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Anna Niarakis

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MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps

Sahar Aghakhani , Anna Niarakis , Sylvain Soliman
Journal of Integrative Bioinformatics, 2024, pp.20230048. ⟨10.1515/jib-2023-0048⟩
Article dans une revue hal-04439008v1
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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Anna Niarakis , Marek Ostaszewski , Alexander Mazein , Inna Kuperstein , Martina Kutmon
Frontiers in Immunology, 2024, 14, ⟨10.3389/fimmu.2023.1282859⟩
Article dans une revue hal-04454379v1
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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⟩
Article dans une revue hal-04187223v1
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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⟩
Article dans une revue hal-04192259v1
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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⟩
Article dans une revue hal-03880870v2

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

Reinhard Laubenbacher , A. Niarakis , Tomáš Helikar , Gary An , Bruce Shapiro
npj Digital Medicine, 2022, 5 (64), ⟨10.1038/s41746-022-00610-z⟩
Article dans une revue hal-03699607v1
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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⟩
Article dans une revue hal-03699702v1

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
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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
Synthetic and Systems Biotechnology, 2022, 7 (2), pp.791-801. ⟨10.1016/j.synbio.2022.03.003⟩
Article dans une revue hal-03626102v1
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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
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Article dans une revue hal-03690604v1
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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⟩
Article dans une revue 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
Journal of Personalized Medicine, 2021, 11 (8), pp.785. ⟨10.3390/jpm11080785⟩
Article dans une revue hal-03344139v1
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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
Journal of Personalized Medicine, 2021, 11 (8), pp.785. ⟨10.3390/jpm11080785⟩
Article dans une revue hal-03515663v1

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 Elati
Revue du Rhumatisme, 2021, 88, pp.A151. ⟨10.1016/j.rhum.2021.10.238⟩
Article dans une revue hal-04504958v1

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
Article dans une revue hal-03344134v1

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
Bioinformatics, 2021, 37 (21), pp.3702-3706. ⟨10.1093/bioinformatics/btab229⟩
Article dans une revue hal-04052751v1
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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
Briefings in Bioinformatics, 2021, 22 (2), pp.1848--1859. ⟨10.1093/bib/bbaa046⟩
Article dans une revue hal-02549796v1
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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
Molecular Systems Biology, 2021, 17 (10), pp.e10387. ⟨10.15252/msb.202110387⟩
Article dans une revue hal-03385317v2
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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
Bioinformatics, 2021, 37 (21), pp.3702 - 3706. ⟨10.1093/bioinformatics/btab229⟩
Article dans une revue hal-03515692v2
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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⟩
Article dans une revue hal-03105351v1
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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
Scientific Data , 2020, 7 (1), pp.247. ⟨10.1038/s41597-020-00589-w⟩
Article dans une revue hal-02958949v1
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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⟩
Article dans une revue hal-03039116v1
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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⟩
Article dans une revue hal-03105365v1
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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
Bioinformatics, 2020, 36 (16), pp.4473-4482. ⟨10.1093/bioinformatics/btaa484⟩
Article dans une revue hal-02590714v1
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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⟩
Article dans une revue hal-02958928v1
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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
Database - The journal of Biological Databases and Curation, 2020, 2020, pp.baaa017. ⟨10.1093/database/baaa017⟩
Article dans une revue hal-02958967v1

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

Community-driven roadmap for integrated disease maps

Marek Ostaszewski , Stephan Gebel , Inna Kuperstein , Alexander Mazein , Andrei Zinovyev
Briefings in Bioinformatics, 2019, 20 (2), pp.659-670. ⟨10.1093/bib/bby024⟩
Article dans une revue hal-02958973v1

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
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 hal-02084421v1
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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
Molecular and Cellular Proteomics, 2013, 12 (10), pp.2874-2889. ⟨10.1074/mcp.M112.025908⟩
Article dans une revue hal-02086260v1

Metabolic analysis of logical models infered from molecular interaction maps

S Aghakhani , A Niarakis , S Soliman
Building Immune digital twins, 2023, Orsay, France
Communication dans un congrès hal-04482069v1

Computational systems biology approaches for deciphering the immune-epithelial cellular interplay in Sjögren syndrome

S E Silva-Saffar , G Nocturne , A Niarakis
Building Immune digital twins, 2023, Orsay, France, France
Communication dans un congrès hal-04482037v1

Computational modeling of the cellular interplay in Rheumatoid Arthritis

N Zerrouk , F Augé , A Niarakis
Building Immune digital twins, 2023, Orsay, France
Communication dans un congrès hal-04482055v1

Computational systems biology approaches for deciphering the immune-epithelial cellular interplay in Sjögren syndrome

S E Silva-Saffar , G Nocturne , A Niarakis
Wellcome Connecting Science, 2022, Hinxton, Cambridge, United Kingdom
Communication dans un congrès hal-04482088v1

GREEKC COST ACTION Workshop

A. Niarakis
Introduction to Disease Maps: successes and challenges, 2021, Virtual conference, France
Communication dans un congrès hal-04482157v1

Do you speak Systems Biology? Shaping a common language for community work

A Niarakis
COMBINE, 2021, Online Conference, France
Communication dans un congrès hal-04482103v1

Invited Lecture at the Summer School, Logical Modeling for Experimental Design

A. Niarakis
Current and Future Biotechnology and Biomedicine, 2021, Trondheim ( Norvège), Norway
Communication dans un congrès hal-04482132v1

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

A. Niarakis
MSM Viral Pandemics meetings, 2021, Virtual conference, France
Communication dans un congrès hal-04482169v1

Executable Disease Networks: Building a large-scale Boolean model of fibroblasts in Rheumatoid Arthritis

A Niarakis
Sanofi Seminar Data Science Webinar Series, 2020, Chilly Mazarin, France
Communication dans un congrès hal-04482315v1

Introductory lecture: Modelling approaches in COVID-19 Disease Map project

A. Niarakis
5th Disease Map Community Meeting, 2020, Virtual conference, France
Communication dans un congrès hal-04482236v1

Automated inference of Boolean models from molecular interaction maps using CaSQ

A Niarakis
COMBINE, 2020, Virtual conference, France
Communication dans un congrès hal-04482251v1

COVID-19 Disease Map, a large-scale community effort to create graphical and executable models of SARS-CoV-2 virus-host interaction mechanisms

A. Niarakis
German Bioinformatics Conference, virtual, 2020, Virtual conference, France
Communication dans un congrès hal-04482258v1

Building graphical and computational models in biology

A Niarakis
ECCB 2020 Sitges Barcelona, 2020, Virtual conference, France
Communication dans un congrès hal-04482263v1

Automated inference of large-scale Boolean models, based on network topology and semantics of static molecular maps. Application on Rheumatoid Arthritis and the RA-map

A. Niarakis
MABioS Seminar I2M, 2020, Virtual conference, France
Communication dans un congrès hal-04482291v1

AI-assisted human biocuration of molecular mechanisms in the COVID-19 Disease Map project

A. Niarakis
AI BioSS, 2020, Virtual conference, France
Communication dans un congrès hal-04482181v1

Inference of a modular, large-scale Boolean network for modelling the Rheumatoid Arthritis fibroblast-like synoviocytes

Vidisha Singh , Soliman S , Anna Niarakis
5th Disease Map Community Meeting, 2020, Virtual conference, France
Communication dans un congrès hal-04482346v1

Automated inference of large-scale Boolean models, based on network topology and semantics of static molecular maps. Application on Rheumatoid Arthritis and the RA-map, I-STEM seminar, virtual, 15th of October 2020

A Niarakis
I-STEM seminar, 2020, Virtual conference, France
Communication dans un congrès hal-04482282v1

Automated inference of annotated Boolean models from molecular interaction maps using CaSQ

A. Niarakis
Workshop CoLoMoTo/SysMod, 2019, Basel, Switzerland
Communication dans un congrès hal-04482431v1

Executable Disease Maps – Addressing the challenges of large scale dynamical modelling

A. Niarakis
4th Disease Map Community Meeting, 2019, Seville, Spain
Communication dans un congrès hal-04482380v1

Executable Disease Networks -Building a large scale Boolean model for Rheumatoid Arthritis,

A Niarakis
Computational Biology for Complex Diseases, ENS, 2019, Cachan (Fr), France
Communication dans un congrès hal-04482356v1

Executable Disease Networks –Modelling the immune system in health and disease

A. Niarakis
Luxembourg Centre of Systems Biomedicine, 2019, Belval, Luxembourg
Communication dans un congrès hal-04482365v1

Automated Inference of Boolean Dynamics from molecular interaction maps

A. Niarakis
[BC]2, 2019, Basel, Switzerland
Communication dans un congrès hal-04482422v1

Automated pipeline for the inference of Boolean models from molecular interaction maps.

S. Pankaew , S. Soliman , T. Helikar , A. Niarakis
Logical modelling of cellular networks ECCB 2018 Workshop, 2018, Athens, Greece
Communication dans un congrès hal-04482462v1

Computational Systems Biology Approach For The Study Of Rheumatoid Arthritis: From A Molecular Map To A Dynamical Model , Invited Speaker, 21-22 June 2018 Institut Curie, Paris

A Niarakis
Disease Maps Community Meeting, 2018, Paris, France
Communication dans un congrès hal-04482487v1

Executable Disease Networks. Adding dynamics to molecular maps, Controlling Complex Networks: When Control Theory Meets Network Science

A Niarakis
Harvard Satellite Symposium of NetSci2018, 2018, Paris, France
Communication dans un congrès hal-04482484v1

Executable Disease Networks: Reconstruction, Topology, Dynamics

A. Niarakis
Cambridge Oncology Seminar Series, Cambridge Institute for Medical Research, 2018, Cambridge, United Kingdom
Communication dans un congrès hal-04482441v1

Disease Networks - Reconstruction, Topology, Dynamics. Towards an automated pipeline from static representations to executable disease models

A. Niarakis
BioNetVisA 2018 ECCB workshop, 2018, Athens, Greece
Communication dans un congrès hal-04482457v1

Integration Analysis And Modelling Of Cellular Networks For Complex Human Diseases

A Niarakis
Invited Speaker, CNRGH, CEA, 2018, Evry, France
Communication dans un congrès hal-04482491v1
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Logical modelling of cellular decision processes with GINsim

Claudine Chaouiya , Aurélien Naldi , Lionel Spinelli , Pedro Monteiro , Duncan Berenguier
JOBIM 2012, Jul 2012, Rennes, France
Communication dans un congrès hal-01261855v1

A Mechanistic Cellular Atlas of the Rheumatic Joint

Naouel Zerrouk , Aghakhani S. , Augé F. , A. Niarakis , V. Singh
21st European Conference on Computational Biology, 2022, Sitges, Spain
Poster de conférence hal-04482553v1

Metabolic reprogramming in rheumatoid arthritis synovial fibroblasts: a hybrid modeling approach

S. Aghakhani , S. Soliman , A. Niarakis
European Conference on Computational Biology, 2022, Sitges, Spain
Poster de conférence hal-04482578v1

A large-scale hybrid model to study metabolic reprogramming in cancer-associated fibroblasts.

S. Aghakhani , S. E Silva-Saffar , S. Soliman , A. Niarakis
ONCOLille Days 2022, 2022, Lille, France
Poster de conférence hal-04482587v1

Computational Modeling of the Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts (RASFs)

S. Aghakhani , S. Soliman , A. Niarakis
6th Disease Maps Community Meeting, 2021, Virtual conference, France
Poster de conférence hal-04482590v1

Computational modelling of the cellular interplay in Rheumatoid Arthritis.Deciphering the role of innate and adaptive immunity in cartilage destruction and bone erosion.

N. Zerrouk , C. Bettembourg , A. Niarakis
Cancer systems biology - Promises of artificial intelligence, 2020, Virtual conference, France
Poster de conférence hal-04482610v1

Fibroblasts as Therapeutic Targets in Rheumatoid Arthritis and Cancer: Computational Modeling of The Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts and Cancer Associated Fibroblasts.

S Aghakhani , A. Niarakis
Computational Systems Biology of Cancer: Promises of Artificial Intelligence – EMBO, 2020, Virtual conference, France
Poster de conférence hal-04482594v1

Computational modelling of the cellular interplay in Rheumatoid Arthritis. Deciphering the role of innate and adaptive immunity in cartilage destruction and bone erosion

N. Zerrouk , F. Augé , A. Niarakis
Disease Map Community Meeting 5th edition, 2020, Virtual conference, France
Poster de conférence hal-04482609v1

Computational Modeling of the Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts and Cancer Associated Fibroblasts

S. Aghakhani , S. Soliman , A. Niarakis
5th Disease Maps Community Meeting, 2020, Virtual conference, France
Poster de conférence hal-04482602v1

Gene co-regulatory inference and modelling of perturbations effects on Rheumatoid Arthritis phenotypes.

Q. Miagoux , N. Zerrouk , V. Singh , E. Petit-Teixeira , A. Niarakis
Genome Campus Advanced Course: Systems Biology: From large datasets to biological insight, 2019, Cambridge, United Kingdom
Poster de conférence hal-04482631v1

Caractérisation de CNV (variants de nombre de copies) à partir de données de séquences exoniques simulées

Q. Miagoux , M. Veyssiere , A. Niarakis , E. Petit-Teixeira , V. Chaudru
JOBIM 2019, 2019, Nantes, France
Poster de conférence hal-04482639v1

Translating Disease Networks to Executable Boolean Models

Ss. Aghamiri , V. Singh , S. Soliman , T. Helikar , A. Niarakis
Young Researchers in Life Sciences Federation, 2019, Paris, France
Poster de conférence hal-04482647v1

Executable Disease Networks: Adding dynamics to molecular maps

V. Singh , S. Pankaew , M. Ostaszewski , Gd. Kalliolias , S. Soliman
ECCB conference, 2018, Athens, Greece
Poster de conférence hal-04482651v1

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

V. Singh , M. Ostaszewski , S. Pankaew , G. Kalliolias , G. Chiocchia
Discrete models and formal verification in biology, Murray Edwards College, 2018, Cambridge, France
Poster de conférence hal-04482656v1

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

V. Singh , M. Ostaszewski , S. Pankaew , G. Kalliolias , G. Chiocchia
Integrating Systems Biology: From Networks to Mechanisms to Models, EMBO WORKSHOP, EMBL, 2018, Heidelberg (Germany), France
Poster de conférence hal-04482671v1

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

V. Singh , M. Ostaszewski , S. Pankaew , G. Kalliolias , G. Chiocchia
Solvay workshop, "Dynamics of biological systems: Modelling genetic, signalling and microbial networks", 2018, Brussel, Belgium
Poster de conférence hal-04482667v1

Executable Disease Networks: Adding dynamics to molecular maps

Vidisha Singh , Saran Pankaew , Marek Ostaszewski , George D. Kalliolias , Sylvain Soliman
ECCB 2018 - 17th European Conference on Computational Biology, Sep 2018, Athens, Greece
Poster de conférence hal-01875418v1

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

V. Singh , M. Ostaszewski , S. Pankaew , G. Kalliolias , G. Chiocchia
Young Researchers in Life Sciences Federation, Ecole Normale Supérieure, 2018, Paris, France
Poster de conférence hal-04482659v1

Integrative Analysis and Dynamical Modelling of Signalling Pathways Involved in Rheumatoid Arthritis

V. Singh , E. Petit-Teixeira , A. Niarakis
Wellcome Trust Advanced Courses Wellcome, 2017, Cambridge, United Kingdom
Poster de conférence hal-04482676v1
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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⟩
Chapitre d'ouvrage hal-03192429v1
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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
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