry, France) Slides

Poster 14: Sparse factor models for gene co-expression networks

Yuna Blum (UCLA, Los Angeles, USA) Slides

Poster 16: Streaming Visualisation for Raw Mass Spectrometry Data Based on a Novel Compression Algorithm

Yan Zhang (University of Manchester. Manchester, UK) Slides


12.20-13.30  Lunch and poster session


Session 2

Data visualisation and analysis in the context of biological networks

Chair: Mario Albrecht (University Medicine Greifswald, Greifswald, Germany)

13.30-13.50  A Pathway-centric Approach to Multiomics Research Powered by GeneSpring Analytics

                    Nigel Skinner (Agilent, Santa-Clara, CA, USA) Slides


13.50-14.10  An integrative network analysis pipeline in Cytoscape

Mohammed   El-Kebir (Centrum Wiskunde & Informatica, Amsterdam, Netherlands) Slides


14.10-14.30  Using network analysis: HyperSet is a novel framework for functional interpretation of ‘omics’ data in global networks

Andrey Alexeyenko (Stockholm Science for Life Laboratory, Solna, Sweden) Slides




Network biology in research and medicine

Chair: Robin Haw (Ontario Institute for Cancer Research, Toronto, Canada)

14.30-14.50  Gene networks, tumor subtypes and patient prognosis signatures associated with ovarian cancer mutations

                    Vladimir Kuznetsov (Bioinformatics Institute, Biopolis Singapore) Slides


14.50-15.10  Decoding Network Dynamics in Cancer

                    Rune Linding (Technical University of Denmark, Lyngby, Denmark) Slides


15.10-15.30  Using Topological Analysis to Study Metabolism of Heterotrophic Plant Cell Network

                    Marie Beurton-Aimar (Université Bordeaux 1, Bordeaux, France) Slides


15.30-15.50  Conserved cross-species network modules elucidate Th17 T cell differentiation in human and mouse

Hayssam Soueidan (NKI-AVL, Amsterdam, Netherlands) Slides


15.50-16.10  Meta expression analysis of regulatory T cell experiments for gene regulatory network reconstruction

Stefan Kroeger (Humboldt-Universität zu Berlin, Berlin, Germany) Slides


16.10-16.30  Coffee break and posters


16.30-17.10 Keynote talk

                    ***THE EMBO LECTURE: HER2 and EGFR: at last, cancer therapy meets systems biology

Yosef Yarden (The Weizmann Institut of Science, Rehovot, Israel) Slides


17.10-17.50  Round table - panel discussion and conclusions


Forum of the Medicine Campus, 4 rue Kirschleger, Strasbourg

Organising Committee


Inna Kuperstein (Institut Curie, France)

Emmanuel Barillot (Institut Curie, France)

Andrei Zinovyev (Institut Curie, France)

Hiroaki Kitano (Okinawa Institute of Science and Technology Graduate University, RIKEN Center for Integrative Medical Sciences, Japan)

Nicolas Le Novère (Babraham Institute, UK)

Robin Haw (Ontario Institute for Cancer Research, Canada)

Mario Albrecht (University Medicine Greifswald, Germany)

Benno Schwikowski (Institut Pasteur, France)


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