Anna Niarakis

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 13

Top Topics

Systems Biology

Mathematical Modeling

Top Venues

Briefings Bioinform.

Database J. Biol. Databases Curation

npj Digit. Medicine

Publications

Sahar Aghakhani, Anna Niarakis, Sylvain Soliman
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. J. Integr. Bioinform. 21 (1) (2024)
Alexander Mazein, Marcio Luis Acencio, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata P. Satagopam, Wei Gu, Andreas Kremer, Reinhard Schneider, Marek Ostaszewski
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers Bioinform. 3 (2023)
Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomás Helikar, Marc R. Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting. Bioinform. 38 (21) (2022)
Sahar Aghakhani, Sylvain Soliman, Anna Niarakis
Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach. PLoS Comput. Biol. 18 (12) (2022)
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
. Briefings Bioinform. 23 (4) (2022)
Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, B. Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier
Building digital twins of the human immune system: toward a roadmap. npj Digit. Medicine 5 (2022)
Anna Niarakis, Tomás Helikar
A practical guide to mechanistic systems modeling in biology using a logic-based approach. Briefings Bioinform. 22 (4) (2021)
Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone
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. Briefings Bioinform. 22 (2) (2021)
Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings Bioinform. 22 (4) (2021)
Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinform. 37 (21) (2021)
Vidisha Singh, George D. Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database J. Biol. Databases Curation 2020 (2020)
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinform. 36 (16) (2020)
Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20 (2) (2019)