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
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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.
Motivation
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.
Topics
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
Scope
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.
Program
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
Session3
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
Venue
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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