Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches

por Aghakhani, Sahar, Zerrouk, Naouel, Niarakis, Anna
Publicado 2020

Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach

por Aghakhani, Sahar, Soliman, Sylvain, Niarakis, Anna
Publicado 2022

A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint

por Singh, Vidisha, Naldi, Aurelien, Soliman, Sylvain, Niarakis, Anna
Publicado 2023

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

por Hemedan, Ahmed Abdelmonem, Niarakis, Anna, Schneider, Reinhard, Ostaszewski, Marek
Publicado 2022

Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts

por Aghakhani, Sahar, Silva-Saffar, Sacha E, Soliman, Sylvain, Niarakis, Anna
Publicado 2023

Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference

por Zerrouk, Naouel, Miagoux, Quentin, Dispot, Aurelien, Elati, Mohamed, Niarakis, Anna
Publicado 2020

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

por Touré, Vasundra, Flobak, Åsmund, Niarakis, Anna, Vercruysse, Steven, Kuiper, Martin
Publicado 2020

Automated inference of Boolean models from molecular interaction maps using CaSQ

por Aghamiri, Sara Sadat, Singh, Vidisha, Naldi, Aurélien, Helikar, Tomáš, Soliman, Sylvain, Niarakis, Anna
Publicado 2020

Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map

por Miagoux, Quentin, Singh, Vidisha, de Mézquita, Dereck, Chaudru, Valerie, Elati, Mohamed, Petit-Teixeira, Elisabeth, Niarakis, Anna
Publicado 2021

Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model

por Singh, Vidisha, Ostaszewski, Marek, Kalliolias, George D., Chiocchia, Gilles, Olaso, Robert, Petit-Teixeira, Elisabeth, Helikar, Tomáš, Niarakis, Anna
Publicado 2017

RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis

por Singh, Vidisha, Kalliolias, George D, Ostaszewski, Marek, Veyssiere, Maëva, Pilalis, Eleftherios, Gawron, Piotr, Mazein, Alexander, Bonnet, Eric, Petit-Teixeira, Elisabeth, Niarakis, Anna
Publicado 2020

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

por Dräger, Andreas, Helikar, Tomáš, Barberis, Matteo, Birtwistle, Marc, Calzone, Laurence, Chaouiya, Claudine, Hasenauer, Jan, Karr, Jonathan R, Niarakis, Anna, Rodríguez Martínez, María, Saez-Rodriguez, Julio, Thakar, Juilee
Publicado 2021

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

por Niarakis, Anna, Waltemath, Dagmar, Glazier, James, Schreiber, Falk, Keating, Sarah M, Nickerson, David, Chaouiya, Claudine, Siegel, Anne, Noël, Vincent, Hermjakob, Henning, Helikar, Tomáš, Soliman, Sylvain, Calzone, Laurence
Publicado 2022

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

por Mazein, Alexander, Acencio, Marcio Luis, Balaur, Irina, Rougny, Adrien, Welter, Danielle, Niarakis, Anna, Ramirez Ardila, Diana, Dogrusoz, Ugur, Gawron, Piotr, Satagopam, Venkata, Gu, Wei, Kremer, Andreas, Schneider, Reinhard, Ostaszewski, Marek
Publicado 2023

Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

por Soudier, Paul, Rodriguez Pinzon, Daniel, Reif-Trauttmansdorff, Tristan, Hijazi, Hassan, Cherrière, Maëva, Goncalves Pereira, Cátia, Blaise, Doriane, Pispisa, Maxime, Saint-Julien, Angelyne, Hamlet, William, Nguevo, Melissa, Gomes, Eva, Belkhelfa, Sophia, Niarakis, Anna, Kushwaha, Manish, Grigoras, Ioana
Publicado 2022

Community-driven roadmap for integrated disease maps

por Ostaszewski, Marek, Gebel, Stephan, Kuperstein, Inna, Mazein, Alexander, Zinovyev, Andrei, Dogrusoz, Ugur, Hasenauer, Jan, Fleming, Ronan M T, Le Novère, Nicolas, Gawron, Piotr, Ligon, Thomas, Niarakis, Anna, Nickerson, David, Weindl, Daniel, Balling, Rudi, Barillot, Emmanuel, Auffray, Charles, Schneider, Reinhard
Publicado 2018

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

por Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2020

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

por Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2020

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

por Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2021

COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

por Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2021