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210 results on '"Fernandez-Cuesta, Lynnette"'

1. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery

Author

Blázquez-Encinas, Ricardo, García-Vioque, Víctor, Caro-Cuenca, Teresa, Moreno-Montilla, María Trinidad, Mangili, Federica, Alors-Pérez, Emilia, Ventura, Sebastian, Herrera-Martínez, Aura D., Moreno-Casado, Paula, Calzado, Marco A., Salvatierra, Ángel, Gálvez-Moreno, María A., Fernandez-Cuesta, Lynnette, Foll, Matthieu, Luque, Raúl M., Alcala, Nicolas, Pedraza-Arevalo, Sergio, Ibáñez-Costa, Alejandro, and Castaño, Justo P.

Published
2023
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2. Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

Author

Mangiante, Lise, Alcala, Nicolas, Sexton-Oates, Alexandra, Di Genova, Alex, Gonzalez-Perez, Abel, Khandekar, Azhar, Bergstrom, Erik N., Kim, Jaehee, Liu, Xiran, Blazquez-Encinas, Ricardo, Giacobi, Colin, Le Stang, Nolwenn, Boyault, Sandrine, Cuenin, Cyrille, Tabone-Eglinger, Severine, Damiola, Francesca, Voegele, Catherine, Ardin, Maude, Michallet, Marie-Cecile, Soudade, Lorraine, Delhomme, Tiffany M., Poret, Arnaud, Brevet, Marie, Copin, Marie-Christine, Giusiano-Courcambeck, Sophie, Damotte, Diane, Girard, Cecile, Hofman, Veronique, Hofman, Paul, Mouroux, Jérôme, Cohen, Charlotte, Lacomme, Stephanie, Mazieres, Julien, de Montpreville, Vincent Thomas, Perrin, Corinne, Planchard, Gaetane, Rousseau, Nathalie, Rouquette, Isabelle, Sagan, Christine, Scherpereel, Arnaud, Thivolet, Francoise, Vignaud, Jean-Michel, Jean, Didier, Ilg, Anabelle Gilg Soit, Olaso, Robert, Meyer, Vincent, Boland-Auge, Anne, Deleuze, Jean-Francois, Altmuller, Janine, Nuernberg, Peter, Ibáñez-Costa, Alejandro, Castaño, Justo P., Lantuejoul, Sylvie, Ghantous, Akram, Maussion, Charles, Courtiol, Pierre, Hernandez-Vargas, Hector, Caux, Christophe, Girard, Nicolas, Lopez-Bigas, Nuria, Alexandrov, Ludmil B., Galateau-Salle, Françoise, Foll, Matthieu, and Fernandez-Cuesta, Lynnette

Published
2023
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3. Detection of acquired TERT amplification in addition to predisposing p53 and Rb pathways alterations in EGFR-mutant lung adenocarcinomas transformed into small-cell lung cancers

Author

Mc Leer, Anne, Foll, Matthieu, Brevet, Marie, Antoine, Martine, Novello, Silvia, Mondet, Julie, Cadranel, Jacques, Girard, Nicolas, Giaj Levra, Matteo, Demontrond, Pierre, Audigier-Valette, Clarisse, Letouzé, Eric, Lantuéjoul, Sylvie, Fernandez-Cuesta, Lynnette, and Moro-Sibilot, Denis

Published
2022
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4. Clinical management of typical and atypical carcinoids/neuroendocrine tumors in ENETS centres of excellence (CoE): Survey from the ENETS lung NET task force.

Author

Koumarianou, Anna, Filosso, Pier Luigi, Bodei, Lisa, Castano, Justo P., Fernandez‐Cuesta, Lynnette, Deroose, Christophe M., Foll, Matthieu, Dromain, Clarisse, Reed, Nicholas Simon, Caplin, Martyn, Capdevila, Jaume, Falkerby, Jenny, Faggiano, Antongiulio, Frilling, Andrea, Grande, Enrique, Hicks, Rodney J., Kasajima, Atsuko, Kos‐Kudla, Beata, Krishna, B. A., and Lim, Eric

Subjects
NEUROENDOCRINE tumors, MEDICAL personnel, NEUROENDOCRINE cells, TASK forces, LUNGS, CARCINOID
Abstract

Lung carcinoid tumours are neuroendocrine neoplasms originating from the bronchopulmonary tract's neuroendocrine cells, accounting for only 1%–3% of all lung cancers but 30% of all neuroendocrine tumours. The incidence of lung carcinoids, both typical and atypical, has been increasing over the years due to improved diagnostic methods and increased awareness among clinicians and pathologists. The most recent WHO classification includes a subgroup of lung carcinoids with atypical morphology and higher mitotic count and/or Ki67 labelling index. Despite appropriate surgery, the 5‐year survival rate for atypical carcinoids barely exceeds 50%–70%. The role of adjuvant therapy in lung carcinoids is not well‐defined, and clinical decisions are generally based on the presence of high‐risk features. Long‐term follow‐up is essential to monitor for recurrence, although the optimal follow‐up protocol remains unclear. To address the lack of consensus in clinical management decisions, the European Neuroendocrine Tumor Society (ENETS) initiated a survey among 20 expert centres. The survey identified varied opinions on approaches to imaging, surgery, use of adjuvant therapy, and follow‐up protocols. Notably, the absence of dedicated multidisciplinary lung neuroendocrine tumour boards in some centres was evident. Experts agreed on the need for a prospective adjuvant trial in high‐risk patients, emphasizing the feasibility of such a study. In conclusion, the study highlights the need for a more uniform adoption of existing guidelines in the management of lung carcinoid tumours and emphasizes the importance of international collaboration to advance research and patient care. Close collaboration between healthcare providers and patients is vital for effective long‐term surveillance and management of these rare tumours. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.

Author

George, Julie, Walter, Vonn, Peifer, Martin, Alexandrov, Ludmil B, Seidel, Danila, Leenders, Frauke, Maas, Lukas, Müller, Christian, Dahmen, Ilona, Delhomme, Tiffany M, Ardin, Maude, Leblay, Noemie, Byrnes, Graham, Sun, Ruping, De Reynies, Aurélien, McLeer-Florin, Anne, Bosco, Graziella, Malchers, Florian, Menon, Roopika, Altmüller, Janine, Becker, Christian, Nürnberg, Peter, Achter, Viktor, Lang, Ulrich, Schneider, Peter M, Bogus, Magdalena, Soloway, Matthew G, Wilkerson, Matthew D, Cun, Yupeng, McKay, James D, Moro-Sibilot, Denis, Brambilla, Christian G, Lantuejoul, Sylvie, Lemaitre, Nicolas, Soltermann, Alex, Weder, Walter, Tischler, Verena, Brustugun, Odd Terje, Lund-Iversen, Marius, Helland, Åslaug, Solberg, Steinar, Ansén, Sascha, Wright, Gavin, Solomon, Benjamin, Roz, Luca, Pastorino, Ugo, Petersen, Iver, Clement, Joachim H, Sänger, Jörg, Wolf, Jürgen, Vingron, Martin, Zander, Thomas, Perner, Sven, Travis, William D, Haas, Stefan A, Olivier, Magali, Foll, Matthieu, Büttner, Reinhard, Hayes, David Neil, Brambilla, Elisabeth, Fernandez-Cuesta, Lynnette, and Thomas, Roman K

Subjects
Humans, Neuroendocrine Tumors, Carcinoma, Neuroendocrine, Carcinoma, Non-Small-Cell Lung, Lung Neoplasms, Immunohistochemistry, In Situ Hybridization, Fluorescence, DNA Mutational Analysis, Genomics, Small Cell Lung Carcinoma, High-Throughput Nucleotide Sequencing, In Vitro Techniques, Carcinoma, Neuroendocrine, Non-Small-Cell Lung, In Situ Hybridization, Fluorescence
Abstract

Pulmonary large-cell neuroendocrine carcinomas (LCNECs) have similarities with other lung cancers, but their precise relationship has remained unclear. Here we perform a comprehensive genomic (n = 60) and transcriptomic (n = 69) analysis of 75 LCNECs and identify two molecular subgroups: "type I LCNECs" with bi-allelic TP53 and STK11/KEAP1 alterations (37%), and "type II LCNECs" enriched for bi-allelic inactivation of TP53 and RB1 (42%). Despite sharing genomic alterations with adenocarcinomas and squamous cell carcinomas, no transcriptional relationship was found; instead LCNECs form distinct transcriptional subgroups with closest similarity to SCLC. While type I LCNECs and SCLCs exhibit a neuroendocrine profile with ASCL1high/DLL3high/NOTCHlow, type II LCNECs bear TP53 and RB1 alterations and differ from most SCLC tumors with reduced neuroendocrine markers, a pattern of ASCL1low/DLL3low/NOTCHhigh, and an upregulation of immune-related pathways. In conclusion, LCNECs comprise two molecularly defined subgroups, and distinguishing them from SCLC may allow stratified targeted treatment of high-grade neuroendocrine lung tumors.

Published
2018

7. Comprehensive Molecular and Pathologic Evaluation of Transitional Mesothelioma Assisted by Deep Learning Approach: A Multi-Institutional Study of the International Mesothelioma Panel from the MESOPATH Reference Center

Author

Galateau Salle, Francoise, Le Stang, Nolwenn, Tirode, Franck, Courtiol, Pierre, Nicholson, Andrew G., Tsao, Ming-Sound, Tazelaar, Henry D., Churg, Andrew, Dacic, Sanja, Roggli, Victor, Pissaloux, Daniel, Maussion, Charles, Moarii, Matahi, Beasley, Mary Beth, Begueret, Hugues, Chapel, David B., Copin, Marie Christine, Gibbs, Allen R., Klebe, Sonja, Lantuejoul, Sylvie, Nabeshima, Kazuki, Vignaud, Jean-Michel, Attanoos, Richard, Brcic, Luka, Capron, Frederique, Chirieac, Lucian R., Damiola, Francesca, Sequeiros, Ruth, Cazes, Aurélie, Damotte, Diane, Foulet, Armelle, Giusiano-Courcambeck, Sophie, Hiroshima, Kenzo, Hofman, Veronique, Husain, Aliya N., Kerr, Keith, Marchevsky, Alberto, Paindavoine, Severine, Picquenot, Jean Michel, Rouquette, Isabelle, Sagan, Christine, Sauter, Jennifer, Thivolet, Francoise, Brevet, Marie, Rouvier, Philippe, Travis, William D., Planchard, Gaetane, Weynand, Birgit, Clozel, Thomas, Wainrib, Gilles, Fernandez-Cuesta, Lynnette, Pairon, Jean-Claude, Rusch, Valerie, and Girard, Nicolas

Published
2020
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8. EURACAN/IASLC Proposals for Updating the Histologic Classification of Pleural Mesothelioma: Towards a More Multidisciplinary Approach

Author

Nicholson, Andrew G., Sauter, Jennifer L., Nowak, Anna K., Kindler, Hedy L., Gill, Ritu R., Remy-Jardin, Martine, Armato, Samuel G., III, Fernandez-Cuesta, Lynnette, Bueno, Raphael, Alcala, Nicolas, Foll, Matthieu, Pass, Harvey, Attanoos, Richard, Baas, Paul, Beasley, Mary Beth, Brcic, Luka, Butnor, Kelly J., Chirieac, Lucian R., Churg, Andrew, Courtiol, Pierre, Dacic, Sanja, De Perrot, Marc, Frauenfelder, Thomas, Gibbs, Allen, Hirsch, Fred R., Hiroshima, Kenzo, Husain, Aliya, Klebe, Sonja, Lantuejoul, Sylvie, Moreira, Andre, Opitz, Isabelle, Perol, Maurice, Roden, Anja, Roggli, Victor, Scherpereel, Arnaud, Tirode, Frank, Tazelaar, Henry, Travis, William D., Tsao, Ming-Sound, van Schil, Paul, Vignaud, Jean Michel, Weynand, Birgit, Lang-Lazdunski, Loic, Cree, Ian, Rusch, Valerie W., Girard, Nicolas, and Galateau-Salle, Francoise

Published
2020
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10. A common classification framework for neuroendocrine neoplasms: an International Agency for Research on Cancer (IARC) and World Health Organization (WHO) expert consensus proposal

Author

Rindi, Guido, Klimstra, David S., Abedi-Ardekani, Behnoush, Asa, Sylvia L., Bosman, Frederik T., Brambilla, Elisabeth, Busam, Klaus J., de Krijger, Ronald R., Dietel, Manfred, El-Naggar, Adel K., Fernandez-Cuesta, Lynnette, Klöppel, Günter, McCluggage, W.Glenn, Moch, Holger, Ohgaki, Hiroko, Rakha, Emad A., Reed, Nicholas S., Rous, Brian A., Sasano, Hironobu, Scarpa, Aldo, Scoazec, Jean-Yves, Travis, William D., Tallini, Giovanni, Trouillas, Jacqueline, van Krieken, J.Han, and Cree, Ian A.

Published
2018
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12. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery

Author

Blázquez-Encinas, Ricardo, primary, García-Vioque, Víctor, additional, Caro-Cuenca, Teresa, additional, Moreno-Montilla, María Trinidad, additional, Mangili, Federica, additional, Alors-Pérez, Emilia, additional, Ventura, Sebastian, additional, Herrera-Martínez, Aura D., additional, Moreno-Casado, Paula, additional, Calzado, Marco A., additional, Salvatierra, Ángel, additional, Gálvez-Moreno, María A., additional, Fernandez-Cuesta, Lynnette, additional, Foll, Matthieu, additional, Luque, Raúl M., additional, Alcala, Nicolas, additional, Pedraza-Arevalo, Sergio, additional, Ibáñez-Costa, Alejandro, additional, and Castaño, Justo P, additional

Published
2023
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15. Data from CD74–NRG1 Fusions in Lung Adenocarcinoma

Author

Fernandez-Cuesta, Lynnette, primary, Plenker, Dennis, primary, Osada, Hirotaka, primary, Sun, Ruping, primary, Menon, Roopika, primary, Leenders, Frauke, primary, Ortiz-Cuaran, Sandra, primary, Peifer, Martin, primary, Bos, Marc, primary, Daßler, Juliane, primary, Malchers, Florian, primary, Schöttle, Jakob, primary, Vogel, Wenzel, primary, Dahmen, Ilona, primary, Koker, Mirjam, primary, Ullrich, Roland T., primary, Wright, Gavin M., primary, Russell, Prudence A., primary, Wainer, Zoe, primary, Solomon, Benjamin, primary, Brambilla, Elisabeth, primary, Nagy-Mignotte, Hélène, primary, Moro-Sibilot, Denis, primary, Brambilla, Christian G., primary, Lantuejoul, Sylvie, primary, Altmüller, Janine, primary, Becker, Christian, primary, Nürnberg, Peter, primary, Heuckmann, Johannes M., primary, Stoelben, Erich, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Sänger, Jörg, primary, Muscarella, Lucia A., primary, la Torre, Annamaria, primary, Fazio, Vito M., primary, Lahortiga, Idoya, primary, Perera, Timothy, primary, Ogata, Souichi, primary, Parade, Marc, primary, Brehmer, Dirk, primary, Vingron, Martin, primary, Heukamp, Lukas C., primary, Buettner, Reinhard, primary, Zander, Thomas, primary, Wolf, Jürgen, primary, Perner, Sven, primary, Ansén, Sascha, primary, Haas, Stefan A., primary, Yatabe, Yasushi, primary, and Thomas, Roman K., primary

Published
2023
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16. Data from Cell-Autonomous and Non–Cell-Autonomous Mechanisms of Transformation by Amplified FGFR1 in Lung Cancer

Author

Malchers, Florian, primary, Dietlein, Felix, primary, Schöttle, Jakob, primary, Lu, Xin, primary, Nogova, Lucia, primary, Albus, Kerstin, primary, Fernandez-Cuesta, Lynnette, primary, Heuckmann, Johannes M., primary, Gautschi, Oliver, primary, Diebold, Joachim, primary, Plenker, Dennis, primary, Gardizi, Masyar, primary, Scheffler, Matthias, primary, Bos, Marc, primary, Seidel, Danila, primary, Leenders, Frauke, primary, Richters, André, primary, Peifer, Martin, primary, Florin, Alexandra, primary, Mainkar, Prathama S., primary, Karre, Nagaraju, primary, Chandrasekhar, Srivari, primary, George, Julie, primary, Silling, Steffi, primary, Rauh, Daniel, primary, Zander, Thomas, primary, Ullrich, Roland T., primary, Reinhardt, H. Christian, primary, Ringeisen, Francois, primary, Büttner, Reinhard, primary, Heukamp, Lukas C., primary, Wolf, Jürgen, primary, and Thomas, Roman K., primary

Published
2023
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17. Supplementary Tables from CD74–NRG1 Fusions in Lung Adenocarcinoma

Author

Fernandez-Cuesta, Lynnette, primary, Plenker, Dennis, primary, Osada, Hirotaka, primary, Sun, Ruping, primary, Menon, Roopika, primary, Leenders, Frauke, primary, Ortiz-Cuaran, Sandra, primary, Peifer, Martin, primary, Bos, Marc, primary, Daßler, Juliane, primary, Malchers, Florian, primary, Schöttle, Jakob, primary, Vogel, Wenzel, primary, Dahmen, Ilona, primary, Koker, Mirjam, primary, Ullrich, Roland T., primary, Wright, Gavin M., primary, Russell, Prudence A., primary, Wainer, Zoe, primary, Solomon, Benjamin, primary, Brambilla, Elisabeth, primary, Nagy-Mignotte, Hélène, primary, Moro-Sibilot, Denis, primary, Brambilla, Christian G., primary, Lantuejoul, Sylvie, primary, Altmüller, Janine, primary, Becker, Christian, primary, Nürnberg, Peter, primary, Heuckmann, Johannes M., primary, Stoelben, Erich, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Sänger, Jörg, primary, Muscarella, Lucia A., primary, la Torre, Annamaria, primary, Fazio, Vito M., primary, Lahortiga, Idoya, primary, Perera, Timothy, primary, Ogata, Souichi, primary, Parade, Marc, primary, Brehmer, Dirk, primary, Vingron, Martin, primary, Heukamp, Lukas C., primary, Buettner, Reinhard, primary, Zander, Thomas, primary, Wolf, Jürgen, primary, Perner, Sven, primary, Ansén, Sascha, primary, Haas, Stefan A., primary, Yatabe, Yasushi, primary, and Thomas, Roman K., primary

Published
2023
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18. Supplementary Methods and Legends from Cell-Autonomous and Non–Cell-Autonomous Mechanisms of Transformation by Amplified FGFR1 in Lung Cancer

Author

Malchers, Florian, primary, Dietlein, Felix, primary, Schöttle, Jakob, primary, Lu, Xin, primary, Nogova, Lucia, primary, Albus, Kerstin, primary, Fernandez-Cuesta, Lynnette, primary, Heuckmann, Johannes M., primary, Gautschi, Oliver, primary, Diebold, Joachim, primary, Plenker, Dennis, primary, Gardizi, Masyar, primary, Scheffler, Matthias, primary, Bos, Marc, primary, Seidel, Danila, primary, Leenders, Frauke, primary, Richters, André, primary, Peifer, Martin, primary, Florin, Alexandra, primary, Mainkar, Prathama S., primary, Karre, Nagaraju, primary, Chandrasekhar, Srivari, primary, George, Julie, primary, Silling, Steffi, primary, Rauh, Daniel, primary, Zander, Thomas, primary, Ullrich, Roland T., primary, Reinhardt, H. Christian, primary, Ringeisen, Francois, primary, Büttner, Reinhard, primary, Heukamp, Lukas C., primary, Wolf, Jürgen, primary, and Thomas, Roman K., primary

Published
2023
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19. Supplementary Figures S1-S14 from Cell-Autonomous and Non–Cell-Autonomous Mechanisms of Transformation by Amplified FGFR1 in Lung Cancer

Author

Malchers, Florian, primary, Dietlein, Felix, primary, Schöttle, Jakob, primary, Lu, Xin, primary, Nogova, Lucia, primary, Albus, Kerstin, primary, Fernandez-Cuesta, Lynnette, primary, Heuckmann, Johannes M., primary, Gautschi, Oliver, primary, Diebold, Joachim, primary, Plenker, Dennis, primary, Gardizi, Masyar, primary, Scheffler, Matthias, primary, Bos, Marc, primary, Seidel, Danila, primary, Leenders, Frauke, primary, Richters, André, primary, Peifer, Martin, primary, Florin, Alexandra, primary, Mainkar, Prathama S., primary, Karre, Nagaraju, primary, Chandrasekhar, Srivari, primary, George, Julie, primary, Silling, Steffi, primary, Rauh, Daniel, primary, Zander, Thomas, primary, Ullrich, Roland T., primary, Reinhardt, H. Christian, primary, Ringeisen, Francois, primary, Büttner, Reinhard, primary, Heukamp, Lukas C., primary, Wolf, Jürgen, primary, and Thomas, Roman K., primary

Published
2023
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20. Supplementary Figures from CD74–NRG1 Fusions in Lung Adenocarcinoma

Author

Fernandez-Cuesta, Lynnette, primary, Plenker, Dennis, primary, Osada, Hirotaka, primary, Sun, Ruping, primary, Menon, Roopika, primary, Leenders, Frauke, primary, Ortiz-Cuaran, Sandra, primary, Peifer, Martin, primary, Bos, Marc, primary, Daßler, Juliane, primary, Malchers, Florian, primary, Schöttle, Jakob, primary, Vogel, Wenzel, primary, Dahmen, Ilona, primary, Koker, Mirjam, primary, Ullrich, Roland T., primary, Wright, Gavin M., primary, Russell, Prudence A., primary, Wainer, Zoe, primary, Solomon, Benjamin, primary, Brambilla, Elisabeth, primary, Nagy-Mignotte, Hélène, primary, Moro-Sibilot, Denis, primary, Brambilla, Christian G., primary, Lantuejoul, Sylvie, primary, Altmüller, Janine, primary, Becker, Christian, primary, Nürnberg, Peter, primary, Heuckmann, Johannes M., primary, Stoelben, Erich, primary, Petersen, Iver, primary, Clement, Joachim H., primary, Sänger, Jörg, primary, Muscarella, Lucia A., primary, la Torre, Annamaria, primary, Fazio, Vito M., primary, Lahortiga, Idoya, primary, Perera, Timothy, primary, Ogata, Souichi, primary, Parade, Marc, primary, Brehmer, Dirk, primary, Vingron, Martin, primary, Heukamp, Lukas C., primary, Buettner, Reinhard, primary, Zander, Thomas, primary, Wolf, Jürgen, primary, Perner, Sven, primary, Ansén, Sascha, primary, Haas, Stefan A., primary, Yatabe, Yasushi, primary, and Thomas, Roman K., primary

Published
2023
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21. BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas

Author

Leblay, Noémie, Leprêtre, Frédéric, Le Stang, Nolwenn, Gautier-Stein, Amandine, Villeneuve, Laurent, Isaac, Sylvie, Maillet, Denis, Galateau-Sallé, Françoise, Villenet, Céline, Sebda, Shéhérazade, Goracci, Alexandra, Byrnes, Graham, McKay, James D, Figeac, Martin, Glehen, Olivier, Gilly, François-Noël, Foll, Matthieu, Fernandez-Cuesta, Lynnette, and Brevet, Marie

Published
2017
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22. Supplementary Figure 3 from Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors

Author

Ortiz-Cuaran, Sandra, primary, Scheffler, Matthias, primary, Plenker, Dennis, primary, Dahmen, llona, primary, Scheel, Andreas H., primary, Fernandez-Cuesta, Lynnette, primary, Meder, Lydia, primary, Lovly, Christine M., primary, Persigehl, Thorsten, primary, Merkelbach-Bruse, Sabine, primary, Bos, Marc, primary, Michels, Sebastian, primary, Fischer, Rieke, primary, Albus, Kerstin, primary, König, Katharina, primary, Schildhaus, Hans-Ulrich, primary, Fassunke, Jana, primary, Ihle, Michaela A., primary, Pasternack, Helen, primary, Heydt, Carina, primary, Becker, Christian, primary, Altmüller, Janine, primary, Ji, Hongbin, primary, Müller, Christian, primary, Florin, Alexandra, primary, Heuckmann, Johannes M., primary, Nuernberg, Peter, primary, Ansén, Sascha, primary, Heukamp, Lukas C., primary, Berg, Johannes, primary, Pao, William, primary, Peifer, Martin, primary, Buettner, Reinhard, primary, Wolf, Jürgen, primary, Thomas, Roman K., primary, and Sos, Martin L., primary

Published
2023
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23. Figure S1 from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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24. Supplementary Figure 2 from Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors

Author

Ortiz-Cuaran, Sandra, primary, Scheffler, Matthias, primary, Plenker, Dennis, primary, Dahmen, llona, primary, Scheel, Andreas H., primary, Fernandez-Cuesta, Lynnette, primary, Meder, Lydia, primary, Lovly, Christine M., primary, Persigehl, Thorsten, primary, Merkelbach-Bruse, Sabine, primary, Bos, Marc, primary, Michels, Sebastian, primary, Fischer, Rieke, primary, Albus, Kerstin, primary, König, Katharina, primary, Schildhaus, Hans-Ulrich, primary, Fassunke, Jana, primary, Ihle, Michaela A., primary, Pasternack, Helen, primary, Heydt, Carina, primary, Becker, Christian, primary, Altmüller, Janine, primary, Ji, Hongbin, primary, Müller, Christian, primary, Florin, Alexandra, primary, Heuckmann, Johannes M., primary, Nuernberg, Peter, primary, Ansén, Sascha, primary, Heukamp, Lukas C., primary, Berg, Johannes, primary, Pao, William, primary, Peifer, Martin, primary, Buettner, Reinhard, primary, Wolf, Jürgen, primary, Thomas, Roman K., primary, and Sos, Martin L., primary

Published
2023
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25. Supplementary Data from Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors

Author

Ortiz-Cuaran, Sandra, primary, Scheffler, Matthias, primary, Plenker, Dennis, primary, Dahmen, llona, primary, Scheel, Andreas H., primary, Fernandez-Cuesta, Lynnette, primary, Meder, Lydia, primary, Lovly, Christine M., primary, Persigehl, Thorsten, primary, Merkelbach-Bruse, Sabine, primary, Bos, Marc, primary, Michels, Sebastian, primary, Fischer, Rieke, primary, Albus, Kerstin, primary, König, Katharina, primary, Schildhaus, Hans-Ulrich, primary, Fassunke, Jana, primary, Ihle, Michaela A., primary, Pasternack, Helen, primary, Heydt, Carina, primary, Becker, Christian, primary, Altmüller, Janine, primary, Ji, Hongbin, primary, Müller, Christian, primary, Florin, Alexandra, primary, Heuckmann, Johannes M., primary, Nuernberg, Peter, primary, Ansén, Sascha, primary, Heukamp, Lukas C., primary, Berg, Johannes, primary, Pao, William, primary, Peifer, Martin, primary, Buettner, Reinhard, primary, Wolf, Jürgen, primary, Thomas, Roman K., primary, and Sos, Martin L., primary

Published
2023
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26. Table S1 from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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27. Supplementary data file from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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28. Supplemental legend from Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome

Author

Derks, Jules L., primary, Leblay, Noémie, primary, Thunnissen, Erik, primary, van Suylen, Robert Jan, primary, den Bakker, Michael, primary, Groen, Harry J.M., primary, Smit, Egbert F., primary, Damhuis, Ronald, primary, van den Broek, Esther C., primary, Charbrier, Amélie, primary, Foll, Matthieu, primary, McKay, James D., primary, Fernandez-Cuesta, Lynnette, primary, Speel, Ernst-Jan M., primary, and Dingemans, Anne-Marie C., primary

Published
2023
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29. Supplementary Figure 4 from Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors

Author

Ortiz-Cuaran, Sandra, primary, Scheffler, Matthias, primary, Plenker, Dennis, primary, Dahmen, llona, primary, Scheel, Andreas H., primary, Fernandez-Cuesta, Lynnette, primary, Meder, Lydia, primary, Lovly, Christine M., primary, Persigehl, Thorsten, primary, Merkelbach-Bruse, Sabine, primary, Bos, Marc, primary, Michels, Sebastian, primary, Fischer, Rieke, primary, Albus, Kerstin, primary, König, Katharina, primary, Schildhaus, Hans-Ulrich, primary, Fassunke, Jana, primary, Ihle, Michaela A., primary, Pasternack, Helen, primary, Heydt, Carina, primary, Becker, Christian, primary, Altmüller, Janine, primary, Ji, Hongbin, primary, Müller, Christian, primary, Florin, Alexandra, primary, Heuckmann, Johannes M., primary, Nuernberg, Peter, primary, Ansén, Sascha, primary, Heukamp, Lukas C., primary, Berg, Johannes, primary, Pao, William, primary, Peifer, Martin, primary, Buettner, Reinhard, primary, Wolf, Jürgen, primary, Thomas, Roman K., primary, and Sos, Martin L., primary

Published
2023
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34. Abstract 3744: Differential Orthopedia Homeobox (OTP) expression in pulmonary carcinoids is associated with changes in DNA methylation

Author

Moonen, Laura, primary, Mangiante, Lise, additional, Leunissen, Daphne J., additional, Lap, Lisa M., additional, Gabriel, Aurelie, additional, Hillen, Lisa M., additional, Roemen, Guido M., additional, Koch, Alexander, additional, van Engeland, Manon, additional, Dingemans, Anne-Marie C., additional, Foll, Matthieu, additional, Alcala, Nicolas, additional, Fernandez-Cuesta, Lynnette, additional, Derks, Jules L., additional, and Speel, Ernst-Jan M., additional

Published
2022
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35. A molecular phenotypic map of malignant pleural mesothelioma.

Author

Di Genova, Alex, Mangiante, Lise, Sexton-Oates, Alexandra, Voegele, Catherine, Fernandez-Cuesta, Lynnette, Alcala, Nicolas, and Foll, Matthieu

Subjects
GENE mapping, MESOTHELIOMA, WHOLE genome sequencing, INDIVIDUALIZED medicine, MULTIOMICS, QUALITY control, NUCLEOTIDE sequencing
Abstract

Background Malignant pleural mesothelioma (MPM) is a rare understudied cancer associated with exposure to asbestos. So far, MPM patients have benefited marginally from the genomics medicine revolution due to the limited size or breadth of existing molecular studies. In the context of the MESOMICS project, we have performed the most comprehensive molecular characterization of MPM to date, with the underlying dataset made of the largest whole-genome sequencing series yet reported, together with transcriptome sequencing and methylation arrays for 120 MPM patients. Results We first provide comprehensive quality controls for all samples, of both raw and processed data. Due to the difficulty in collecting specimens from such rare tumors, a part of the cohort does not include matched normal material. We provide a detailed analysis of data processing of these tumor-only samples, showing that all somatic alteration calls match very stringent criteria of precision and recall. Finally, integrating our data with previously published multiomic MPM datasets (n = 374 in total), we provide an extensive molecular phenotype map of MPM based on the multitask theory. The generated map can be interactively explored and interrogated on the UCSC TumorMap portal (https://tumormap.ucsc.edu/?p=RCG%5fMESOMICS/MPM%5fArchetypes). Conclusions This new high-quality MPM multiomics dataset, together with the state-of-art bioinformatics and interactive visualization tools we provide, will support the development of precision medicine in MPM that is particularly challenging to implement in rare cancers due to limited molecular studies. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Lung cancers with acquired resistance to EGFR inhibitors occasionally harbor BRAF gene mutations but lack mutations in KRAS, NRAS, or MEK1

Author

Ohashi, Kadoaki, Sequist, Lecia V., Arcila, Maria E., Moran, Teresa, Chmielecki, Juliann, Lin, Ya-Lun, Pan, Yumei, Wang, Lu, de Stanchina, Elisa, Shien, Kazuhiko, Aoe, Keisuke, Toyooka, Shinichi, Kiura, Katsuyuki, Fernandez-Cuesta, Lynnette, Fidias, Panos, Yang, James Chih-Hsin, Miller, Vincent A., Riely, Gregory J., Kris, Mark G., Engelman, Jeffrey A., Vnencak-Jones, Cindy L., Dias-Santagata, Dora, Ladanyi, Marc, and Pao, William

Published
2012

37. Differential Orthopedia Homeobox expression in pulmonary carcinoids is associated with changes in DNA methylation

Author

Moonen, Laura, primary, Mangiante, Lise, additional, Leunissen, Daphne J. G., additional, Lap, Lisa M. V., additional, Gabriel, Aurelie, additional, Hillen, Lisa M., additional, Roemen, Guido M., additional, Koch, Alexander, additional, Engeland, Manon, additional, Dingemans, Anne‐Marie C., additional, Foll, Matthieu, additional, Alcala, Nicolas, additional, Fernandez‐Cuesta, Lynnette, additional, Derks, Jules L., additional, and Speel, Ernst‐Jan M., additional

Published
2022
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38. Disentangling heterogeneity of Malignant Pleural Mesothelioma through deep integrative omics analyses

Author

Mangiante, Lise, primary, Alcala, Nicolas, additional, Di Genova, Alex, additional, Sexton-Oates, Alexandra, additional, Gonzalez-Perez, Abel, additional, Khandekar, Azhar, additional, Bergstrom, Erik N., additional, Kim, Jaehee, additional, Giacobi, Colin, additional, Le Stang, Nolwenn, additional, Boyault, Sandrine, additional, Cuenin, Cyrille, additional, Tabone-Eglinger, Severine, additional, Damiola, Francesca, additional, Voegele, Catherine, additional, Ardin, Maude, additional, Michallet, Marie-Cecile, additional, Soudade, Lorraine, additional, Delhomme, Tiffany M., additional, Poret, Arnaud, additional, Brevet, Marie, additional, Copin, Marie-Christine, additional, Giusiano-Courcambeck, Sophie, additional, Damotte, Diane, additional, Girard, Cecile, additional, Hofman, Veronique, additional, Hofman, Paul, additional, Mouroux, Jérôme, additional, Lacomme, Stephanie, additional, Mazieres, Julien, additional, de Montpreville, Vincent Thomas, additional, Perrin, Corinne, additional, Planchard, Gaetane, additional, Rouquette, Isabelle, additional, Sagan, Christine, additional, Scherpereel, Arnaud, additional, Thivolet, Francoise, additional, Vignaud, Jean-Michel, additional, Jean, Didier, additional, Gilg Soit Ilg, Anabelle, additional, Olaso, Robert, additional, Meyer, Vincent, additional, Boland, Anne, additional, Deleuze, Jean-Francois, additional, Altmuller, Janine, additional, Nuernberg, Peter, additional, Lantuejoul, Sylvie, additional, Ghantous, Akram, additional, Maussion, Charles, additional, Courtiol, Pierre, additional, Hernandez-Vargas, Hector, additional, Caux, Christophe, additional, Girard, Nicolas, additional, Lopez-Bigas, Nuria, additional, Alexandrov, Ludmil B., additional, Salle, Françoise Galateau, additional, Foll, Matthieu, additional, and Fernandez-Cuesta, Lynnette, additional

Published
2021
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39. Altered splicing machinery as a source of biomarkers in lung neuroendocrine neoplasms

Author

Blazquez-Encinas, Ricardo, primary, Caro, Maria T., additional, Garcia-Vioque, Victor, additional, Pedraza-Arevalo, Sergio, additional, Alors-Perez, Emilia, additional, Moreno-Montilla, M. Trinidad, additional, Herrera-Martinez, Aura D., additional, Sanchez-Sanchez, Rafael, additional, Salvatierra, A., additional, Serrano-Blanch, Raquel, additional, Gahete, Manuel D., additional, Foll, Matthieu, additional, Luque, Raul M, additional, Fernandez-Cuesta, Lynnette, additional, Ibanez, Costa Alejandro, additional, and Castano, Justo P., additional

Published
2021
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40. A molecular map of lung neuroendocrine neoplasms

Author

Gabriel, Aurélie A G, primary, Mathian, Emilie, additional, Mangiante, Lise, additional, Voegele, Catherine, additional, Cahais, Vincent, additional, Ghantous, Akram, additional, McKay, James D, additional, Alcala, Nicolas, additional, Fernandez-Cuesta, Lynnette, additional, and Foll, Matthieu, additional

Published
2020
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43. Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data

Author

Delhomme, Tiffany M, primary, Avogbe, Patrice H, additional, Gabriel, Aurélie A G, additional, Alcala, Nicolas, additional, Leblay, Noemie, additional, Voegele, Catherine, additional, Vallée, Maxime, additional, Chopard, Priscilia, additional, Chabrier, Amélie, additional, Abedi-Ardekani, Behnoush, additional, Gaborieau, Valérie, additional, Holcatova, Ivana, additional, Janout, Vladimir, additional, Foretová, Lenka, additional, Milosavljevic, Sasa, additional, Zaridze, David, additional, Mukeriya, Anush, additional, Brambilla, Elisabeth, additional, Brennan, Paul, additional, Scelo, Ghislaine, additional, Fernandez-Cuesta, Lynnette, additional, Byrnes, Graham, additional, Calvez-Kelm, Florence L, additional, McKay, James D, additional, and Foll, Matthieu, additional

Published
2020
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45. Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions

Author

Alcala, Nicolas, primary, Mangiante, Lise, additional, Le-Stang, Nolwenn, additional, Gustafson, Corinne E., additional, Boyault, Sandrine, additional, Damiola, Francesca, additional, Alcala, Karine, additional, Brevet, Marie, additional, Thivolet-Bejui, Françoise, additional, Blanc-Fournier, Cécile, additional, Le Rochais, Jean-Philippe, additional, Planchard, Gaëtane, additional, Rousseau, Nathalie, additional, Damotte, Diane, additional, Pairon, Jean Claude, additional, Copin, Marie Christine, additional, Scherpereel, Arnaud, additional, Wasielewski, Eric, additional, Wicquart, Laurence, additional, Lacomme, Stéphanie, additional, Vignaud, Jean-Michel, additional, Ancelin, Gaspard, additional, Girard, Cécile, additional, Sagan, Christine, additional, Bonnetaud, Christelle, additional, Hofman, Véronique, additional, Hofman, Paul, additional, Mouroux, Jérôme, additional, Thomas de Montpreville, Vincent, additional, Clermont-Taranchon, Estelle, additional, Mazieres, Julien, additional, Rouquette, Isabelle, additional, Begueret, Hugues, additional, Blay, Jean-Yves, additional, Lantuejoul, Sylvie, additional, Bueno, Raphael, additional, Caux, Christophe, additional, Girard, Nicolas, additional, McKay, James D., additional, Foll, Matthieu, additional, Galateau-Salle, Françoise, additional, and Fernandez-Cuesta, Lynnette, additional

Published
2019
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46. Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data

Author

Delhomme, Tiffany M., primary, Avogbe, Patrice H., additional, Gabriel, Aurélie, additional, Alcala, Nicolas, additional, Leblay, Noemie, additional, Voegele, Catherine, additional, Vallée, Maxime, additional, Chopard, Priscilia, additional, Chabrier, Amélie, additional, Abedi-Ardekani, Behnoush, additional, Gaborieau, Valérie, additional, Holcatova, Ivana, additional, Janout, Vladimir, additional, Foretová, Lenka, additional, Milosavljevic, Sasa, additional, Zaridze, David, additional, Mukeriya, Anush, additional, Brambilla, Elisabeth, additional, Brennan, Paul, additional, Scelo, Ghislaine, additional, Fernandez-Cuesta, Lynnette, additional, Byrnes, Graham, additional, Le Calvez-Kelm, Florence, additional, McKay, James D., additional, and Foll, Matthieu, additional

Published
2019
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48. Multi-omics comparative analyses of pulmonary typical carcinoids, atypical carcinoids, and large-cell neuroendocrine carcinoma

Author

Leblay, Noemie, Alcala, Nicolas, Marin, David Hervas, Delhomme, Tiffany M., Giffon, Theo, Ghantous, Akram, Chabrier, Amelie, Cuenin, Cyrille, Altmueller, Janine, Durand, Geoffroy, Voegele, Catherine, Lorimier, Philippe, Toffart, Anne-Claire, Derks, Jules, Brustugun, Odd Terje, Clement, Joachim H., Saenger, Joerg, Field, John K., Soltermann, Alex, Wright, Gavin M., Roz, Luca, Muscarella, Lucia Anna, Graziano, Paolo, Herceg, Zdenko, Speel, Ernst-Jan, Nuernberg, Peter, McKay, James, Girard, Nicolas, Lantuejoul, Sylvie, Sandoval, Juan, Brambilla, Elisabeth, Foll, Matthieu, Fernandez-Cuesta, Lynnette, Leblay, Noemie, Alcala, Nicolas, Marin, David Hervas, Delhomme, Tiffany M., Giffon, Theo, Ghantous, Akram, Chabrier, Amelie, Cuenin, Cyrille, Altmueller, Janine, Durand, Geoffroy, Voegele, Catherine, Lorimier, Philippe, Toffart, Anne-Claire, Derks, Jules, Brustugun, Odd Terje, Clement, Joachim H., Saenger, Joerg, Field, John K., Soltermann, Alex, Wright, Gavin M., Roz, Luca, Muscarella, Lucia Anna, Graziano, Paolo, Herceg, Zdenko, Speel, Ernst-Jan, Nuernberg, Peter, McKay, James, Girard, Nicolas, Lantuejoul, Sylvie, Sandoval, Juan, Brambilla, Elisabeth, Foll, Matthieu, and Fernandez-Cuesta, Lynnette

Published
2018

49. A Case-Control Study to Test the Use of ctDNA in the Early Detection of SCLC Reveals TP53 Mutations in Non-Cancer Controls

Author

Fernandez-Cuesta, Lynnette Perdomo, Sandra Avogbe, Patrice and Leblay, Noemie Delhomme, Tiffany Gaborieau, Valerie and Abedi-Ardekani, Behnoush Chanudet, Estelle Olivier, Magali and Zaridze, David Mukeria, Anush Vilensky, Marta Holcatova, Ivana Polesel, Jerry Simonato, Lorenzo Canova, Cristina and Lagiou, Pagona Brambilla, Christian Brambilla, Elisabeth and Byrnes, Graham Scelo, Ghislaine Le Calvez-Kelm, Florence Fo, Matthieu Mckay, James Brennan, Paul

Published
2017

50. Abstract 5358: Multi-omics comparative analyses of pulmonary typical carcinoids, atypical carcinoids, and large-cell neuroendocrine carcinoma

Author

Leblay, Noémie, primary, Alcala, Nicolas, additional, Marin, David Hervás, additional, Delhomme, Tiffany M., additional, Giffon, Théo, additional, Ghantous, Akram, additional, Chabrier, Amélie, additional, Cuenin, Cyrille, additional, Altmueller, Janine, additional, Durand, Geoffroy, additional, Voegele, Catherine, additional, Lorimier, Philippe, additional, Toffart, Anne-Claire, additional, Derks, Jules, additional, Brustugun, Odd Terje, additional, Clement, Joachim H., additional, Saenger, Joerg, additional, Field, John K., additional, Soltermann, Alex, additional, Wright, Gavin M., additional, Roz, Luca, additional, Muscarella, Lucia Anna, additional, Graziano, Paolo, additional, Herceg, Zdenko, additional, Speel, Ernst-Jan, additional, Nuernberg, Peter, additional, McKay, James, additional, Girard, Nicolas, additional, Lantuejoul, Sylvie, additional, Sandoval, Juan, additional, Brambilla, Elisabeth, additional, Foll, Matthieu, additional, and Fernandez-Cuesta, Lynnette, additional

Published
2018
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