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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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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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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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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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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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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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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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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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Approche globale intégrative pour l’identification de nouvelles cibles moléculaires dans la polyarthrite rhumatoïde
Quentin Miagoux
Theses
tel-03675227v1
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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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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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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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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-03344134v1
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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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Identification of biological pathways specific to phases preceding rheumatoid arthritis development through gene expression profiling
Cyril Dalmasso
,
Céline Derbois
,
Maeva Veyssière
,
Robert Olaso
,
Céline Lamacchia
,
et al.
Journal articles
hal-03120585v1
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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
,
Valérie Chaudru
,
Mohamed Elati
,
et al.
Journal articles
hal-03515663v1
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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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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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Data integration in logic-based models of biological mechanisms
Benjamin A Hall
,
Anna Niarakis
Journal articles
hal-03515653v1
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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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Integrative analysis and modeling of molecular pathways dysregulated in rheumatoid arthritis
Vidisha Singh
Theses
tel-03202163v1
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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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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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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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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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RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis
Vidisha Singh
,
George Kalliolias
,
Marek Ostaszewski
,
Maeva Veyssière
,
Eleftherios Pilalis
,
et al.
Journal articles
hal-02958967v1
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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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Association study of copy number variants in CCL3L1, FCGR3A and FCGR3B genes with risk of ankylosing spondylitis in a West Algerian population
Chahinez Amira Dahmani
,
Ahmed Benzaoui
,
Habiba Amroun
,
Faouzia Zemani‐fodil
,
Elisabeth Petit-Teixeira
,
et al.
Journal articles
hal-02958980v1
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Community-driven roadmap for integrated disease maps
Marek Ostaszewski
,
Stephan Gebel
,
Inna Kuperstein
,
Alexander Mazein
,
Andrei Zinovyev
,
et al.
Journal articles
hal-02958973v1
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Investigation of candidate gene copy number identifies FCGR3B as a potential biomarker for rheumatoid arthritis.
Mohamed Sahbi Ben Kilani
,
François Cornelis
,
Robert E Olaso
,
Valérie Chaudru
,
Elisabeth Petit-Teixeira
Clinical and experimental rheumatology, 2019
Journal articles
hal-02268137v1
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