Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map
Quentin Miagoux
,
Vidisha Singh
,
Dereck de Mézquita
,
Valérie Chaudru
,
Mohamed Elati
,
et al.
Journal articles
hal-03515663v1
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Boolean modelling as a logic-based dynamic approach in systems medicine
Ahmed Abdelmonem Hemedan
,
Anna Niarakis
,
Reinhard Schneider
,
Marek Ostaszewski
Journal articles
hal-03699613v1
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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
Anna Niarakis
,
Dagmar Waltemath
,
James Glazier
,
Falk Schreiber
,
Sarah Keating
,
et al.
Journal articles
hal-03690604v1
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Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop
Anna Niarakis
,
Martin Kuiper
,
Marek Ostaszewski
,
Rahuman Malik Sheriff
,
Cristina Casals-Casas
,
et al.
Journal articles
hal-02549796v1
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Automated inference of Boolean models from molecular interaction maps using CaSQ
Sara Sadat Aghamiri
,
Vidisha Singh
,
Aurélien Naldi
,
Tomáš Helikar
,
Sylvain Soliman
,
et al.
Journal articles
hal-02590714v1
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Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches
Sahar Aghakhani
,
Naouel Zerrouk
,
Anna Niarakis
Journal articles
hal-03105351v1
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Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome
Yacine Bounab
,
Anne-Marie- Hesse
,
Bruno Iannascoli
,
Luca Grieco
,
Yohann Couté
,
et al.
Journal articles
hal-02086260v1
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Executable Disease Networks: Adding dynamics to molecular maps
Vidisha Singh
,
Saran Pankaew
,
Marek Ostaszewski
,
George D. Kalliolias
,
Sylvain Soliman
,
et al.
ECCB 2018 - 17th European Conference on Computational Biology , Sep 2018, Athens, Greece
Poster communications
hal-01875418v1
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COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
Marek Ostaszewski
,
Anna Niarakis
,
Alexander Mazein
,
Inna Kuperstein
,
Robert Phair
,
et al.
Journal articles
hal-03385317v2
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Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference
Naouel Zerrouk
,
Quentin Miagoux
,
Aurelien Dispot
,
Mohamed Elati
,
Anna Niarakis
Journal articles
hal-02958928v1
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SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
Andreas Dräger
,
Tomáš Helikar
,
Matteo Barberis
,
Marc Birtwistle
,
Laurence Calzone
,
et al.
Journal articles
hal-03515692v2
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Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model
Vidisha Singh
,
Marek Ostaszewski
,
George D. Kalliolias
,
Gilles Chiocchia
,
Robert Olaso
,
et al.
Journal articles
hal-02084429v1
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Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima
Paul Soudier
,
Daniel Rodriguez Pinzon
,
Tristan Reif-Trauttmansdorff
,
Hassan Hijazi
,
Maëva Cherrière
,
et al.
Journal articles
hal-03626102v1
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A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
Vidisha Singh
,
Aurélien Naldi
,
Sylvain Soliman
,
Anna Niarakis
Journal articles
hal-04187223v1
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Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: a Hybrid Modeling Approach
Sahar Aghakhani
,
Sylvain Soliman
,
Anna Niarakis
Journal articles
hal-03880870v2
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Modélisation Logique et Analyse Intégrative Des Voies Moléculaires Impliquées Dans La Polyarthrite Rhumatoïde
Anna Niarakis
,
V. Singh
,
Elisabeth Petit-Teixeira
Journal articles
hal-02084421v1
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A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms
Anna Niarakis
,
Marek Ostaszewski
,
Alexander Mazein
,
Inna Kuperstein
,
Martina Kutmon
,
et al.
2022
Preprints, Working Papers, ...
hal-03907738v1
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Logical modelling of cellular decision processes with GINsim
Claudine Chaouiya
,
Aurélien Naldi
,
Lionel Spinelli
,
Pedro Monteiro
,
Duncan Berenguier
,
et al.
JOBIM 2012 , Jul 2012, Rennes, France
Conference papers
hal-01261855v1
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The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
Vasundra Touré
,
Åsmund Flobak
,
Anna Niarakis
,
Steven Vercruysse
,
Martin Kuiper
Journal articles
hal-03105365v1
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Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts
Sahar Aghakhani
,
Sacha E Silva-Saffar
,
Sylvain Soliman
,
Anna Niarakis
Journal articles
hal-04192259v1
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Building digital twins of the human immune system: toward a roadmap
Reinhard Laubenbacher
,
A. Niarakis
,
Tomáš Helikar
,
Gary An
,
Bruce Shapiro
,
et al.
Journal articles
hal-03699607v1
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Activating and Inhibitory Receptors on Mast Cells
Anna Niarakis
,
Marc Daëron
Book sections
hal-03192429v1
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A practical guide to mechanistic systems modeling in biology using a logic-based approach
Anna Niarakis
,
Tomáš Helikar
Journal articles
hal-03039116v1
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Data integration in logic-based models of biological mechanisms
Benjamin A Hall
,
Anna Niarakis
Journal articles
hal-03515653v1
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Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map
Quentin Miagoux
,
Vidisha Singh
,
Dereck de Mézquita
,
Valerie Chaudru
,
Mohamed Elati
,
et al.
Journal articles
hal-03344139v1
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A Mechanistic Cellular Atlas of the Rheumatic Joint
Naouel Zerrouk
,
Sahar Aghakhani
,
Vidisha Singh
,
Franck Augé
,
Anna Niarakis
Journal articles
hal-03699702v1
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Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
Marek Ostaszewski
,
Alexander Mazein
,
Marc Gillespie
,
Inna Kuperstein
,
Anna Niarakis
,
et al.
Journal articles
hal-02958949v1
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Effects of proteasome inhibitors on cytokines, metalloproteinases and their inhibitors and collagen type-I expression in periprosthetic tissues and fibroblasts from loose arthroplasty endoprostheses
Anna Niarakis
,
Eleftheria Giannopoulou
,
Spyros Syggelos
,
Elias Panagiotopoulos
Journal articles
hal-02958968v1
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SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins
Samuel Alizon
,
Frédéric Cazals
,
Stéphane Guindon
,
Claire Lemaitre
,
Tristan Mary-Huard
,
et al.
[Research Report] CNRS. 2021, pp.1-35
Reports
hal-03170023v1
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Computational Modeling of the Main Signaling Pathways Involved in Mast Cell Activation
Anna Niarakis
,
Yacine Bounab
,
Luca Grieco
,
Romain Roncagalli
,
Anne-Marie Hesse
,
et al.
Book sections
hal-02086273v1
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