W2 – BioNetVisA: from biological network reconstruction to data visualization and analysis in molecular biology and medicine




Workshop details

Date: Sunday September 9, 2018

Time: 9:00 – 17:00

Venue: Eugenides Foundation

Room: Andrea Puccio

Abstract submission deadline: August 10, 2018


Workshop website: https://bionetvisa.github.io/



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.



Graphical representation of biological knowledge

Pathway and network resources

Networks annotation and curation

Multi-omics data visualization and analysis in the context of networks

Network modelling

Basic research and clinical application of networks

Microbiome and networks

Networks for single-cell data interpretation

Metabolomics and networks

Networks applications for drug repositioning

Networks in disease comorbidity studies


BioNetVisA program

09:00 – 10:30 Session 1: Signalling and metabolic network resources
09:00 – 09:20 Samik Ghosh
The Systems Biology Institute, Tokyo, Japan
Towards a network-centric approach in systems toxicology
09:20 – 09:35 Cristobal Monraz Gomez
Institut Curie, Paris, France
Atlas of Cancer Signaling Network: a resource of multi-scale biological maps to study disease mechanisms
09:35 – 09:55 Joaquin Dopazo
Fundación Progreso y Salud, Seville, Spain
Navigating through disease maps
09:55 – 10:10 Antonio Fabregat
EMBL-EBI, Hinxton, UK
The Reactome Pathway Knowledgebase
10:10 – 10:30 Augustin Luna
Dana-Farber Cancer Institute/Harvard University, Boston, United States
Access and Discover Biological Pathway Information from Pathway Commons


10:30 – 11:00 Coffee break


11:00 – 12:30 Session 2: Platforms and methods for analysis of complex networks
11:00 – 11:20 Georgios Pavlopoulos
Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
Using HipMCL, a high-performance parallel implementation of the Markov clustering algorithm, to understand microbial diversity
11:20 – 11:40 Anna Niarakis
GenHotel EA3886, Univ Evry, Université Paris-Saclay, France
Disease Networks – Reconstruction, Topology, Dynamics. Towards an automated pipeline from static representations to executable disease models
11:40 – 11: 55 Josephine Daub
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
Genetic interactions in childhood cancer
11:55 – 12: 10 Barbara Shih
The Roslin Institute and Royal (Dick) School of Veterinary Studies, the University of Edinburgh, Easter Bush, Midlothian, Edinburgh, UK
A platform for the network assembly and visual analysis of transcript isoforms from short-read RNA-sequencing data
12:10 – 12:30 Talks selected from abstracts


12:30 – 13:30 Lunch


13:30 – 15:00 Session 3: Biological networks in single-cell data analysis
13:30 – 13:50 Yvan Saeys
VIB-Ghent University, Gent, Belgium
Inferring dynamic regulatory networks from single cell data
13:50 – 14:10 Andrei Zinovyev
Institute Curie, Paris, France
Biological networks help unraveling tumoral heterogeneity at single cell level
14:10 – 14:25 Anirudh Patir
The University of Edinburgh, Edinburgh, UK
Evaluation of network methods for the analysis scRNA-seq data and development of a new KNN-based method based on identified caveats
14:25 – 14:40 Vassili Soumelis
Institut Curie, FR
Immune cell diversification in response to a single stimulus: from single cells to subsets and back
14:40 – 15:00 Talks selected from Abstracts


15:00 – 15:30 Coffee break


15:30 – 17:00 Session 4: Biological network in drug repositioning and disease comorbidity
15:30 – 16:10 Alfonso Valencia Keynote Lecturer
Barcelona Supercomputing Center, Barcelona, Spain
Disease networks for the study of the molecular basis of disease comorbidity
16:10 – 16:25 Celine Hernandez
Institut de Biologie de l’Ecole Normale Supérieure, Paris, France
Dynamical modelling of T cell co-inhibitory pathways to predict anti-tumour responses to checkpoint inhibitors
16:25 – 16:40 Sven Bergmann
University of Lausanne & Swiss Institute of Bioinformatics, Switzerland
Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
16:40 – 17:00 Round table discussion



Abstract submission

We invite to submit your abstract for talk and/or poster in the topics descried above

The submission deadline is August 10, 2018

For further details and submission link please access https://bionetvisa.github.io/





Important dates

May 15 Call for abstract submission
July 15 Workshop’s final program announcement
August 10 Extended abstract submission deadline
August 12 Abstract acceptance notificationt


Abstract submission

We invite to submit your abstract for talk and/or poster in the topics descried above


The submission deadline is August 10, 2018

For further details and submission link please access https://bionetvisa.github.io/



The registration has to be performed via ECCB website





Organising committee

Inna Kuperstein (Institut Curie, France)

Emmanuel Barillot (Institut Curie, France)

Andrei Zinovyev (Institut Curie, France)

Luis Cristobal Monraz Gomez (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)