Anna Niarakis

Publications

Article dans une revue (32)

Design specifications for biomedical virtual twins in engineered adoptive cellular immunotherapies Ulrike Weirauch,Markus Kreuz,Colin Birkenbihl,Miriam Alb,Maria Quarantaet al. npj Digital Medicine, 2025, 8 (1), pp.493. ⟨10.1038/s41746-025-01809-6⟩ Article dans une revue hal-05534994v1
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches Anna Niarakis,Marek Ostaszewski,Alexander Mazein,Inna Kuperstein,Martina Kutmonet al. Frontiers in Immunology, 2024, 14, ⟨10.3389/fimmu.2023.1282859⟩ Article dans une revue hal-04454379v1
Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis Naouel Zerrouk,Rachel Alcraft,Benjamin A Hall,Franck Augé,Anna Niarakis npj Systems Biology and Applications, 2024, 10 (1), pp.10. ⟨10.1038/s41540-024-00337-5⟩ Article dans une revue hal-04909278v1
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps Sahar Aghakhani,Anna Niarakis,Sylvain Soliman Journal of Integrative Bioinformatics, 2024, 21 (1), pp.20230048. ⟨10.1515/jib-2023-0048⟩ Article dans une revue hal-04439008v1
Immune digital twins for complex human pathologies: applications, limitations, and challenges Anna Niarakis,Reinhard Laubenbacher,Gary An,Yaron Ilan,Jasmin Fisheret al. npj Systems Biology and Applications, 2024, 10 (1), pp.141. ⟨10.1038/s41540-024-00450-5⟩ Article dans une revue hal-04909272v1
Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis Naouel Zerrouk,Franck Augé,Anna Niarakis npj Digital Medicine, 2024, 7 (1), pp.379. ⟨10.1038/s41746-024-01396-y⟩ Article dans une revue hal-04909267v1
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⟩ Article dans une revue hal-04187223v1
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⟩ Article dans une revue hal-04192259v1
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⟩ Article dans une revue hal-03699613v1
Building digital twins of the human immune system: toward a roadmap Reinhard Laubenbacher,A. Niarakis,Tomáš Helikar,Gary An,Bruce Shapiroet al. npj Digital Medicine, 2022, 5 (64), ⟨10.1038/s41746-022-00610-z⟩ Article dans une revue hal-03699607v1
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⟩ Article dans une revue hal-03880870v2
Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima Paul Soudier,Daniel Rodriguez Pinzon,Tristan Reif-Trauttmansdorff,Hassan Hijazi,Maëva Cherrièreet al. Synthetic and Systems Biotechnology, 2022, 7 (2), pp.791-801. ⟨10.1016/j.synbio.2022.03.003⟩ Article dans une revue hal-03626102v1
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology Anna Niarakis,Dagmar Waltemath,James Glazier,Falk Schreiber,Sarah Keatinget al. Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩ Article dans une revue hal-03690604v1
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⟩ Article dans une revue hal-03699702v1
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 Elatiet al. Journal of Personalized Medicine, 2021, 11 (8), pp.785. ⟨10.3390/jpm11080785⟩ Article dans une revue hal-03515663v1
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-Casaset al. Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩ Article dans une revue hal-02549796v1
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms Marek Ostaszewski,Anna Niarakis,Alexander Mazein,Inna Kuperstein,Robert Phairet al. Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩ Article dans une revue hal-03385317v2
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 Calzoneet al. Bioinformatics, 2021, 37 (21), pp.3702 - 3706. ⟨10.1093/bioinformatics/btab229⟩ Article dans une revue hal-03515692v2
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⟩ Article dans une revue hal-03105351v1
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⟩ Article dans une revue hal-03515653v1
De la création d’un réseau intégratif spécifique de la polyarthrite rhumatoïde à l’étude d’un modèle personnalisé relié au traitement des patients Q. Miagoux,V. Singh,D.M. Dereck,V. Chaudru,Mohamed Elatiet al. Revue du Rhumatisme, 2021, 88, pp.A151. ⟨10.1016/j.rhum.2021.10.238⟩ Article dans une revue hal-04504958v1
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis Vidisha Singh,George Kalliolias,Marek Ostaszewski,Maeva Veyssière,Eleftherios Pilaliset al. Database - The journal of Biological Databases and Curation, 2020, 2020, pp.baaa017. ⟨10.1093/database/baaa017⟩ Article dans une revue hal-02958967v1
Automated inference of Boolean models from molecular interaction maps using CaSQ Sara Sadat Aghamiri,Vidisha Singh,Aurélien Naldi,Tomáš Helikar,Sylvain Solimanet al. Bioinformatics, 2020, 36 (16), pp.4473-4482. ⟨10.1093/bioinformatics/btaa484⟩ Article dans une revue hal-02590714v1
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⟩ Article dans une revue hal-02958928v1
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⟩ Article dans une revue hal-03105365v1
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⟩ Article dans une revue hal-03039116v1
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 Niarakiset al. Scientific Data , 2020, 7 (1), pp.247. ⟨10.1038/s41597-020-00589-w⟩ Article dans une revue hal-02958949v1
Community-driven roadmap for integrated disease maps Marek Ostaszewski,Stephan Gebel,Inna Kuperstein,Alexander Mazein,Andrei Zinovyevet al. Briefings in Bioinformatics, 2019, 20 (2), pp.659-670. ⟨10.1093/bib/bby024⟩ Article dans une revue hal-02958973v1
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⟩ Article dans une revue hal-02958968v1
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 Olasoet al. Genomics and Computational Biology, 2018, 4 (1), pp.e100050. ⟨10.18547/gcb.2018.vol4.iss1.e100050⟩ Article dans une revue hal-02084429v1
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⟩ Article dans une revue istex hal-02084421v1
Proteomic Analysis of the SH2Domain-containing Leukocyte Protein of 76 kDa (SLP76) Interactome Yacine Bounab,Anne-Marie- Hesse,Bruno Iannascoli,Luca Grieco,Yohann Coutéet al. Molecular and Cellular Proteomics, 2013, 12 (10), pp.2874-2889. ⟨10.1074/mcp.M112.025908⟩ Article dans une revue hal-02086260v1

Chapitre d'ouvrage (2)

Computational Modeling of the Main Signaling Pathways Involved in Mast Cell Activation Anna Niarakis,Yacine Bounab,Luca Grieco,Romain Roncagalli,Anne-Marie Hesseet 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⟩ Chapitre d'ouvrage hal-02086273v1
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⟩ Chapitre d'ouvrage hal-03192429v1