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292 results on '"De Meulder, Bertrand"'

1. PIONEER big data platform for prostate cancer: lessons for advancing future real-world evidence research

Author: Lawlor, Ailbhe, Beyer, Katharina, Russell, Beth, Steinbeisser, Carl, Bjartell, Anders, De Meulder, Bertrand, Omar, Muhammad Imran, Hulsen, Tim, Butler, John, N’Dow, James, Rivas, Juan Gómez, Gandaglia, Giorgio, Nicoletti, Rossella, Sakalis, Vasileios, Smith, Emma Jane, Maass, Monika, Zong, Jihong, Fullwood, Louise, Abbott, Thomas, Tafreshiha, Azadeh, Papineni, Kishore, Snijder, Robert, Horgan, Denis, Seager, Sarah, Evans-Axelsson, Susan, Ribal, Maria J., Roobol, Monique J., and Van Hemelrijck, Mieke
Published: 2025
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2. Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management: A PIONEER Analysis Based on Big Data

Author: Gandaglia, Giorgio, Pellegrino, Francesco, Golozar, Asieh, De Meulder, Bertrand, Abbott, Thomas, Achtman, Ariel, Imran Omar, Muhammad, Alshammari, Thamir, Areia, Carlos, Asiimwe, Alex, Beyer, Katharina, Bjartell, Anders, Campi, Riccardo, Cornford, Philip, Falconer, Thomas, Feng, Qi, Gong, Mengchun, Herrera, Ronald, Hughes, Nigel, Hulsen, Tim, Kinnaird, Adam, Lai, Lana Y.H., Maresca, Gianluca, Mottet, Nicolas, Oja, Marek, Prinsen, Peter, Reich, Christian, Remmers, Sebastiaan, Roobol, Monique J., Sakalis, Vasileios, Seager, Sarah, Smith, Emma J., Snijder, Robert, Steinbeisser, Carl, Thurin, Nicolas H., Hijazy, Ayman, van Bochove, Kees, Van den Bergh, Roderick C.N., Van Hemelrijck, Mieke, Willemse, Peter-Paul, Williams, Andrew E., Zounemat Kermani, Nazanin, Evans-Axelsson, Susan, Briganti, Alberto, and N'Dow, James
Published: 2024
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3. Unanswered questions in prostate cancer — findings of an international multi-stakeholder consensus by the PIONEER consortium

Author: Omar, Muhammad Imran, MacLennan, Steven, Ribal, Maria J., Roobol, Monique J., Dimitropoulos, Konstantinos, van den Broeck, Thomas, MacLennan, Sara J., Axelsson, Susan Evans, Gandaglia, Giorgio, Willemse, Peter-Paul, Mastris, Ken, Ransohoff, John Butler, Devecseri, Zsuzsanna, Abbott, Thomas, De Meulder, Bertrand, Bjartell, Anders, Asiimwe, Alex, and N’Dow, James
Published: 2023
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4. Artificial Intelligence and Deep Phenotyping in COVID-19

Author: Giacó, Luciano, De Meulder, Bertrand, Valentini, Vincenzo, Scambia, Giovanni, Cesario, Alfredo, Auffray, Charles, Cesario, Alfredo, editor, D'Oria, Marika, editor, Auffray, Charles, editor, and Scambia, Giovanni, editor
Published: 2023
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5. The role of inflammation in anxiety and depression in the European U-BIOPRED asthma cohorts

Author: Hou, Ruihua, Ye, Gang, Cheng, Xiaojing, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Barbro, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Howarth, Peter, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Auffray, Charles, De Meulder, Bertrand, Sousa, Ana R., Adcock, Ian M., Fan Chung, Kian, Sterk, Peter J., Skipp, Paul J., Schofield, James, and Djukanović, Ratko
Published: 2023
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6. The Key Role of Patient Involvement in the Development of Core Outcome Sets in Prostate Cancer

Author: Smith, Emma Jane, N'Dow, James, Plass, Karin, Ribal, Maria, Mottet, Nicolas, Shepherd, Robert, Moris, Lisa, Lardas, Michael, Van den Broeck, Thomas, Willemse, Peter-Paul, Campi, Riccardo, Gacci, Mauro, Bjartell, Anders, Evans-Axelsson, LU Susan, Briganti, Alberto, Gandaglia, Giorgio, Crosti, Daniele, Meoni, Massimiliano, Garzonio, Roberto, Bangma, Chris, Roobol, Monique, Remmers, Sebastiaan, Tilki, Derya, Auvinen, Anssi, Murtola, Teemu, Visakorpi, Tapio, Talala, Kirsi, Tammela, Teuvo, Siltari, Aino, Van Hemelrijck, Mieke, Beyer, Katharina, Lejeune, Stephane, van Diggelen, Femke, Byrne, Sophie, Fialho, Luz, Cardone, Antonella, Gono, Paulina, De Meulder, Bertrand, Auffray, Charles, Balaur, Irina-Afrodita, Taibi, Nesrine, Power, Shaun, Kermani, Nazanin Zounemat, van Bochove, Kees, Cirillo, Elisa, Moinat, Maxim, Voss, Emma, Horgan, Denis, Fullwood, Louise, Holtorf, Marc, Lancet, Doron, Bernstein, Gabi, Omar, Imran, MacLennan, Sara, MacLennan, Steven, Tripathee, Sheela, Huber, Johannes, Wirth, Manfred, Froehner, Michael, Brenner, Beate, Borkowetz, Angelika, Thomas, Christian, Horn, Friedemann, Reiche, Kristin, Kreuz, Markus, Josefsson, Andreas, Tandefelt, Delila Gasi, Hugosson, Jonas, Schalken, Jack, Huisman, Henkjan, Hofmarcher, Thomas, Lindgren, Peter, Andersson, Emelie, Fridhammar, Adam, Asiimwe, Alex, Verholen, Frank, Zong, Jihong, Butler-Ransohoff, John-Edward, Williamson, Todd, Chandrawansa, Kumari, Waldeck, Reg, Molnar, Megan, Bruno, Amanda, Herrera, Ronald, Nevedomskaya, Ekaterina, Fatoba, Samuel, Constantinovici, Niculae, Mohamed, Ateesha, Steinbeißer, Carl, Kedhagae, Siddhanth, Maass, Monika, Torremante, Patrizia, Voss, Marc Dietrich, Devecseri, Zsuzsanna, Abbott, Tom, Kiran, Amit, Dau, Chad, Papineni, Kishore, Wang-silvanto, Jing, Hass, Steve, Snijder, Robert, Doyé, Verena, Wang, Xuewei, Garnham, Andy, Lambrecht, Mark, Wolfinger, Russ, Rogiers, Stijn, Servan, Angela, Casariego, Joaquin, Samir, Mohamed, Pascoe, Katie, Robinson, Paul, Reich, Christian, Ratwani, Shilpa, Longden-Chapman, Elaine, Burke, Danny, Agapow, Paul, Derkits, Sahra, Licour, Muriel, Ang, Michelle, Payne, Sarah, Yong, Alan, Thompson, Lucy, Le Mare, Sophia, Bussmann, Michael, Köhler, Inken, Juckeland, Guido, Kotik, Daniel, MacLennan, Sara J., Mastris, Ken, Hooker, Gary, Greene, Robert, Briers, Erik, Omar, Muhammad Imran, Healey, Jemma, Venderbos, Lionne D.F., Smith, Emma J., Bjorkqvist, Josefine, Roobol, Monique J., and N’Dow, James
Published: 2021
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7. Abstract 14044: Leveraging Multi-Omics to Identify Biologically-Informed Clusters of Individuals With Differing Underlying Disease Risk Mechanisms Using an Innovative Network Modelling Approach

Author: Bagheri Naraghi, Minoo, De Meulder, Bertrand, Annis, Jeffrey, Brittain, Evan, Mosley, Jonathan, and Ferguson, Jane F
Published: 2022
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8. MP14-08 REAL-WORD CLINICAL CHARACTERIZATION OF METASTATIC HORMONE SENSITIVE PROSTATE CANCER: DATA FROM THE EUROPEAN NETWORK OF EXCELLENCE FOR BIG DATA IN PROSTATE CANCER (PIONEER)

Author: Nicoletti, Rossella, primary, Rivas, Juan Gomez, additional, Ibáñez, Laura, additional, Steinbeisserc, Carl, additional, de Meulder, Bertrand, additional, France, Lyon, additional, Golozar, Asieh, additional, Axelsson, Susan Evans, additional, Snijder, Robert, additional, Bjartell, Anders, additional, Cornford, Philip, additional, Van Hemelrijck, Mieke, additional, Beyer, Katharina, additional, Willemse, Peter-Paul, additional, Murtola, Teemu, additional, Robool, Monique J., additional, Sierra, Jesus Moreno, additional, Campi, Riccardo, additional, Gacci, Mauro, additional, Mottet, Nicolas, additional, Merseburger, Axel, additional, and Ndow, James, additional
Published: 2024
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9. Research Protocol for an Observational Health Data Analysis on the Adverse Events of Systemic Treatment in Patients with Metastatic Hormone-sensitive Prostate Cancer: Big Data Analytics Using the PIONEER Platform

Author: Rajwa, Pawel, primary, Borkowetz, Angelika, additional, Abbott, Thomas, additional, Alberti, Andrea, additional, Bjartell, Anders, additional, Brash, James T., additional, Campi, Riccardo, additional, Chilelli, Andrew, additional, Conover, Mitchell, additional, Constantinovici, Niculae, additional, Davies, Eleanor, additional, De Meulder, Bertrand, additional, Eid, Sherrine, additional, Gacci, Mauro, additional, Golozar, Asieh, additional, Hafeez, Haroon, additional, Haque, Samiul, additional, Hijazy, Ayman, additional, Hulsen, Tim, additional, Josefsson, Andreas, additional, Khalid, Sara, additional, Kolde, Raivo, additional, Kotik, Daniel, additional, Kurki, Samu, additional, Lambrecht, Mark, additional, Leung, Chi-Ho, additional, Moreno, Julia, additional, Nicoletti, Rossella, additional, Nieboer, Daan, additional, Oja, Marek, additional, Palanisamy, Soundarya, additional, Prinsen, Peter, additional, Reich, Christian, additional, Raffaele Resta, Giulio, additional, Ribal, Maria J., additional, Gómez Rivas, Juan, additional, Smith, Emma, additional, Snijder, Robert, additional, Steinbeisser, Carl, additional, Vandenberghe, Frederik, additional, Cornford, Philip, additional, Evans-Axelsson, Susan, additional, N'Dow, James, additional, and Willemse, Peter-Paul M., additional
Published: 2024
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10. MP14-09 DEVELOPMENT OF A PREDICTION MODEL OF SURVIVAL AMONGST PATIENTS WITH METASTATIC HORMONE SENSITIVE PROSTATE CANCER (MHSPC) USING BIG DATA: INTERIM RESULTS FROM THE EUROPEAN NETWORK OF EXCELLENCE FOR BIG DATA IN PROSTATE CANCER (PIONEER)

Author: Nicoletti, Rossella, primary, Rivas, Juan Gomez, additional, Ibáñez, Laura, additional, Steinbeisserc, Carl, additional, de Meulder, Bertrand, additional, Golozar, Asieh, additional, Axelsson, Susan Evans, additional, Snijder, Robert, additional, Bjartell, Anders, additional, Cornford, Philip, additional, Van Hemelrijck, Mieke, additional, Beyer, Katharina, additional, Willemse, Peter-Paul, additional, Murtola, Teemu, additional, Robool, Monique J., additional, Sierra, Jesus Moreno, additional, Campi, Riccardo, additional, Gacci, Mauro, additional, Mottet, Nicolas, additional, Merseburger, Axel, additional, Ndow, James, additional, and Nicoletti, Rossella, additional
Published: 2024
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11. Research protocol for an observational health data analysis to assess the applicability of randomized controlled trials focusing on newly diagnosed metastatic prostate cancer using real-world data: PIONEER IMI’s “big data for better outcomes” program

Author: Gandaglia, Giorgio, primary, Pellegrino, Francesco, additional, De Meulder, Bertrand, additional, Hijazy, Ayman, additional, Abbott, Thomas, additional, Golozar, Asieh, additional, Nicoletti, Rossella, additional, Gomez-Rivas, Juan, additional, Steinbeisser, Carl, additional, Evans-Axelsson, Susan, additional, Briganti, Alberto, additional, and N’Dow, James, additional
Published: 2024
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12. Suboptimal response to biologics in severe asthma - a marker of humoral immunodeficiencies

Author: Tiotiu, Angelica, primary, De Meulder, Bertrand, additional, Vaillant, Pierre, additional, Mouton-Faivre, Claudie, additional, and Jaussaud, Roland, additional
Published: 2024
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13. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author: Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Naldi, Aurélien, Helikar, Tomáš, Singh, Vidisha, Fernández, Marco Fariñas, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce-de-Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam Arokia Balaya, Orlic-Milacic, Marija, Gomez, Luis Cristobal Monraz, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard
Abstract: Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors. Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies., Peer Reviewed
Published: 2024

14. Research protocol for an observational health data analysis on the adverse events of systemic treatment in patients with metastatic hormone-sensitive prostate cancer : big data analytics using the PIONEER platform

Author: Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T., Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi-Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J., Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, Willemse, Peter-Paul M., Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T., Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi-Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J., Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, and Willemse, Peter-Paul M.
Abstract: Combination therapies in metastatic hormone-sensitive prostate cancer (mHSPC), which include the addition of an androgen receptor signaling inhibitor and/or docetaxel to androgen deprivation therapy, have been a game changer in the management of this disease stage. However, these therapies come with their fair share of toxicities and side effects. The goal of this observational study is to report drug-related adverse events (AEs), which are correlated with systemic combination therapies for mHSPC. Determining the optimal treatment option requires large cohorts to estimate the tolerability and AEs of these combination therapies in “real-life” patients with mHSPC, as provided in this study. We use a network of databases that includes population-based registries, electronic health records, and insurance claims, containing the overall target population and subgroups of patients defined by unique certain characteristics, demographics, and comorbidities, to compute the incidence of common AEs associated with systemic therapies in the setting of mHSPC. These data sources are standardised using the Observational Medical Outcomes Partnership Common Data Model. We perform the descriptive statistics as well as calculate the AE incidence rate separately for each treatment group, stratified by age groups and index year. The time until the first event is estimated using the Kaplan-Meier method within each age group. In the case of episodic events, the anticipated mean cumulative counts of events are calculated. Our study will allow clinicians to tailor optimal therapies for mHSPC patients, and they will serve as a basis for comparative method studies.
Published: 2024
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15. Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management:A PIONEER Analysis Based on Big Data

Author: Gandaglia, Giorgio, Pellegrino, Francesco, Golozar, Asieh, De Meulder, Bertrand, Abbott, Thomas, Achtman, Ariel, Imran Omar, Muhammad, Alshammari, Thamir, Areia, Carlos, Asiimwe, Alex, Beyer, Katharina, Bjartell, Anders, Campi, Riccardo, Cornford, Philip, Falconer, Thomas, Feng, Qi, Gong, Mengchun, Herrera, Ronald, Hughes, Nigel, Hulsen, Tim, Kinnaird, Adam, Lai, Lana Y.H., Maresca, Gianluca, Mottet, Nicolas, Oja, Marek, Prinsen, Peter, Reich, Christian, Remmers, Sebastiaan, Roobol, Monique J., Sakalis, Vasileios, Seager, Sarah, Smith, Emma J., Snijder, Robert, Steinbeisser, Carl, Thurin, Nicolas H., Hijazy, Ayman, van Bochove, Kees, Van den Bergh, Roderick C.N., Van Hemelrijck, Mieke, Willemse, Peter Paul, Williams, Andrew E., Zounemat Kermani, Nazanin, Evans-Axelsson, Susan, Briganti, Alberto, N'Dow, James, Gandaglia, Giorgio, Pellegrino, Francesco, Golozar, Asieh, De Meulder, Bertrand, Abbott, Thomas, Achtman, Ariel, Imran Omar, Muhammad, Alshammari, Thamir, Areia, Carlos, Asiimwe, Alex, Beyer, Katharina, Bjartell, Anders, Campi, Riccardo, Cornford, Philip, Falconer, Thomas, Feng, Qi, Gong, Mengchun, Herrera, Ronald, Hughes, Nigel, Hulsen, Tim, Kinnaird, Adam, Lai, Lana Y.H., Maresca, Gianluca, Mottet, Nicolas, Oja, Marek, Prinsen, Peter, Reich, Christian, Remmers, Sebastiaan, Roobol, Monique J., Sakalis, Vasileios, Seager, Sarah, Smith, Emma J., Snijder, Robert, Steinbeisser, Carl, Thurin, Nicolas H., Hijazy, Ayman, van Bochove, Kees, Van den Bergh, Roderick C.N., Van Hemelrijck, Mieke, Willemse, Peter Paul, Williams, Andrew E., Zounemat Kermani, Nazanin, Evans-Axelsson, Susan, Briganti, Alberto, and N'Dow, James
Abstract: BACKGROUND: Conservative management is an option for prostate cancer (PCa) patients either with the objective of delaying or even avoiding curative therapy, or to wait until palliative treatment is needed. PIONEER, funded by the European Commission Innovative Medicines Initiative, aims at improving PCa care across Europe through the application of big data analytics.OBJECTIVE: To describe the clinical characteristics and long-term outcomes of PCa patients on conservative management by using an international large network of real-world data.DESIGN, SETTING, AND PARTICIPANTS: From an initial cohort of >100 000 000 adult individuals included in eight databases evaluated during a virtual study-a-thon hosted by PIONEER, we identified newly diagnosed PCa cases (n = 527 311). Among those, we selected patients who did not receive curative or palliative treatment within 6 mo from diagnosis (n = 123 146).OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Patient and disease characteristics were reported. The number of patients who experienced the main study outcomes was quantified for each stratum and the overall cohort. Kaplan-Meier analyses were used to estimate the distribution of time to event data.RESULTS AND LIMITATIONS: The most common comorbidities were hypertension (35-73%), obesity (9.2-54%), and type 2 diabetes (11-28%). The rate of PCa-related symptomatic progression ranged between 2.6% and 6.2%. Hospitalization (12-25%) and emergency department visits (10-14%) were common events during the 1st year of follow-up. The probability of being free from both palliative and curative treatments decreased during follow-up. Limitations include a lack of information on patients and disease characteristics and on treatment intent.CONCLUSIONS: Our results allow us to better understand the current landscape of patients with PCa managed with conservative treatment. PIONEER offers a unique opportunity to characterize the baseline features and
Published: 2024

16. Research Protocol for an Observational Health Data Analysis on the Adverse Events of Systemic Treatment in Patients with Metastatic Hormone-sensitive Prostate Cancer: Big Data Analytics Using the PIONEER Platform

Author: MS Urologische Oncologie, Cancer, Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T, Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi-Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J, Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, Willemse, Peter-Paul M, MS Urologische Oncologie, Cancer, Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T, Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi-Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J, Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, and Willemse, Peter-Paul M
Published: 2024

17. Research Protocol for an Observational Health Data Analysis on the Adverse Events of Systemic Treatment in Patients with Metastatic Hormone-sensitive Prostate Cancer:Big Data Analytics Using the PIONEER Platform

Author: Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T., Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J., Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, Willemse, Peter Paul M., Rajwa, Pawel, Borkowetz, Angelika, Abbott, Thomas, Alberti, Andrea, Bjartell, Anders, Brash, James T., Campi, Riccardo, Chilelli, Andrew, Conover, Mitchell, Constantinovici, Niculae, Davies, Eleanor, De Meulder, Bertrand, Eid, Sherrine, Gacci, Mauro, Golozar, Asieh, Hafeez, Haroon, Haque, Samiul, Hijazy, Ayman, Hulsen, Tim, Josefsson, Andreas, Khalid, Sara, Kolde, Raivo, Kotik, Daniel, Kurki, Samu, Lambrecht, Mark, Leung, Chi Ho, Moreno, Julia, Nicoletti, Rossella, Nieboer, Daan, Oja, Marek, Palanisamy, Soundarya, Prinsen, Peter, Reich, Christian, Raffaele Resta, Giulio, Ribal, Maria J., Gómez Rivas, Juan, Smith, Emma, Snijder, Robert, Steinbeisser, Carl, Vandenberghe, Frederik, Cornford, Philip, Evans-Axelsson, Susan, N'Dow, James, and Willemse, Peter Paul M.
Abstract: Combination therapies in metastatic hormone-sensitive prostate cancer (mHSPC), which include the addition of an androgen receptor signaling inhibitor and/or docetaxel to androgen deprivation therapy, have been a game changer in the management of this disease stage. However, these therapies come with their fair share of toxicities and side effects. The goal of this observational study is to report drug-related adverse events (AEs), which are correlated with systemic combination therapies for mHSPC. Determining the optimal treatment option requires large cohorts to estimate the tolerability and AEs of these combination therapies in “real-life” patients with mHSPC, as provided in this study. We use a network of databases that includes population-based registries, electronic health records, and insurance claims, containing the overall target population and subgroups of patients defined by unique certain characteristics, demographics, and comorbidities, to compute the incidence of common AEs associated with systemic therapies in the setting of mHSPC. These data sources are standardised using the Observational Medical Outcomes Partnership Common Data Model. We perform the descriptive statistics as well as calculate the AE incidence rate separately for each treatment group, stratified by age groups and index year. The time until the first event is estimated using the Kaplan-Meier method within each age group. In the case of episodic events, the anticipated mean cumulative counts of events are calculated. Our study will allow clinicians to tailor optimal therapies for mHSPC patients, and they will serve as a basis for comparative method studies.
Published: 2024

18. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author: 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, and Schneider, Reinhard
Published: 2021
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19. Stratification of asthma phenotypes by airway proteomic signatures

Author: Ahmed, H., Allen, D., Badorrek, P., Ballereau, S., Baribaud, F., Bedding, A., Behndig, A.F., Berglind, A., Berton, A., Bigler, J., Boedigheimer, M.J., Bønnelykke, K., Brinkman, P., Bush, A., Campagna, D., Casaulta, C., Chaiboonchoe, A., Davison, T., De Meulder, B., Delin, I., Dennison, P., Dodson, P., El Hadjam, L., Erzen, D., Faulenbach, C., Fichtner, K., Fitch, N., Formaggio, E., Gahlemann, M., Galffy, G., Garissi, D., Garret, T., Gent, J., Guillmant-Farry, E., Henriksson, E., Hoda, U., Hohlfeld, J.M., Hu, X., James, A., Johnson, K., Jullian, N., Kerry, G., Klüglich, M., Knowles, R., Konradsen, J.R., Kretsos, K., Krueger, L., Lantz, A.-S., Larminie, C., Latzin, P., Lefaudeux, D., Lemonnier, N., Lowe, L.A., Lutter, R., Manta, A., Mazein, A., McEvoy, L., Menzies-Gow, A., Mores, N., Murray, C.S., Nething, K., Nihlén, U., Niven, R., Nordlund, B., Nsubuga, S., Pellet, J., Pison, C., Praticò, G., Valls, M. Puig, Riemann, K., Rocha, J.P., Rossios, C., Santini, G., Saqi, M., Scott, S., Sehgal, N., Selby, A., Söderman, P., Sogbesan, A., Spycher, F., Stephan, S., Stokholm, J., Sunther, M., Szentkereszty, M., Tamasi, L., Tariq, K., Valente, S., van Aalderen, W.M., van Drunen, C.M., Van Eyll, J., Vyas, A., Yu, W., Zetterquist, W., Zolkipli, Z., Zwinderman, A.H., Schofield, James P.R., Burg, Dominic, Nicholas, Ben, Strazzeri, Fabio, Brandsma, Joost, Staykova, Doroteya, Folisi, Caterina, Bansal, Aruna T., Xian, Yang, Guo, Yike, Rowe, Anthony, Corfield, Julie, Wilson, Susan, Ward, Jonathan, Lutter, Rene, Shaw, Dominick E., Bakke, Per S., Caruso, Massimo, Dahlen, Sven-Erik, Fowler, Stephen J., Horváth, Ildikó, Howarth, Peter, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Sun, Kai, Pandis, Ioannis, Riley, John, Auffray, Charles, De Meulder, Bertrand, Lefaudeux, Diane, Sousa, Ana R., Adcock, Ian M., Chung, Kian Fan, Sterk, Peter J., Skipp, Paul J., and Djukanović, Ratko
Published: 2019
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20. Identification and prospective stability of electronic nose (eNose)–derived inflammatory phenotypes in patients with severe asthma

Author: Brinkman, Paul, Wagener, Ariane H., Hekking, Pieter-Paul, Bansal, Aruna T., Maitland-van der Zee, Anke-Hilse, Wang, Yuanyue, Weda, Hans, Knobel, Hugo H., Vink, Teunis J., Rattray, Nicholas J., D'Amico, Arnaldo, Pennazza, Giorgio, Santonico, Marco, Lefaudeux, Diane, De Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Chung, Kian F., Corfield, Julie, Dahlén, Sven-Erik, Djukanovic, Ratko, Geiser, Thomas, Horvath, Ildiko, Krug, Nobert, Musial, Jacek, Sun, Kai, Riley, John H., Shaw, Dominic E., Sandström, Thomas, Sousa, Ana R., Montuschi, Paolo, Fowler, Stephen J., and Sterk, Peter J.
Published: 2019
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21. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author: 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, 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, and Schneider, Reinhard
Published: 2021
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22. Baseline characteristics and clinical outcomes of prostate cancer patients on delayed palliative management: a PIONEER analysis based on big data.

Author: Lai, Lana Y. H., Sakalis, Vasileios, Chatzichristos, Christos, de la Parra, Irene, Steinbeisser, Carl, Golozar, Asieh, de Meulder, Bertrand, Hijazy, Ayman, Snijder, Robert, Qi Feng, Falconer, Thomas, Cornford, Philip, Bjartell, Anders, Evans-Axelsson, Susan, N’Dow, James, Gandaglia, Giorgio, and Gómez Rivas, Juan
Subjects: CHRONIC obstructive pulmonary disease, EMERGENCY room visits, PROSTATE cancer patients, TYPE 2 diabetes, DATA analytics
Abstract: Introduction Delayed palliative management (DPM) is an alternative for prostate cancer (PCa) patients with poor performance status, or those who received radical treatment but progressed and no longer meet the criteria for curative treatment. PIONEER is a large network of federated data analytic platforms in PCa that aims to improve its care through the application of big data analytics. The objective of this study was to describe clinical baseline characteristics and outcomes of PCa patients receiving DPM using big data. Material and methods Descriptive study of patients on DPM from four databases in PIONEER (Pharmetrics Plus, Optum Clinformatics, Marketscan and Columbia University Irving Medical Center (CUIMC)). Baseline characteristics, including comorbidities (hypertension, type 2 diabetes (T2DM), asthma/chronic obstructive pulmonary disease (COPD) and obesity), were stratified by age. Outcomes of interest were annual emergency department (ED) visits, hospitalization and symptomatic progression. Additional outcomes were time to death, hospitalization and time to symptomatic progression for CUIMC. Results We included 13246 men with a median age of 68–75 and Charlson Comorbidity index of 6–8. The three most common comorbidities were hypertension (80–93% [>80 years] vs 69–80% [55–80 years] vs 59–64% [<55 years]), T2DM (29–41% [>80 years] vs 26–38% [55–80 years] vs 23–26% [<55 years] and asthma/COPD (28–37% [>80 years] vs 19–30% [55–80 years] vs 16–19% [<55 years]). ED visits and hospitalizations were highest in the first year of follow-up (19–33% and 21–48% respectively). The median time to death was 548 days (IQR 1265 days) and to symptomatic progression was 408 days (IQR 1125 days) in CUIMC. Conclusions Men on DPM were in their mid-seventies, with the three most common comorbidities being hypertension, T2DM and asthma/COPD, regardless of age groups. This study reflects the potential of PIONEER as a federated network of databases that may be used to harness big data in PCa research. [ABSTRACT FROM AUTHOR]
Published: 2024
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23. Epithelial IL-6 trans-signaling defines a new asthma phenotype with increased airway inflammation

Author: Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Bansal, A.T., Baribaud, F., Bates, S., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, F.K., Compton, C.H., Corfield, J., D'Amico, A., Dahlen, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Goss, V., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., James, A.J., Knowles, R., Knox, A.J., Krug, N., Lefaudeux, D., Loza, M.J., Manta, A., Matthews, J.G., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Postle, A., Powel, P., Praticò, G., Rao, N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Schofield, J.P.R., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Jevnikar, Zala, Östling, Jörgen, Ax, Elisabeth, Calvén, Jenny, Thörn, Kristofer, Israelsson, Elisabeth, Öberg, Lisa, Singhania, Akul, Lau, Laurie C.K., Wilson, Susan J., Ward, Jonathan A., Chauhan, Anoop, Sousa, Ana R., De Meulder, Bertrand, Loza, Matthew J., Baribaud, Frédéric, Sterk, Peter J., Chung, Kian Fan, Sun, Kai, Guo, Yike, Adcock, Ian M., Payne, Debbie, Dahlen, Barbro, Chanez, Pascal, Shaw, Dominick E., Krug, Norbert, Hohlfeld, Jens M., Sandström, Thomas, Djukanovic, Ratko, James, Anna, Hinks, Timothy S.C., Howarth, Peter H., Vaarala, Outi, van Geest, Marleen, and Olsson, Henric
Published: 2019
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24. Pathway discovery using transcriptomic profiles in adult-onset severe asthma

Author: Adcock, I.M., Ahmed, H., Auffray, C., Bakke, P., Bansal, A.T., Baribaud, F., Bates, S., Bel, E.H., Bigler, J., Bisgaard, H., Boedigheimer, M.J., Bønnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, F.K., Compton, C.H., Corfield, J., D'Amico, A., Dahlen, S.E., De Meulder, B., Djukanovic, R., Erpenbeck, V.J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L.J., Formaggio, E., Fowler, S.J., Frey, U., Gahlemann, M., Geiser, T., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P.W., Higenbottam, T., Hohlfeld, J.M., Holweg, C., Horváth, I., Howarth, P., James, A.J., Knowles, R., Krug, N., Lefaudeux, D., Loza, M.J., Lutter, R., Manta, A., Masefield, S., Matthews, J.G., Mazein, A., Meiser, A., Middelveld, R.J.M., Miralpeix, M., Mores, N., Murray, C.S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Powel, P., Praticò, G., Valls, M Puig, Rao, N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandström, T., Seibold, W., Selby, A., Shaw, D.E., Sigmund, R., Singer, F., Skipp, P.J., Sousa, A.R., Sterk, P.J., Sun, K., Thornton, B., van Aalderen, W.M., van Geest, M., Vestbo, J., Vissing, N.H., Wagener, A.H., Wagers, S.S., Weiszhart, Z., Wheelock, C.E., Wilson, S.J., Hekking, Pieter-Paul, Loza, Matt J., Pavlidis, Stelios, de Meulder, Bertrand, Lefaudeux, Diane, Baribaud, Fred, Auffray, Charles, Wagener, Ariane H., Brinkman, Paul, Ir, Lutter, Rene, Ir, Bansal, Aruna T., Sousa, Ana R., Bates, Steve A., Pandis, Yannis, Fleming, Louise J., Shaw, Dominique E., Fowler, Stephen J., Meiser, Andrea, Sun, Kai, Corfield, Julie, Howarth, Peter H., Bel, Elisabeth H., Adcock, Ian M., Chung, Kian Fan, Djukanovic, Ratko, and Sterk, Peter J.
Published: 2018
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25. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection

Author: Do, Lien Anh Ha, Pellet, Johann, van Doorn, H. Rogier, Tran, Anh Tuan, Nguyen, Bach Hue, Tran, Thi Thu Loan, Tran, Quynh Huong, Vo, Quoc Bao, Dac, Nguyen Anh Tran, Trinh, Hong Nhien, Nguyen, Thi Thanh Hai, Le Binh, Bao Tinh, Nguyen, Huu Mai Khanh, Nguyen, Minh Tien, Thai, Quang Tung, Vo, Thanh Vu, Ngo, Ngoc Quang Minh, Dang, Thi Kim Huyen, Cao, Ngoc Huong, Van Tran, Thu, Ho, Lu Viet, De Meulder, Bertrand, Auffray, Charles, Hofstra, Jorrit-Jan, Farrar, Jeremy, Bryant, Juliet E., de Jong, Menno, and Hibberd, Martin L.
Published: 2018

26. Data-driven model links BMIz to gene expression in pediatric asthma

Author: Dandenault, Vincent, primary, Hachem, Nehme, additional, Adcock, Ian M, additional, Andersson, Lars I., additional, Auffray, Charles, additional, Chung, Fan K, additional, Dahlén, Sven-Erik, additional, De Meulder, Bertrand, additional, Djukanovic, Ratko, additional, Howarth, Peter, additional, Knowles, Richard G, additional, Krug, Norbert, additional, Roberts, Amanda, additional, Sousa, Ana R, additional, Sterk, Peter J., additional, Supple, David, additional, Rao, Navin, additional, Roberts, Graham, additional, Uddin, Mohib, additional, Wagers, Scott, additional, Maitland-Van Der Zee, Anke-Hilse, additional, and Longo, Cristina, additional
Published: 2023
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27. Prediction of severe asthma clinical phenotypes using molecular profiles of urine eicosanoids

Author: Kolmert, Johan, primary, Sparreman-Mikus, Maria, additional, De Meulder, Bertrand, additional, Andersson, Lars I, additional, Adcook, Ian, additional, Djukanovic, Ratko, additional, Dahlén, Sven-Erik, additional, and Wheeelock, Craig E., additional
Published: 2023
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28. U-BIOPRED clinical adult asthma clusters linked to a subset of sputum omics

Author: Adriaens, Nora, Ahmed, Hassan, Aliprantis, Antonios, Alving, Kjell, Badorek, Philipp, Balgoma, David, Barber, Clair, Bautmans, An, Behndig, Annelie F., Bel, Elisabeth, Beleta, Jorge, Berglind, Ann, Berton, Alix, Bigler, Jeanette, Bisgaard, Hans, Bochenek, Grazyna, Boedigheimer, Michael J., Bøonnelykke, Klaus, Brandsma, Joost, Braun, Armin, Brinkman, Paul, Burg, Dominic, Campagna, Davide, Carayannopoulos, Leon, Carvalho da Purfição Rocha, João P., Chaiboonchoe, Amphun, Chaleckis, Romanas, Coleman, Courtney, Compton, Chris, D'Amico, Arnaldo, Dahlén, Barbro, De Alba, Jorge, de Boer, Pim, De Lepeleire, Inge, Dekker, Tamara, Delin, Ingrid, Dennison, Patrick, Dijkhuis, Annemiek, Draper, Aleksandra, Edwards, Jessica, Emma, Rosalia, Ericsson, Magnus, Erpenbeck, Veit, Erzen, Damijan, Faulenbach, Cornelia, Fichtner, Klaus, Fitch, Neil, Flood, Breda, Frey, Urs, Gahlemann, Martina, Galffy, Gabriella, Gallart, Hector, Garret, Trevor, Geiser, Thomas, Gent, Jilaiha, Gerhardsson de Verdier, Maria, Gibeon, David, Gomez, Cristina, Gove, Kerry, Gozzard, Neil, Guo, Yi-Ke, Hashimoto, Simone, Haughney, John, Hedlin, Gunilla, Hekking, Pieter-Paul, Henriksson, Elisabeth, Hewitt, Lorraine, Higgenbottam, Tim, Hoda, Uruj, Hohlfeld, Jans, Holweg, Cecile, Howarth, Peter, Hu, Richard, Hu, Sile, Hu, Xugang, Hudson, Val, James, Anna J., Kamphuis, Juliette, Kennington, Erika J., Kerry, Dyson, Klüglich, Matthias, Knobel, Hugo, Knowles, Richard, Knox, Alan, Kolmert, Johan, Konradsen, Jon, Kots, Maxim, Krueger, Linn, Kuo, Scott, Kupczyk, Maciej, Lambrecht, Bart, Lantz, Ann-Sofie, Larsson, Lars, Lazarinis, Nikos, Lone-Satif, Saeeda, Marouzet, Lisa, Martin, Jane, Masefield, Sarah, Mathon, Caroline, Matthews, John G., Mazein, Alexander, Meah, Sally, Maiser, Andrea, Menzies-Gow, Andrew, Metcalf, Leanne, Middelveld, Roelinde, Mikus, Maria, Miralpeix, Montse, Monk, Philips, Mores, Nadia, Murray, Clare S., Musial, Jacek, Myles, David, Naz, Shama, Nething, Katja, Nicholas, Ben, Nihlen, Ulf, Nilsson, Peter, Nordlund, Björn, Östling, Jörgen, Pacino, Antonio, Pahus, Laurie, Palkonnen, Susanna, Pavlidis, Stelios, Pennazza, Giorgio, Petrén, Anne, Pink, Sandy, Postle, Anthony, Powel, Pippa, Rahman-Amin, Malayka, Rao, Navin, Ravanetti, Lara, Ray, Emma, Reinke, Stacey, Reynolds, Leanne, Riemann, Kathrin, Riley, John, Robberechts, Martine, Roberts, Amanda, Rossios, Christos, Russell, Kirsty, Rutgers, Michael, Santini, Giuseppe, Sentoninco, Marco, Schoelch, Corinna, Schofield, James P.R., Seibold, Wolfgang, Sigmund, Ralf, Sjödin, Marcus, Skipp, Paul J., Smids, Barbara, Smith, Caroline, Smith, Jessica, Smith, Katherine M., Söderman, Päivi, Sogbesan, Adesimbo, Staykova, Doroteya, Strandberg, Karin, Sun, Kai, Supple, David, Szentkereszty, Marton, Tamasi, Lilla, Tariq, Kamran, Thörngren, John-Olof, Thornton, Bob, Thorsen, Jonathan, Valente, Salvatore, van Aalderenm, Wim, van de Pol, Marianne, van Drunen, Kees, van Geest, Marleen, Versnel, Jenny, Vestbo, Jorgen, Vink, Anton, Vissing, Nadja, von Garnier, Christophe, Wagerner, Arianne, Wagers, Scott, Wald, Frans, Walker, Samantha, Ward, Jonathan, Weiszhart, Zsoka, Wetzel, Kristiane, Wheelock, Craig E., Wiegman, Coen, Williams, Siân, Wilson, Susan J., Woosdcock, Ashley, Yang, Xian, Yeyashingham, Elizabeth, Yu, Wen, Zetterquist, Wilhelm, Zwinderman, Koos, Lefaudeux, Diane, De Meulder, Bertrand, Loza, Matthew J., Peffer, Nancy, Rowe, Anthony, Baribaud, Frédéric, Bansal, Aruna T., Lutter, Rene, Sousa, Ana R., Corfield, Julie, Pandis, Ioannis, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Dahlén, Sven-Erik, Fleming, Louise J., Fowler, Stephen J., Horvath, Ildiko, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandstrom, Thomas, Shaw, Dominic E., Singer, Florian, Sterk, Peter J., Roberts, Graham, Adcock, Ian M., Djukanovic, Ratko, Auffray, Charles, and Chung, Kian Fan
Published: 2017
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29. Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management: A PIONEER Analysis Based on Big Data

Author: Gandaglia, Giorgio, primary, Pellegrino, Francesco, additional, Golozar, Asieh, additional, De Meulder, Bertrand, additional, Abbott, Thomas, additional, Achtman, Ariel, additional, Imran Omar, Muhammad, additional, Alshammari, Thamir, additional, Areia, Carlos, additional, Asiimwe, Alex, additional, Beyer, Katharina, additional, Bjartell, Anders, additional, Campi, Riccardo, additional, Cornford, Philip, additional, Falconer, Thomas, additional, Feng, Qi, additional, Gong, Mengchun, additional, Herrera, Ronald, additional, Hughes, Nigel, additional, Hulsen, Tim, additional, Kinnaird, Adam, additional, Lai, Lana Y.H., additional, Maresca, Gianluca, additional, Mottet, Nicolas, additional, Oja, Marek, additional, Prinsen, Peter, additional, Reich, Christian, additional, Remmers, Sebastiaan, additional, Roobol, Monique J., additional, Sakalis, Vasileios, additional, Seager, Sarah, additional, Smith, Emma J., additional, Snijder, Robert, additional, Steinbeisser, Carl, additional, Thurin, Nicolas H., additional, Hijazy, Ayman, additional, van Bochove, Kees, additional, Van den Bergh, Roderick C.N., additional, Van Hemelrijck, Mieke, additional, Willemse, Peter-Paul, additional, Williams, Andrew E., additional, Zounemat Kermani, Nazanin, additional, Evans-Axelsson, Susan, additional, Briganti, Alberto, additional, and N'Dow, James, additional
Published: 2023
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30. Survivorship Data in Prostate Cancer: Where Are We and Where Do We Need To Be?

Author: Smith, Emma, N'Dow, James, Plass, Karin, Ribal, Maria, Mottet, Nicolas, Shepherd, Robert, Abbott, Tom, Mastris, Ken, Moris, Lisa, Lardas, Michael, Van den Broeck, Thomas, Willemse, Peter-Paul, Fossati, Nicola, Pang, Karl, Campi, Riccardo, Greco, Isabella, Gacci, Mauro, Serni, Sergio, Bjartell, Anders, Lonnerbro, Ragnar, Briganti, Alberto, Crosti, Daniele, Garzonio, Roberto, Gandaglia, Giorgio, Faticoni, Martina, Grant office, Bangma, Chris, Jongerden, Maria, Tilki, Derya, Auvinen, Anssi, Murtola, Teemu, Visakorpi, Tapio, Talala, Kirsi, Tammela, Teuvo, Siltari, Aino, Lejeune, Stephane, Colette, Laurence, Caputova, Simona, Poli, Delielena, Byrne, Sophie, Fialho, Luz, Rowland, Ashley, Tapela, Neo, Di Flora, Nicola, Apostolidis, Kathi, Lemair, Valerie, De Meulder, Bertrand, Auffray, Charles, Taibi, Nesrine, Hijazy, Ayman, Saporta, Albert, Sun, Kai, Power, Shaun, Zounemat Kermani, Nazanin, van Bochove, Kees, Tafreshiha, Azadeh, Bernini, Chiara, Horgan, Denis, Fullwood, Louise, Holtorf, Marc, Lancet, Doron, Bernstein, Gabi, Tripathee, Sheela, Wirth, Manfred, Froehner, Michael, Brenner, Beate, Borkowetz, Angelika, Thomas, Christian, Horn, Friedemann, Reiche, Kristin, Kreuz, Markus, Josefsson, Andreas, Gasi Tandefelt, Delila, Hugosson, Jonas, Schalken, Jack, Huisman, Henkjan, Hofmarcher, Thomas, Lindgren, Peter, Andersson, Emelie, Fridhammar, Adam, Tames Grijalva, Monica, Evans-Axelsson, Susan, Verholen, Frank, Zong, Jihong, Butler-Ransohoff, John-Edward, Williamson, Todd, Waldeck, Reg, Bruno, Amanda, Nevedomskaya, Ekaterina, Fatoba, Samuel, Constantinovici, Niculae, Steinbeisser, Carl, Maass, Monika, Torremante, Patrizia, Dochy, Emmanuelle, Pisa, Federica, Voss, Marc Dietrich, Papineni, Kishore, Wang-silvanto, Jing, Snijder, Robert, Wang, Xuewei, Lambrecht, Mark, Wolfinger, Russ, Eid, Sherinne, Palanisamy, Soundarya, Haque, Samiul, Antoni, Laurent, Servan, Angela, Pascoe, Katie, Robinson, Paul, Lencart, Joana, Jaton, Bertrand, Turunen, Heidi, Kilkku, Olavi, Pohjanjousi, Pasi, Voima, Olli, Nevalaita, Liina, Punakivi, Keijo, Seager, Sarah, Ratwani, Shilpa, Grzeslak, Katarzyna, Brash, James, Longden-Chapman, Elaine, Burke, Danny, Licour, Muriel, Payne, Sarah, Yong, Alan, Lujan, Flavia, Le Mare, Sophia, Hendrich, Jan, Bussmann, Michael, Juckeland, Kotik, Reich, Christian, Russell, Beth, Beyer, Katharina, Lawlor, Ailbhe, Roobol, Monique J., Venderbos, Lionne D.F., Remmers, Sebastiaan, Briers, Erik, MacLennan, Sara J., MacLennan, Steven, Omar, Muhammad Imran, and Van Hemelrijck, Mieke
Published: 2024
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31. Research protocol to identify progression and death amongst patients with metastatic hormone-sensitive prostate cancer treated with available treatments: PIONEER IMI's 'big data for better outcomes' program

Author: MS Urologische Oncologie, Cancer, Gomez Rivas, Juan, Nicoletti, Rossella, Ibáñez, Laura, Steinbeisser, Carl, de Meulder, Bertrand, Golozar, Asieh, Axelsson, Susan Evans, Snijder, Robert, Bjartell, Anders, Cornford, Philip, Van Hemelrijck, Mieke, Beyer, Katharina, Willemse, Peter-Paul, Murtola, Teemu, Roobol, Monique J, Moreno-Sierra, Jesús, Campi, Riccardo, Gacci, Mauro, Mottet, Nicolas, Merseburger, Axel, Ndow, James, MS Urologische Oncologie, Cancer, Gomez Rivas, Juan, Nicoletti, Rossella, Ibáñez, Laura, Steinbeisser, Carl, de Meulder, Bertrand, Golozar, Asieh, Axelsson, Susan Evans, Snijder, Robert, Bjartell, Anders, Cornford, Philip, Van Hemelrijck, Mieke, Beyer, Katharina, Willemse, Peter-Paul, Murtola, Teemu, Roobol, Monique J, Moreno-Sierra, Jesús, Campi, Riccardo, Gacci, Mauro, Mottet, Nicolas, Merseburger, Axel, and Ndow, James
Published: 2023

32. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author: Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, COVID- Disease Map Community the COVID-19 Disease Map Community, Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US), Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, and COVID- Disease Map Community the COVID-19 Disease Map Community
Abstract: Introduction: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing., Methods: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors., Results: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19., Discussion: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Published: 2023

33. Research protocol to identify progression and death amongst patients with metastatic hormone-sensitive prostate cancer treated with available treatments: PIONEER IMI's "big data for better outcomes" program.

Author: Gomez Rivas, Juan, Nicoletti, Rossella, Ibáñez, Laura, Steinbeisser, Carl, de Meulder, Bertrand, Golozar, Asieh, Evans Axelsson, Susan, Snijder, Robert, Bjartell, Anders, Cornford, Philip, Van Hemelrijck, Mieke, Beyer, Katharina, Willemse, Peter-Paul, Murtola, Teemu, Roobol, Monique J., Moreno-Sierra, Jesús, Campi, Riccardo, Gacci, Mauro, Mottet, Nicolas, and Merseburger, Axel
Published: 2023
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34. A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Author: Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc, Funahashi, Akira, Acencio, Marcio, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro, Hiki, Yusuke, Hiroi, Noriko, Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon, Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Pena-Chilet, Maria, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara, Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Farinas Fernandez, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noel, Vincent, Ponce de Leon, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin, Bachman, John, Luna, Agustin, Pinero, Janet, Furlong, Laura, Balaur, Irina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert, Phair, Robert, Perfetto, Livia, Matthews, Lisa, Rex, Devasahayam, Orlic-Milacic, Marija, Monraz Gomez, Luis, de Meulder, Bertrand, Ravel, Jean, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques, Evelo, Chris, d'Eustachio, Peter, Schreiber, Falk, Saez-Rodriguez, Julio, Dopazo, Joaquin, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire de recherche européen pour la polyarthrite rhumatoïde (GenHotel), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, University of Luxembourg [Luxembourg], Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris sciences et lettres (PSL), Maastricht Centre for Systems Biology [Maastricht] (MaCSBio), Maastricht University [Maastricht], Ontario Institute for Cancer Research [Canada] (OICR), Ontario Institute for Cancer Research, Keio University, Luxembourg Centre For Systems Biomedicine (LCSB), University of Konstanz, Hochschule Mittweida - University of Applied Sciences, Kanagawa Institute of Technology, Heidelberg University Hospital [Heidelberg], National Institute for Infectious Diseases 'Lazzaro Spallanzani', Hospital Universitario Virgen del Rocío [Sevilla], Biomedicine Institute of Sevilla [Seville, Spain], University of Nebraska–Lincoln, University of Nebraska System, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Harvard Medical School [Boston] (HMS), Universitat Pompeu Fabra [Barcelona] (UPF), National Institute of Advanced Industrial Science and Technology (AIST), Humboldt University Of Berlin, Integrative Bioinformatics Inc [Mountain View], Department of Informatics and System Sciences (Sapienza University of Rome), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), New York University Langone Medical Center (NYU Langone Medical Center), NYU System (NYU), Yenepoya University, Janet Piñero, Laura I. Furlong: IMI2-JU grants, resources which are composed of financial contributions from the European Union’s Horizon 2020 Research and Innovation Programme and EFPIA [GA: 777365 eTRANSAFE], and the EU H2020 Programme [GA:964537 RISKHUNT3R], Project 001-P-001647—Valorisation of EGA for Industry and Society funded by the European Regional Development Fund (ERDF) and Generalitat de Catalunya, and Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, 'A way to make Europe').
Subjects: SARS-CoV-2, disease maps, systems biology, dynamic models, systems medicine, large-scale community effort, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], mechanistic models
Abstract: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.
Published: 2022

35. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Author: Mazein, Alexander, Ostaszewski, Marek, Kuperstein, Inna, Watterson, Steven, Le Novère, Nicolas, Lefaudeux, Diane, De Meulder, Bertrand, Pellet, Johann, Balaur, Irina, Saqi, Mansoor, Nogueira, Maria Manuela, He, Feng, Parton, Andrew, Lemonnier, Nathanaël, Gawron, Piotr, Gebel, Stephan, Hainaut, Pierre, Ollert, Markus, Dogrusoz, Ugur, Barillot, Emmanuel, Zinovyev, Andrei, Schneider, Reinhard, Balling, Rudi, and Auffray, Charles
Published: 2018
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36. A computational framework for complex disease stratification from multiple large-scale datasets

Author: De Meulder, Bertrand, Lefaudeux, Diane, Bansal, Aruna T., Mazein, Alexander, Chaiboonchoe, Amphun, Ahmed, Hassan, Balaur, Irina, Saqi, Mansoor, Pellet, Johann, Ballereau, Stéphane, Lemonnier, Nathanaël, Sun, Kai, Pandis, Ioannis, Yang, Xian, Batuwitage, Manohara, Kretsos, Kosmas, van Eyll, Jonathan, Bedding, Alun, Davison, Timothy, Dodson, Paul, Larminie, Christopher, Postle, Anthony, Corfield, Julie, Djukanovic, Ratko, Chung, Kian Fan, Adcock, Ian M., Guo, Yi-Ke, Sterk, Peter J., Manta, Alexander, Rowe, Anthony, Baribaud, Frédéric, Auffray, Charles, and the U-BIOPRED Study Group and the eTRIKS Consortium
Published: 2018
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37. Faculty Opinions recommendation of Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome.

Author: Auffray, Charles, primary and De Meulder, Bertrand, additional
Published: 2022
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38. Clinical and transcriptomic features of persistent exacerbation-prone severe asthma in U-BIOPRED cohort

Author: Hoda, Uruj, Pavlidis, Stelios, Bansal, Aruna T, Takahashi, Kentaro, Hu, Sile, Ng Kee Kwong, Francois, Rossios, Christos, Sun, Kai, Bhavsar, Pankaj, Loza, Matthew, Baribaud, Frederic, Chanez, Pascal, Fowler, Stephen J, Horvath, Ildiko, Montuschi, Paolo, Singer, Florian, Musial, Jacek, Dahlen, Barbro, Krug, Norbert, Sandstrom, Thomas, Shaw, Dominic E, Lutter, Rene, Fleming, Louise J, Howarth, Peter H, Caruso, Massimo, Sousa, Ana R, Corfield, Julie, Auffray, Charles, De Meulder, Bertrand, Lefaudeux, Diane, Dahlen, Sven-Erik, Djukanovic, Ratko, Sterk, Peter J, Guo, Yike, Adcock, Ian M, Chung, Kian Fan, Pulmonology, AII - Inflammatory diseases, and Commission of the European Communities
Subjects: severe asthma, Bronchi/pathology, Medicine (miscellaneous), PHENOTYPES, 1110 Nursing, 610 Medicine & health, Bronchi, Research & Experimental Medicine, Sputum/metabolism, Cohort Studies, Humans, CEACAM5, Asthma/genetics, Science & Technology, STATEMENT, Sputum, Transcriptome/genetics, Asthma, frequent exacerbators, Oncology, Medicine, Research & Experimental, asthma exacerbations, Molecular Medicine, U-BIOPRED study group, 610 Medizin und Gesundheit, Transcriptome, Life Sciences & Biomedicine, persistent frequent exacerbators, LUNG
Abstract: BACKGROUND: Exacerbation-prone asthma is a feature of severe disease. However, the basis for its persistency remains unclear.OBJECTIVES: To determine the clinical and transcriptomic features of frequent exacerbators (FEs) and persistent FEs (PFEs) in the U-BIOPRED cohort.METHODS: We compared features of FE (≥2 exacerbations in past year) to infrequent exacerbators (IE, RESULTS: Of 317 patients, 62.4% had FE, of whom 63.6% had PFE, while 37.6% had IE, of whom 61.3% had PIE. Using multivariate analysis, FE was associated with short-acting beta-agonist use, sinusitis and daily oral corticosteroid use, while PFE was associated with eczema, short-acting beta-agonist use and asthma control index. CEA cell adhesion molecule 5 (CEACAM5) was the only differentially expressed transcript in bronchial biopsies between PE and IE. There were no differentially expressed genes in the other four compartments. There were higher expression scores for type 2, T-helper type-17 and type 1 pathway signatures together with those associated with viral infections in bronchial biopsies from FE compared to IE, while there were higher expression scores of type 2, type 1 and steroid insensitivity pathway signatures in bronchial biopsies of PFE compared to PIE.CONCLUSION: The FE group and its PFE subgroup are associated with poor asthma control while expressing higher type 1 and type 2 activation pathways compared to IE and PIE, respectively.
Published: 2022
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39. Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

Author: Sparreman Mikus, Maria, Kolmert, Johan, Andersson, Lars I., Östling, Jörgen, Knowles, Richard G., Gómez, Cristina, Ericsson, Magnus, Thörngren, John-Olof, Emami Khoonsari, Payam, Dahlén, Barbro, Kupczyk, Maciej, De Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Beghe, Bianca, Bel, Elisabeth H., Caruso, Massimo, Chanez, Pascal, Chawes, Bo, Fowler, Stephen J., Gaga, Mina, Geiser, Thomas, Gjomarkaj, Mark, Horváth, Ildikó, Howarth, Peter H., Johnston, Sebastian L., Joos, Guy, Krug, Norbert, Montuschi, Paolo, Musial, Jacek, Niżankowska-Mogilnicka, Ewa, Olsson, Henric K., Papi, Alberto, Rabe, Klaus F., Sandström, Thomas, Shaw, Dominick E., Siafakas, Nikolaos M., Uhlén, Mathias, Riley, John H., Bates, Stewart, Middelveld, Roelinde J M, Wheelock, Craig E., Chung, Kian Fan, Adcock, Ian M., Sterk, Peter J., Djukanovic, Ratko, Nilsson, Peter, Dahlén, Sven-Erik, James, Anna, Sparreman Mikus, Maria, Kolmert, Johan, Andersson, Lars I., Östling, Jörgen, Knowles, Richard G., Gómez, Cristina, Ericsson, Magnus, Thörngren, John-Olof, Emami Khoonsari, Payam, Dahlén, Barbro, Kupczyk, Maciej, De Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Beghe, Bianca, Bel, Elisabeth H., Caruso, Massimo, Chanez, Pascal, Chawes, Bo, Fowler, Stephen J., Gaga, Mina, Geiser, Thomas, Gjomarkaj, Mark, Horváth, Ildikó, Howarth, Peter H., Johnston, Sebastian L., Joos, Guy, Krug, Norbert, Montuschi, Paolo, Musial, Jacek, Niżankowska-Mogilnicka, Ewa, Olsson, Henric K., Papi, Alberto, Rabe, Klaus F., Sandström, Thomas, Shaw, Dominick E., Siafakas, Nikolaos M., Uhlén, Mathias, Riley, John H., Bates, Stewart, Middelveld, Roelinde J M, Wheelock, Craig E., Chung, Kian Fan, Adcock, Ian M., Sterk, Peter J., Djukanovic, Ratko, Nilsson, Peter, Dahlén, Sven-Erik, and James, Anna
Published: 2022
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40. Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

Author: Mikus, Maria Sparreman, Kolmert, Johan, Andersson, Lars I., Östling, Jörgen, Knowles, Richard G., Gómez, Cristina, Ericsson, Magnus, Thörngren, John Olof, Khoonsari, Payam Emami, Dahlén, Barbro, Kupczyk, Maciej, de Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Beghe, Bianca, Bel, Elisabeth H., Caruso, Massimo, Chanez, Pascal, Chawes, Bo, Fowler, Stephen J., Gaga, Mina, Geiser, Thomas, Gjomarkaj, Mark, Horváth, Ildikó, Howarth, Peter H., Johnston, Sebastian L., Joos, Guy, Krug, Norbert, Montuschi, Paolo, Musial, Jacek, Niżankowska-Mogilnicka, Ewa, Olsson, Henric K., Papi, Alberto, Rabe, Klaus F., Sandström, Thomas, Shaw, Dominick E., Siafakas, Nikolaos M., Uhlén, Mathias, Riley, John H., Bates, Stewart, Middelveld, Roelinde J.M., Wheelock, Craig E., Chung, Kian Fan, Adcock, Ian M., Sterk, Peter J., Bisgaard, Hans, Bønnelykke, Klaus, Vestbo, Jørgen, Vissing, Nadja H., Olsson, Marianne, Mikus, Maria Sparreman, Kolmert, Johan, Andersson, Lars I., Östling, Jörgen, Knowles, Richard G., Gómez, Cristina, Ericsson, Magnus, Thörngren, John Olof, Khoonsari, Payam Emami, Dahlén, Barbro, Kupczyk, Maciej, de Meulder, Bertrand, Auffray, Charles, Bakke, Per S., Beghe, Bianca, Bel, Elisabeth H., Caruso, Massimo, Chanez, Pascal, Chawes, Bo, Fowler, Stephen J., Gaga, Mina, Geiser, Thomas, Gjomarkaj, Mark, Horváth, Ildikó, Howarth, Peter H., Johnston, Sebastian L., Joos, Guy, Krug, Norbert, Montuschi, Paolo, Musial, Jacek, Niżankowska-Mogilnicka, Ewa, Olsson, Henric K., Papi, Alberto, Rabe, Klaus F., Sandström, Thomas, Shaw, Dominick E., Siafakas, Nikolaos M., Uhlén, Mathias, Riley, John H., Bates, Stewart, Middelveld, Roelinde J.M., Wheelock, Craig E., Chung, Kian Fan, Adcock, Ian M., Sterk, Peter J., Bisgaard, Hans, Bønnelykke, Klaus, Vestbo, Jørgen, Vissing, Nadja H., and Olsson, Marianne
Published: 2022

41. A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes

Author: Abdel-Aziz, Mahmoud I., Vijverberg, Susanne J.H., Neerincx, Anne H., Brinkman, Paul, Wagener, Ariane H., Riley, John H., Sousa, Ana R., Bates, Stewart, Wagers, Scott S., De Meulder, Bertrand, Auffray, Charles, Wheelock, Åsa M., Bansal, Aruna T., Caruso, Massimo, Chanez, Pascal, Uddin, Mohib, Corfield, Julie, Horvath, Ildiko, Krug, Norbert, Musial, Jacek, Sun, Kai, Shaw, Dominick E., Sandström, Thomas, Montuschi, Paolo, Fowler, Stephen J., Lutter, René, Djukanovic, Ratko, Howarth, Peter, Skipp, Paul, Sanak, Marek, Adcock, Ian M., Chung, Kian Fan, Sterk, Peter J., Kraneveld, Aletta D., Maitland-Van der Zee, Anke H., Abdel-Aziz, Mahmoud I., Vijverberg, Susanne J.H., Neerincx, Anne H., Brinkman, Paul, Wagener, Ariane H., Riley, John H., Sousa, Ana R., Bates, Stewart, Wagers, Scott S., De Meulder, Bertrand, Auffray, Charles, Wheelock, Åsa M., Bansal, Aruna T., Caruso, Massimo, Chanez, Pascal, Uddin, Mohib, Corfield, Julie, Horvath, Ildiko, Krug, Norbert, Musial, Jacek, Sun, Kai, Shaw, Dominick E., Sandström, Thomas, Montuschi, Paolo, Fowler, Stephen J., Lutter, René, Djukanovic, Ratko, Howarth, Peter, Skipp, Paul, Sanak, Marek, Adcock, Ian M., Chung, Kian Fan, Sterk, Peter J., Kraneveld, Aletta D., and Maitland-Van der Zee, Anke H.
Abstract: A multi-omics approach revealed the underlying biological pathways in the microbiome-driven severe asthma phenotypes. This may help to elucidate new leads for treatment development, particularly for the therapeutically challenging neutrophilic asthma.
Published: 2022
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42. A Transcriptome-driven Analysis of Epithelial Brushings and Bronchial Biopsies to Define Asthma Phenotypes in U-BIOPRED

Author: Kuo, Chih-Hsi Scott, Pavlidis, Stelios, Loza, Matthew, Baribaud, Fred, Rowe, Anthony, Pandis, Ioannis, Hoda, Uruj, Rossios, Christos, Sousa, Ana, Wilson, Susan J., Howarth, Peter, Dahlen, Barbro, Dahlen, Sven-Erik, Chanez, Pascal, Shaw, Dominick, Krug, Norbert, Sandström, Thomas, De Meulder, Bertrand, Lefaudeux, Diane, Fowler, Stephen, Fleming, Louise, Corfield, Julie, Auffray, Charles, Sterk, Peter J., Djukanovic, Ratko, Guo, Yike, Adcock, Ian M., and Chung, Kian Fan
Published: 2017
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43. Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness

Author: Saqi, Mansoor, primary, Pellet, Johann, additional, Roznovat, Irina, additional, Mazein, Alexander, additional, Ballereau, Stéphane, additional, De Meulder, Bertrand, additional, and Auffray, Charles, additional
Published: 2016
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44. Association of Differential Mast Cell Activation with Granulocytic Inflammation in Severe Asthma

Author: Tiotiu, Angelica, primary, Badi, Yusef, additional, Kermani, Nazanin Zounemat, additional, Sanak, Marek, additional, Kolmert, Johan, additional, Wheelock, Craig E., additional, Hansbro, Philip M., additional, Dahlén, Sven-Erik, additional, Sterk, Peter J., additional, Djukanovic, Ratko, additional, Guo, Yike, additional, Mumby, Sharon, additional, Adcock, Ian M., additional, Chung, Kian Fan, additional, Hoda, Uruj, additional, Rossios, Christos, additional, Bel, Elisabeth, additional, Rao, Navin, additional, Myles, David, additional, Compton, Chris, additional, Van Geest, Marleen, additional, Howarth, Peter, additional, Roberts, Graham, additional, Lefaudeux, Diane, additional, De Meulder, Bertrand, additional, Bansal, Aruna T., additional, Knowles, Richard, additional, Erzen, Damijn, additional, Wagers, Scott, additional, Krug, Norbert, additional, Higenbottam, Tim, additional, Matthews, John, additional, Erpenbeek, Veit, additional, Carayannopoulos, Leon, additional, Roberts, Amanda, additional, Supple, David, additional, deBoer, Pim, additional, Caruso, Massimo, additional, Chanez, Pascal, additional, Horváth, Ildikó, additional, Musial, Jacek, additional, and Sandström, Thomas, additional
Published: 2022
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45. A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes

Author: Abdel-Aziz, Mahmoud I., primary, Vijverberg, Susanne J.H., additional, Neerincx, Anne H., additional, Brinkman, Paul, additional, Wagener, Ariane H., additional, Riley, John H., additional, Sousa, Ana R., additional, Bates, Stewart, additional, Wagers, Scott S., additional, De Meulder, Bertrand, additional, Auffray, Charles, additional, Wheelock, Åsa M., additional, Bansal, Aruna T., additional, Caruso, Massimo, additional, Chanez, Pascal, additional, Uddin, Mohib, additional, Corfield, Julie, additional, Horvath, Ildiko, additional, Krug, Norbert, additional, Musial, Jacek, additional, Sun, Kai, additional, Shaw, Dominick E., additional, Sandström, Thomas, additional, Montuschi, Paolo, additional, Fowler, Stephen J., additional, Lutter, René, additional, Djukanovic, Ratko, additional, Howarth, Peter, additional, Skipp, Paul, additional, Sanak, Marek, additional, Adcock, Ian M., additional, Chung, Kian Fan, additional, Sterk, Peter J., additional, Kraneveld, Aletta D., additional, and Maitland-van der Zee, Anke H., additional
Published: 2021
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46. Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

Author: Sparreman Mikus, Maria, primary, Kolmert, Johan, additional, Andersson, Lars I., additional, Östling, Jörgen, additional, Knowles, Richard G., additional, Gómez, Cristina, additional, Ericsson, Magnus, additional, Thörngren, John-Olof, additional, Emami Khoonsari, Payam, additional, Dahlén, Barbro, additional, Kupczyk, Maciej, additional, De Meulder, Bertrand, additional, Auffray, Charles, additional, Bakke, Per S., additional, Beghe, Bianca, additional, Bel, Elisabeth H., additional, Caruso, Massimo, additional, Chanez, Pascal, additional, Chawes, Bo, additional, Fowler, Stephen J., additional, Gaga, Mina, additional, Geiser, Thomas, additional, Gjomarkaj, Mark, additional, Horváth, Ildikó, additional, Howarth, Peter H., additional, Johnston, Sebastian L., additional, Joos, Guy, additional, Krug, Norbert, additional, Montuschi, Paolo, additional, Musial, Jacek, additional, Niżankowska-Mogilnicka, Ewa, additional, Olsson, Henric K., additional, Papi, Alberto, additional, Rabe, Klaus F., additional, Sandström, Thomas, additional, Shaw, Dominick E., additional, Siafakas, Nikolaos M., additional, Uhlén, Mathias, additional, Riley, John H., additional, Bates, Stewart, additional, Middelveld, Roelinde J.M., additional, Wheelock, Craig E., additional, Chung, Kian Fan, additional, Adcock, Ian M., additional, Sterk, Peter J., additional, Djukanovic, Ratko, additional, Nilsson, Peter, additional, Dahlén, Sven-Erik, additional, and James, Anna, additional
Published: 2021
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47. Faculty Opinions recommendation of Harmonization of quality metrics and power calculation in multi-omic studies.

Author: Auffray, Charles, primary and De Meulder, Bertrand, additional
Published: 2021
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48. The Key Role of Patient Involvement in the Development of Core Outcome Sets in Prostate Cancer

Author: Beyer, Katharina, primary, MacLennan, Sara J., additional, Moris, Lisa, additional, Lardas, Michael, additional, Mastris, Ken, additional, Hooker, Gary, additional, Greene, Robert, additional, Briers, Erik, additional, Omar, Muhammad Imran, additional, Healey, Jemma, additional, Tripathee, Sheela, additional, Gandaglia, Giorgio, additional, Venderbos, Lionne D.F., additional, Smith, Emma J., additional, Bjorkqvist, Josefine, additional, Asiimwe, Alex, additional, Huber, Johannes, additional, Roobol, Monique J., additional, Zong, Jihong, additional, Bjartell, Anders, additional, N’Dow, James, additional, Briganti, Alberto, additional, MacLennan, Steven, additional, Van Hemelrijck, Mieke, additional, Smith, Emma Jane, additional, N'Dow, James, additional, Plass, Karin, additional, Ribal, Maria, additional, Mottet, Nicolas, additional, Shepherd, Robert, additional, Van den Broeck, Thomas, additional, Willemse, Peter-Paul, additional, Campi, Riccardo, additional, Gacci, Mauro, additional, Evans-Axelsson, LU Susan, additional, Crosti, Daniele, additional, Meoni, Massimiliano, additional, Garzonio, Roberto, additional, Bangma, Chris, additional, Roobol, Monique, additional, Remmers, Sebastiaan, additional, Tilki, Derya, additional, Auvinen, Anssi, additional, Murtola, Teemu, additional, Visakorpi, Tapio, additional, Talala, Kirsi, additional, Tammela, Teuvo, additional, Siltari, Aino, additional, Beyer, Katharina, additional, Lejeune, Stephane, additional, van Diggelen, Femke, additional, Byrne, Sophie, additional, Fialho, Luz, additional, Cardone, Antonella, additional, Gono, Paulina, additional, De Meulder, Bertrand, additional, Auffray, Charles, additional, Balaur, Irina-Afrodita, additional, Taibi, Nesrine, additional, Power, Shaun, additional, Kermani, Nazanin Zounemat, additional, van Bochove, Kees, additional, Cirillo, Elisa, additional, Moinat, Maxim, additional, Voss, Emma, additional, Horgan, Denis, additional, Fullwood, Louise, additional, Holtorf, Marc, additional, Lancet, Doron, additional, Bernstein, Gabi, additional, Omar, Imran, additional, MacLennan, Sara, additional, Wirth, Manfred, additional, Froehner, Michael, additional, Brenner, Beate, additional, Borkowetz, Angelika, additional, Thomas, Christian, additional, Horn, Friedemann, additional, Reiche, Kristin, additional, Kreuz, Markus, additional, Josefsson, Andreas, additional, Tandefelt, Delila Gasi, additional, Hugosson, Jonas, additional, Schalken, Jack, additional, Huisman, Henkjan, additional, Hofmarcher, Thomas, additional, Lindgren, Peter, additional, Andersson, Emelie, additional, Fridhammar, Adam, additional, Verholen, Frank, additional, Butler-Ransohoff, John-Edward, additional, Williamson, Todd, additional, Chandrawansa, Kumari, additional, Waldeck, Reg, additional, Molnar, Megan, additional, Bruno, Amanda, additional, Herrera, Ronald, additional, Nevedomskaya, Ekaterina, additional, Fatoba, Samuel, additional, Constantinovici, Niculae, additional, Mohamed, Ateesha, additional, Steinbeißer, Carl, additional, Kedhagae, Siddhanth, additional, Maass, Monika, additional, Torremante, Patrizia, additional, Voss, Marc Dietrich, additional, Devecseri, Zsuzsanna, additional, Abbott, Tom, additional, Kiran, Amit, additional, Dau, Chad, additional, Papineni, Kishore, additional, Wang-silvanto, Jing, additional, Hass, Steve, additional, Snijder, Robert, additional, Doyé, Verena, additional, Wang, Xuewei, additional, Garnham, Andy, additional, Lambrecht, Mark, additional, Wolfinger, Russ, additional, Rogiers, Stijn, additional, Servan, Angela, additional, Casariego, Joaquin, additional, Samir, Mohamed, additional, Pascoe, Katie, additional, Robinson, Paul, additional, Reich, Christian, additional, Ratwani, Shilpa, additional, Longden-Chapman, Elaine, additional, Burke, Danny, additional, Agapow, Paul, additional, Derkits, Sahra, additional, Licour, Muriel, additional, Ang, Michelle, additional, Payne, Sarah, additional, Yong, Alan, additional, Thompson, Lucy, additional, Le Mare, Sophia, additional, Bussmann, Michael, additional, Köhler, Inken, additional, Juckeland, Guido, additional, and Kotik, Daniel, additional
Published: 2021
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49. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Author: Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], 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, Groues, 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, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], 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, Groues, 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, and Schneider, Reinhard
Abstract: We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
Published: 2021

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

Author: Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, 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, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, 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, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, 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, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, 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, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, and Czauderna, Tobias
Abstract: We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
Published: 2021

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