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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 of Personalized Medicine, 2021, 11 (8), pp.785. ⟨10.3390/jpm11080785⟩
Journal articles hal-03515663v1

Boolean modelling as a logic-based dynamic approach in systems medicine

Ahmed Abdelmonem Hemedan , Anna Niarakis , Reinhard Schneider , Marek Ostaszewski
Computational and Structural Biotechnology Journal, 2022, ⟨10.1016/j.csbj.2022.06.035⟩
Journal articles hal-03699613v1

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.
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
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.
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
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.
Bioinformatics, 2020, 36 (16), pp.4473-4482. ⟨10.1093/bioinformatics/btaa484⟩
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
Cancers, 2021, 13 (1), pp.35. ⟨10.3390/cancers13010035⟩
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.
Molecular and Cellular Proteomics, 2013, 12 (10), pp.2874-2889. ⟨10.1074/mcp.M112.025908⟩
Journal articles hal-02086260v1

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.
Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩
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
Scientific Reports, 2020, 10 (1), pp.16236. ⟨10.1038/s41598-020-73147-4⟩
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.
Bioinformatics, 2021, 37 (21), pp.3702 - 3706. ⟨10.1093/bioinformatics/btab229⟩
Journal articles hal-03515692v2

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.
Genomics and Computational Biology, 2018, 4 (1), pp.e100050. ⟨10.18547/gcb.2018.vol4.iss1.e100050⟩
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.
Synthetic and Systems Biotechnology, 2022, 7 (2), pp.791-801. ⟨10.1016/j.synbio.2022.03.003⟩
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
npj Systems Biology and Applications, 2023, 9 (33), ⟨10.1038/s41540-023-00294-5⟩
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
PLoS Computational Biology, 2022, 18 (12), pp.e1010408. ⟨10.1371/journal.pcbi.1010408⟩
Journal articles hal-03880870v2

Modélisation Logique et Analyse Intégrative Des Voies Moléculaires Impliquées Dans La Polyarthrite Rhumatoïde

Anna Niarakis , V. Singh , Elisabeth Petit-Teixeira
Revue du Rhumatisme, 2016, 83, pp.A297. ⟨10.1016/S1169-8330(16)30689-5⟩
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.
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
Briefings in Bioinformatics, 2020, pp.bbaa390. ⟨10.1093/bib/bbaa390⟩
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
Computational and Structural Biotechnology Journal, 2023, 21, pp.4196-4206. ⟨10.1016/j.csbj.2023.08.015⟩
Journal articles hal-04192259v1

Building digital twins of the human immune system: toward a roadmap

Reinhard Laubenbacher , A. Niarakis , Tomáš Helikar , Gary An , Bruce Shapiro , et al.
npj Digital Medicine, 2022, 5 (64), ⟨10.1038/s41746-022-00610-z⟩
Journal articles hal-03699607v1
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Activating and Inhibitory Receptors on Mast Cells

Anna Niarakis , Marc Daëron
Encyclopedia of Medical Immunology, Springer New York, pp.1-10, 2014, ⟨10.1007/978-1-4614-9194-1_92⟩
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
Briefings in Bioinformatics, 2020, 22 (4), ⟨10.1093/bib/bbaa236⟩
Journal articles hal-03039116v1
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Data integration in logic-based models of biological mechanisms

Benjamin A Hall , Anna Niarakis
Current Opinion in Systems Biology, 2021, 28, pp.100386. ⟨10.1016/j.coisb.2021.100386⟩
Journal articles hal-03515653v1

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 of Personalized Medicine, 2021, 11 (8), pp.785. ⟨10.3390/jpm11080785⟩
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
Frontiers in Systems Biology, 2022, ⟨10.3389/fsysb.2022.925791⟩
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.
Scientific Data , 2020, 7 (1), pp.247. ⟨10.1038/s41597-020-00589-w⟩
Journal articles hal-02958949v1

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
Connective Tissue Research, 2019, 60 (6), pp.555-570. ⟨10.1080/03008207.2019.1601186⟩
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.
Marc Daëron; Falk Nimmerjahn. Fc Receptors, 382, Springer, pp.69-93, 2014, Current Topics in Microbiology and Immunology, 978-3-319-07911-0. ⟨10.1007/978-3-319-07911-0_4⟩
Book sections hal-02086273v1