Network-based approaches for drug response prediction and targeted therapy development in cancer

Dorel, Mathurin; Barillot, Emmanuel; Zinovyev, Andrei; Kuperstein, Inna

doi:10.1016/j.bbrc.2015.06.094

Cited by 32 publications

(19 citation statements)

References 60 publications

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“…Complex networks, redundancy of the inflammatory pathways, plasticity of the immune response, and complex interplay between inflammation and healing response pose challenges. 21 However, oral synthetic targeted therapies may offer unique opportunities to try new strategies without being too concerned about immunogenicity and loss of response. These will include stop-start strategies, intercalated short-term additional therapy to background maintenance therapy, combining therapies with complementary mechanism of action as well as novel topical therapies.…”

Section: Targeting Integrins and Safety In An Emerging Class Of Targementioning

confidence: 99%

Targeting Integrins and Safety in an Emerging Class of Targeted Oral Therapies: Are We Prepared for Rational and Precision Choices?

Levesque

Ghosh

2015

Gastroenterology

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Intragastric pressure during food intake: a physiological and minimally invasive method to assess gastric accommodation. Neurogastroenterol Motil 2011; 23:316-322, e153-154. 29. McCallum RW, Lembo A, Esfandyari T, et al; TZP-102 Phase 2b Study Group. Phase 2b, randomized, doubleblind 12-week studies of TZP-102, a ghrelin receptor agonist for diabetic gastroparesis. Neurogastroenterol Motil 2013;25:e705-e717.

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Section: Targeting Integrins and Safety In An Emerging Class Of Targementioning

confidence: 99%

Targeting Integrins and Safety in an Emerging Class of Targeted Oral Therapies: Are We Prepared for Rational and Precision Choices?

Levesque

Ghosh

2015

Gastroenterology

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“…Data visualization is a possible solution to obtain an integrated overview of the data and understanding their characteristic patterns. Making biological sense out of the molecular data requires visualizing them in the context of cell signalling processes (5, 6). A lot of information about molecular mechanisms is available in the scientific literature, and is also integrated into signalling pathway databases.…”

Section: Introductionmentioning

confidence: 99%

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

Dorel

Viara²,

Barillot

et al. 2017

Database

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Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of regulation of molecular functions reflected by an omics profile. In order to make this task easy, we developed NaviCom, a Python package and web platform for visualization of multi-level omics data on top of biological network maps. NaviCom is bridging the gap between cBioPortal, the most used resource of large-scale cancer omics data and NaviCell, a data visualization web service that contains several molecular network map collections. NaviCom proposes several standardized modes of data display on top of molecular network maps, allowing addressing specific biological questions. We illustrate how users can easily create interactive network-based cancer molecular portraits via NaviCom web interface using the maps of Atlas of Cancer Signalling Network (ACSN) and other maps. Analysis of these molecular portraits can help in formulating a scientific hypothesis on the molecular mechanisms deregulated in the studied disease. Database URL: NaviCom is available at https://navicom.curie.fr

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“…This complexity explains frequent failure of one-drug-one-target paradigm of treatment, resulting in drug resistance in patients. To overcome the robustness of cell signaling network, the treatment should be extended to a combination therapy scheme [67].…”

Section: Personalization Of Models Using Datamentioning

confidence: 99%

Community-driven roadmap for integrated disease maps

Ostaszewski¹,

Gebel²,

Kuperstein³

et al. 2018

Preprint

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The Disease Maps Project builds upon 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 in order to predict disease comorbidity or drug response and to suggest drug repositioning, altogether supporting clinical decisions.

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Network-based approaches for drug response prediction and targeted therapy development in cancer

Cited by 32 publications

References 60 publications

Targeting Integrins and Safety in an Emerging Class of Targeted Oral Therapies: Are We Prepared for Rational and Precision Choices?

Targeting Integrins and Safety in an Emerging Class of Targeted Oral Therapies: Are We Prepared for Rational and Precision Choices?

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

Community-driven roadmap for integrated disease maps

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