BioNetVisA 2017 workshop
From biological network reconstruction to data
visualization and analysis in molecular biology and medicine
https://www.bc2.ch/2017/program/workshops/ws2/
12 September
2017
University of Basel
Kollegienhaus
Petersplatz
1, CH-4001
Basel,
Switzerland
https://www.bc2.ch/2017/travel-venue/
Program
and abstracts booklet 2017
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 network biology
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.
BioNetVisA program
Session 1
Signaling and metabolic network databases
Chair: Andrei Zinovyev
09.00-09.20
Stephan Gebel (University of Luxembourg, Luxembourg)
A comprehensive map of signalling
in Parkinson’s disease
09.20-09.35
Konstantinos Sidiropoulos
(EMBL-EBI,
Hinxton, UK)
Reactome: New features for
enhanced pathway visualisation
09.35-10.55
Falk Schreiber (University of Konstanz, Konstanz, Germany)
From static visualisation
to immersive analytics of biological networks
10.55-10.10
Björn Sommer (Monash University, Melbourne, Australia)
Multiscale Modeling and 3D Visualization of
spatially-embedded Cytological Networks
10.10-10.25
Marcus Krantz (Humboldt-Universität zu Berlin, Berlin,
Germany)
Formalisation, visualisation and analysis of signal transduction
networks with rxncon
10.25-11.00 Coffee break
Session 2
Platforms and method for analysis of complex
biological networks
Chair: Patrick Kemmeren
11.00-11.30
Keynote lecture
Alfonso
Valencia (Spanish
National Bioinformatics Institute, Madrid, Spain)
Networks and Co-evolution in the Interpretation
of Epigenetic Regulation
11.30-11.50
Andrei Zinovyev (Institut Curie, Paris, France)
Application of the reduced Google Matrix
approach for the analysis of directed biological networks
11.50-12.10
Ugur Dogrusoz (Bilkent University, Ankara, Turkey)
Interactive web based curation of
biological pathways with advanced layout and complexity management support
12.10-12.25
Aura Ileana Moreno-Vega (Institut Curie, Paris, France)
Characterization of the FGFR3 regulatory network in bladder tumors
12.30-13.30 Lunch
Session 3
Biological networks in drug discovery and
toxicology studies
Chair: Ugur Dogrusoz
13.30-14.00
Keynote lecture
Minoru Kanehisa (Institute for Chemical Research, Kyoto University)
From gene variants to network variants: a new database
for understanding diseases and drugs
14.00-14.20
Mark Ibberson (Swiss
Institute of Bioinformatics)
Biomarker discovery in diabetes: A
network-based approach
14.20-14.40
Tatyana Doktorova (Douglas Connect GmbH, Basel, Switzerland)
Integrated
Modelling and Testing Strategies supporting Systems Toxicology and
Evidence-based
Safety Assessment
14.40-14.55
Justyna Szostak
(Philip Morris International group, Neuchâtel,
Switzerland)
Detect Liver Toxicity through Causal Biological Network Model and
Computational Algorithm
15.00-15.30 Coffee break
Session 4
Biological networks modelling in medicine
Chair: Matteo Barberis
15.30-15.50
Gregory
Batt (Institut Pasteur, Paris,
France)
A multi-scale model for investigating TRAIL
resistance in multi-cellular tumor spheroids
15.50-16.10
Patrick Kemmeren (Princess Maxima Center
for Pediatric Oncology, Utrecht, Netherlands)
Exhaustive Petri net modeling to infer
mechanisms of genetic interactions
16.10-16.25
Valeriya Malysheva (Université de Strasbourg, Illkirch, France)
Integration of chromatin structure dynamics
in the regulatory network governing cell fate acquisition
16.25-16.45
Matteo Barberis (University
of Amsterdam, Amsterdam, The Netherlands)
GEMMER: GEnome-wide
software for Multi-scale Modeling data Extraction and
Representation
16.45-17.00
Closing remarks and
discussion
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)
Minoru Kanehisa (Institute for Chemical
Research, Kyoto University, Japan)
Samik Ghosh (Systems Biology
Institute, Tokyo, Japan)
Nicolas Le Novère (Babraham Institute, UK)
Robin Haw (Ontario Institute for Cancer Research, Canada)
Alfonso Valencia (Spanish National Bioinformatics Institute,
Madrid, Stain)
Lodewyk Wessels (Netherlands Cancer Institute, Amsterdam,
Netherlands)
Patrick Kemmeren (Princess
Maxima Center for Pediatric
Oncology, Utrecht, Netherands)
Downloads
Program and abstracts booklet 2014 Presentations 2014
Program and abstracts booklet 2015 Presentations 2015
Program and abstracts booklet 2016 Presentations 2016
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