Browsing by Author "Auffray, C."

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Open Access
Community-driven roadmap for integrated disease maps
(Oxford University Press, 2018) Ostaszewski, M.; Gebel, S.; Kuperstein, I.; Mazein, A.; Zinovyev, A.; Doğrusöz, Uğur; Hasenauer, J.; Fleming, R. M. T.; Novere, N. L.; Gawron, P.; Ligon, T.; Niarakis, A.; Nickerson, D.; Weindl, D.; Balling, R.; Barillot, E.; Auffray, C.; Schneider, R.
The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. The involvement of domain experts ensures that the key disease hallmarks are covered and relevant, up-to-date knowledge is adequately represented. Expert-curated and computer readable, disease maps may serve as a compendium of knowledge, allow for data-supported hypothesis generation or serve as a scaffold for the generation of predictive mathematical models. This article summarizes the 2nd Disease Maps Community meeting, highlighting its important topics and outcomes. We outline milestones on the roadmap for the future development of disease maps, including creating and maintaining standardized disease maps; sharing parts of maps that encode common human disease mechanisms; providing technical solutions for complexity management of maps; and Web tools for in-depth exploration of such maps. A dedicated discussion was focused on mathematical modeling approaches, as one of the main goals of disease map development is the generation of mathematically interpretable representations to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions.
Open Access
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps
(Oxford University Press, 2021-05-15) Balcı, Hasan; Siper, Metin Can; Saleh, Nasim; Safarli, İlkin; Roy, L.; Kılıçarslan, Merve; Özaydın, Rümeysa; Mazein, A.; Auffray, C.; Babur, Ö.; Demir, E.; Doğrusöz, Uğur
Motivation Visualization of cellular processes and pathways is a key recurring requirement for effective biological data analysis. There is a considerable need for sophisticated web-based pathway viewers and editors operating with widely accepted standard formats, using the latest visualization techniques and libraries. Results We developed a web-based tool named Newt for viewing, constructing and analyzing biological maps in standard formats such as SBGN, SBML and SIF. Availability and implementation Newt’s source code is publicly available on GitHub and freely distributed under the GNU LGPL. Ample documentation on Newt can be found on http://newteditor.org and on YouTube.
Open Access
Systems medicine and integrated care to combat chronic noncommunicable diseases
(BioMed Central Ltd., 2011) Bousquet, J.; Anto, J. M.; Sterk, P. J.; Adcock, I. M.; Chung, K. F.; Roca, J.; Agusti, A.; Brightling, C.; Cambon-Thomsen, A.; Cesario, A.; Abdelhak, S.; Antonarakis, S. E.; Avignon, A.; Ballabio, A.; Baraldi, E.; Baranov, A.; Bieber, T.; Bockaert, J.; Brahmachari, S.; Brambilla, C.; Bringer, J.; Dauzat, M.; Ernberg, I.; Fabbri, L.; Frogue, P.; Galas, D.; Gojobori2, T.; Hunter, P.; Jorgensen, C.; Kauffmann, F.; Kourilsky, P.; Kowalski, M. L.; Lancet, D.; Le Pen, C.; Mallet, J.; Mayosi, B.; Mercier, J.; Metspalu, A.; Nadeau, J. H.; Ninot, G.; Noble, D.; Öztürk, M.; Palkonen, S.; Préfaut, C.; Rabe, K.; Renard, E.; Roberts, R. G.; Samolinski, B.; Schünemann, H. J.; Simon, H. U.; Soares, M. B.; Superti-Furga, G.; Tegner, J.; Verjovski-Almeida, S.; Wellstead, P.; Wolkenhauer, O.; Wouters, E.; Balling, R.; Brookes, A. J.; Charron, D.; Pison, C.; Chen, Z.; Hood, L.; Auffray, C.
We propose an innovative, integrated, cost-e ective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders and cancers, which together are the predominant health problem of the 21st century. This proposed holistic strategy involves comprehensive patient-centered integrated care and multi-scale, multi-modal and multilevel systems approaches to tackle NCDs as a common group of diseases. Rather than studying each disease individually, it will take into account their intertwined gene-environment, socio-economic interactions and co-morbidities that lead to individual-speci c complex phenotypes. It will implement a road map for predictive, preventive, personalized and participatory (P4) medicine based on a robust and extensive knowledge management infrastructure that contains individual patient information. It will be supported by strategic partnerships involving all stakeholders, including general practitioners associated with patient-centered care. This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and speci cities of local economies and health systems.
Open Access
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms
(Nature Publishing Group, 2018) Mazein, A.; Ostaszewski, M.; Kuperstein, I.; Watterson, S.; Le Novère, N.; Lefaudeux, D.; De Meulder, B.; Pellet, J.; Balaur, I.; Saqi, M.; Nogueira, M. M.; He, F.; Parton, A.; Lemonnier, N.; Gawron, P.; Gebel, S.; Hainaut, P.; Ollert, M.; Doğrusöz, Uğur; Barillot, E.; Zinovyev, A.; Schneider, R.; Balling, R.; Auffray, C.
The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.
Open Access
Viva Europa, a land of excellence in research and innovation for health and wellbeing
(Wolters Kluwer Health, 2017-06-07) Auffray, C.; Sagner, M.; Abdelhak, S; Adcock, I.; Antonarakis, S.; Arena, R.; Argoul, F.; Balling, R.; Barabasi, Albert-Laszlo; Beckmann, J.; Bjartell, A.; Bourgeon, T.; Boutron, B.; Brahmachari, S.; Brechot, C.; Brightling, C.; Cascante, M.; Cesario, A.; Charron, D.; Chen, Sai-Juan; Chen, Z.; Chung, F.; Clement, K.; Conesa, A.; Cozzone, A.; de Jong, M.; Deleuze, Jean-François; Demotes, J.; di Meglio, A.; Djukanovic, R.; Dogrusoz, U.; Epel, E.; Fischer, A.; Gelemanovic, A.; Goble, C.; Gojobori, T.; Goldman, M.; Goossens, H.; Gros, F.; Hainaut, P.; Guo, Yi-Ke; Harrison, D.; Hoffmann, H.; Hood, L.; Hunter, P.; Jacob, Y.; Kitano, H.; Klingmuller, U.; Knoppers, B.; Kolch, W.; Koopmans, M.; Lancet, D.; Laville, M.; Lehn, Jean-Marie; Lévi, F.; Lisistsa, A.; Lotteau, V.; Mayosi, B.; Metspalu, A.; Moreau, Y.; N'Dow, J.; Nicod, L.; Noble, D.; Nogueira, Maria-Manuela; Norrby-Teglund, A.; Openshaw, P.; Ozturk, M.; Palkonen, S.; Parodi, S.; Pellet, J.; Polasek, O.; Price, N.; Pristipino, C.; Radstake, T.; Raes, M.; Roca, J.; Rozman, D.; Sabatier, P.; Sasson, S.; Schmeck, B.; Serageldin, I.; Simonds, A.; Soares, B.; Sterk, P.; Superti-Furga, G.; Supple, D.; Tegner, J.; Uhlen, M.; van der Werf, S.; Villoslada, P.; Vinciguerra, M.; Volpert, V.; Webb, S.; Wouters, E.; Sanz, F.; Nobrega, F.