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The 3rd Disease Maps Community Meeting (DMCM2018) is hosted by the Computational Systems Biology of Cancer group, Institut Curie.

The programme and the abstract booklet are available here

Photos from the meeting are available at CurieSysBio Instagram


Objectives

The objective of the 3rd DMCM is to consolidate efforts around the disease map projects and extend the Disease Maps Community. The 3rd DMCM will expose progress of the projects from the Disease Maps Community and beyond. The representative examples of network maps generation, their applications for disease data analysis, disease comorbidity, drug response prediction, advances in tools development and modelling approaches will be presented.

Topics

Among others, the following topics will be discussed: biocuration of prior knowledge related to different human diseases; creation and maintenance of disease network maps following common standards; sharing sub-maps with mechanisms implemented into different human diseases; providing technical solutions for network maps complexity management, mathematical modelling of maps and web-tools for explorations in maps. Topic-specific roundtable discussions will be organised to identify bottleneck problems and ways to overcome them.

Hands-on tutorials

Part of the meeting will be dedicated to demos and hands-on tutorials on major tools supporting the disease maps. The downloadable materials are available at the tutorial description in the meeting programme.

Programme

21 June

Amphithéâtre BDD

08:30 - 09:00 Arrival and registration
09:00 - 09:05 Opening session and welcome
Emmanuel Barillot, Institute Curie, Paris, France
Reinhard Schneider, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
09:05 - 09:15 Aims and perspectives of the DMCM2018 meeting
Alexander Mazein, European Institute for Systems Biology and Medicine, Lyon, France
Inna Kuperstein, Institute Curie, Paris, France

Session 1: Disease maps resources

09:15 - 09:30 Integrating disease maps using a graph database approach
Irina Balaur, European Institute for Systems Biology and Medicine, Lyon, France
Abstract
09:30 - 09:45 A disease map for the blood pressure and glomerular filtration regulatory network on which antihypertensive and analgesic drugs act
Francisco J. Lopez Hernandez, University of Salamanca, Salamanca, Spain
Abstract
09:45 - 10:00 Towards a molecular map of cystic fibrosis mechanisms
Catarina Pereira and Andre Falcao, University of Lisbon, Lisbon, Portugal
Abstract

10:00 - 10:30 Coffee break at BDD Hall

Session 2: Disease maps resources II

10:30 - 10:45 The AsthmaMap: computational representation of disease mechanisms using domain expert knowledge
Alexander Mazein, European Institute for Systems Biology and Medicine, Lyon, France
Abstract
10:45 - 11:00 A multiscale signalling network map of immune response in cancer reveals signatures of cell heterogeneity and functional polarization
Maria Kondratova, Institute Curie, Paris, France
Abstract
11:00 - 11:15 Parkinson's disease map facilitated gene expression analysis reveals new insights in PD pathogenesis
Stephan Gebel, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
Abstract
11:15 - 11:30 Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model
Anna Niarakis, Universite d' Evry Val d' Essonne, Evry Val d' Essonne, France
Abstract
11:30 - 12:30 Invited talk: WikiPathways: curation, visualization and analysis of biological pathways
Martina-Summer Kutmon Maastricht University, Maastricht, the Netherlands
Abstract

12:30 - 13:30 Lunch and collaborations discussion at BDD Hall

13:30 - 15:00 Hands-on tutorials: parallel sessions

Time/Place Amphi BDD Annexes 1-3 BDD
13:30 - 14:10 Tutorial 1 Tutorial 3
14:10 - 14:15 Break Break
14:15 - 14:55 Tutorial 2 Tutorial 4

Tutorial 1: Constructing and visualizing pathways with web-based SBGN editor Newt
Ugur Dogrusoz, Bilkent University, Ankara, Turkey
Abstract
Tutorial 2: MINERVA for visualization of disease maps
Piotr Gawron, Marek Ostaszewski, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
Abstract
Requirements and downloads: To follow this tutorial, is recommended to install CellDesigner. All tutorial files are available here. Additionally, all files will be available on LCSB’s ownCloud (Password: DMCM2018)
Tutorial 3: rROMA, a tool for module activity calculation from omics data and networks
Luca Albergante, Urszula Czerwinska, Andrei Zinovyev, Loredana Martignetti, Institute Curie, Paris, France
Abstract
Requirements and downloads: To follow this tutorial, is recommended to install R or R Studio and to download these files
Tutorial 4: COBRA toolbox for visualisation and map manipulation through CellDesigner and MatLab environment
Jennifer Modamio, Ronan Fleming, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
Nicolas Sompairac, Andrei Zinovyev, Inna Kuperstein, Institute Curie, Paris, France
Abstract
Requirements and downloads: To follow this tutorial, is recommended to install MATLAB (Paying license needed), CellDesigner and the COBRAToolBox . The files for the tutorial can be downloaded here

Session 3:Maps of biological processes and disease

15:00 - 15:10 The adult neurogenesis map
Rupert Overall, German Center for Neurodegenerative Diseases, Dresden, Germany
Abstract
15:10 - 15:20 The Ras/Raf/Mek/Erk Signaling Pathway - Attention to Details
Maria Dost, Humboldt-Universität zu Berlin, Berlin, Germany
Abstract
15:20 - 15:30 Is cellular senescence a prerequisite for tumor invasion?
Mathieu Boissan, Centre de recherche St-Antoine, Paris, France
Abstract

15:30 - 16:00 Coffee break at BDD Hall

Session 4: Maps for drug assessment and disease comorbidity

16:00 - 16:10 Comprehensive signaling network of regulated cell death: comparison of cell death modes in Alzheimer's neurodegenerative disease and cancer
Cristobal Monraz, Institute Curie, Paris, France
Abstract
16:10 - 16:20 Predicting personal activation potential of CD4 T cells
Feng He, Luxembourg Institute of Health, Luxembourg, Luxembourg
Abstract
16:20 - 16:30 Reconstruction of integrated maps for drug efficacy assessment
Tatiana Serebriyskaya, Moscow Institute of Physics and Technology, Moscow, Russia
Abstract
16:30- 16:40 Metabolic and signalling network map integration: application to cross-talk studies and omics data analysis in cancer
Nicolas Sompairac, Institute Curie, Paris, France
Abstract

16:45- 17:00 Group photo

17:00 - 18:15 Marie Curie museum and garden visit
http://musee.curie.fr

22 June

Amphithéâtre BDD

Session 5:Methods resources and models

09:00 - 09:15 Access and Discover Biological Pathway Information from Pathway Commons
Augustin Luna, Dana-Farber Cancer Institute/Harvard University, Boston, United States
Abstract
09:15 - 09:30 Community resources connecting chemistry and toxicity knowledge to environmental observations
Emma Schymanski, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
Antony Williams, National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Durham,USA
Abstract
09:30 - 09:45 Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
Joaquin Dopazo, Fundación Progreso y Salud, Sevilla, Spain
Abstract
09:45 - 10:00 A computational model of the circadian clock and its application to understanding renal disease
Tom Freeman, The University of Edinburgh, Edinburgh, United Kingdom
Abstract

10:00 - 10:30 Coffee break at BDD Hall

Session 6: Large Reconstructions and integrations

10:30 - 10:45 Status report: parameter estimation of a large-scale mechanistic model for mast cells in asthma
Thomas S. Ligon, Ludwig-Maximilians-Universitat, Munich, Germany
Jan Hasenauer, Helmholtz Zentrum Munchen, Munich, Germany
Abstract
10:45 - 11:00 Application of disease maps to rare diseases: as muscular dystrophies
Cecilia Jimenez Mallebrera, Hospital Sant Joan de Deu, Barcelona, Spain
Abstract
11:00 - 11:15 Maps of influence and interactions of infectious and cancer diseases from Wikipedia networks
Dima Shepelyansky, Laboratoire de Physique Theorique CNRS, Universite Paul Sabatier, Toulouse, France
Abstract
11:15 - 11:30 Integrating ontological representation and reasoning into a disease map: application to Alzheimer’s disease
Vincent Henry, ICM Brain and Spine Institute, Paris, France
Abstract
11:30 - 12:30 Invited talk: Reactome multi-scale pathway visualization
Henning Hermjakob, Molecular Systems services EMBL-EBI, Cambridge, United Kingdom
Abstract

12:30 - 13:30 Lunch and collaborations discussion at BDD Hall

13:30 - 15:00 Hands-on tutorials: parallel sessions

Time/Place Amphi BDD Annexes 1-3 BDD
13:30 - 14:10 Tutorial 5 Tutorial 7
14:10 - 14:15 Break Break
14:15 - 14:55 Tutorial 6

Tutorial 5: From interaction maps to dynamical models with Cell Collective: a hands-on tutorial
Tomas Helikar, University of Nebraska-Lincoln, Lincoln, United States
Abstract
Requirements and downloads: To follow this tutorial, is recommended to create a free acount on the Cell Colective website
Tutorial 6: mEPN and yEd: a graphical and computational modelling platform for biological pathways
Tom C. Freeman, University of Edinburgh, Edinburgh, UK
Abstract
Requirements and downloads: To follow this tutorial, is recommended to download and install yEd and Graphia Professional
Tutorial 7: A tutorial of hipathia, a mechanistic model of pathway activity
Martha R Hidalgo, Centro de Investigación Principe Felipe, Valencia, Spain
Joaquin Dopazo, Fundación Progreso y Salud, Sevilla, Spain
Abstract
15:00 - 15:30 Invited talk: Share FAIR – Data management and standards for Systems Medicine
Martin Golebiewski, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
Abstract

15:30 - 16:00 Coffee break at BDD Hall

Session 7: Visualization and modeling frameworks

16:00 - 16:10 Instantiation of patient-specific network-based logical models with multi-omics data allows clinical stratification of patients
Jonas Beal, Institute Curie, Paris, France
Abstract
16:10 - 16:20 Visual analytics of biological networks using VANTED and its SBGN-ED add-on
Hanna Borlinghaus, University of Konstanz, Konstanz, Germany
Abstract
16:20 - 16:30 MINERVA API and plugin architecture: new data visualization interfaces for disease maps
Piotr Gawron, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg
Abstract
16:40 - 17:15 Thematic discussion groups (suggested topics):
Integration of maps in a shared repository
Tools for maps generation
Applications of disease maps in research and clinics: what is missing to close the gap?
Maps to models: curation standards to allow easy transformation of networks into executable models
Maps' complexity management approaches
Disease pathways vs. healthy pathways: how different are they?
17:15 - 17:30 Conclusions and closing session
Emmanuel Barillot, Institute Curie, Paris, France
Reinhard Schneider, Luxembourg Centre for Systems Biomedicine, Belval, Luxembourg

Abstract submission

Submit abstracts (up to 400 words) via the submission link for oral presentations and/or posters. Indicate 4 keywords to allocate it into the suitable session.

Registration

The registration is free but mandatory. Fill in the registration form here.

Location

Batiment de biologie du developpement et cancer (BDD building)
11 rue Pierre et Marie Curie
75005, Paris
France


Accommodation

Recommended hotels:

Les Jardins Du Luxembourg
5 Impasse Royer-Collard, 75005 Paris, France

Hotel Elysa-Luxembourg
6 Rue Gay Lussac, 75005 Paris, France

Hotel du Brésil
10 rue Le Goff, 75005 Paris, France

Hotel Michelet Odeon
6 Place De L Odeon, 75006 Paris, France

Hotel de l'Avenir
65 rue Madame, 75006 Paris, France

Hôtel Des Mines
125 Bd Saint Michel, 75005 Paris, France

Contact

disease-maps-coord@googlegroups.com

Organisers

Computational Systems Biology of Cancer group, Institut Curie:
Emmanuel Barillot
Maria Kondratova
Inna Kuperstein
Cristobal Monraz
Andrei Zinovyev
Irina Balaur

Disease Maps Project Coordinators

Alexander Mazein
Marek Ostaszewski
Inna Kuperstein
Andrei Zinovyev
Reinhard Schneider
Emmanuel Barillot
Rudi Balling
Charles Auffray