Publications
2024
The genomic and transcriptomic landscape of metastastic urothelial cancer
Yohann Loriot, Maud Kamal, Laurene Syx, Remy Nicolle, Celia Dupain, Naoual Menssouri, Igor Duquesne, Pernelle Lavaud, Claudio Nicotra, Maud Ngocamus, Ludovic Lacroix, Lambros Tselikas, Gilles Crehange, Luc Friboulet, Zahra Castel-Ajgal, Yann Neuzillet, Edith Borcoman, Philippe Beuzeboc, Grégoire Marret, Tom Gutman, Jennifer Wong, Francois Radvanyi, Sylvain Dureau, Jean-Yves Scoazec, Nicolas Servant, Yves Allory, Benjamin Besse, Fabrice Andre, Christophe Le Tourneau, Christophe Massard, Ivan Bieche
Nature communications
2024 Oct 4
Sopa: a technology-invariant pipeline for analyses of image-based spatial omics
Quentin Blampey, Kevin Mulder, Margaux Gardet, Stergios Christodoulidis, Charles-Antoine Dutertre, Fabrice André, Florent Ginhoux, Paul-Henry Cournède
Nature communications
2024 Jun 4
Forget lung, breast or prostate cancer: why tumour naming needs to change
Fabrice André, Elie Rassy, Aurélien Marabelle, Stefan Michiels, Benjamin Besse
Nature
2024 Jan 31
Moving toward precision medicine to predict drug sensitivity in patients with metastatic breast cancer
M Bottosso, F Mosele, S Michiels, P-H Cournède, S Dogan, C Labaki, F André
ESMO open
2024 Mar
Moving to ultra-short therapy to cure patients with cancer: a solution for sustainable cancer care
J M Ribeiro, J Dixon-Douglas, F André
ESMO open
2024 Feb
2023
Moving toward precision oncology centers V2.0
S Dogan, P-H Cournède, E Solary, J-M Heard, M Aldea, T Conroy, C Robert, F André
Annals of oncology
2023 Dec
Genomic Profiling of Metastatic Castration-Resistant Prostate Cancer Samples Resistant to Androgen Receptor Pathway Inhibitors
Naoual Menssouri, Loïc Poiraudeau, Carole Helissey, Ludovic Bigot, Jonathan Sabio, Tony Ibrahim, Cédric Pobel, Claudio Nicotra, Maud Ngo-Camus, Ludovic Lacroix, Etienne Rouleau, Lambros Tselikas, Anne Chauchereau, Félix Blanc-Durand, Alice Bernard-Tessier, Anna Patrikidou, Natacha Naoun, Ronan Flippot, Emeline Colomba, Alina Fuerea, Laurence Albiges, Pernelle Lavaud, Paul van de Wiel, Eveline den Biezen, Yvonne Wesseling-Rozendaal, Santiago Ponce, Stefan Michiels, Christophe Massard, Daniel Gautheret, Fabrice Barlesi, Fabrice André, Benjamin Besse, Jean-Yves Scoazec, Luc Friboulet, Karim Fizazi, Yohann Loriot
Clinical cancer research
2023 Nov
Clinicopathological features and survival outcomes of luminal-like breast tumors with estrogen receptor loss at metastatic recurrence: A case-control study
Stefania Morganti, Antonio Marra, Sara Gandini, Liliana Ascione, Mariia Ivanova, Konstantinos Venetis, Elham Sajjadi, Paola Zagami, Federica Giugliano, Beatrice Taurelli Salimbeni, Pier Paolo Maria Berton Giachetti, Chiara Corti, Elisa De Camilli, Giuseppe Curigliano, Nicola Fusco, Carmen Criscitiello
European journal of cancer
2023 Dec
Blampey Q, Bercovici N, Dutertre CA, Pic I, Ribeiro JM, André F, Cournède PH.
A biology-driven deep generative model for cell-type annotation in cytometry
39.
Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F.
Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision?
ESMO Open. 2023 Sep 26;8(5):101642.
38.
Rosenquist R, Bernard E, Erkers T, Scott DW, Itzykson R, Rousselot P, Soulier J, Hutchings M, Östling P, Cavelier L, Fioretos T, Smedby KE.
Novel precision medicine approaches and treatment strategies in hematological malignanciesESMO expert consensus statements (ECS) on the definition, diagnosis, and management of HER2-low breast cancer
J Intern Med. 2023 Oct;294(4):413-436.
37.
Mosele F, Deluche E, Lusque A, Le Bescond L, Filleron T, Pradat Y, Ducoulombier A, Pistilli B, Bachelot T, Viret F, Levy C, Signolle N, Alfaro A, Tran DTN, Garberis IJ, Talbot H, Christodoulidis S, Vakalopoulou M, Droin N, Stourm A, Kobayashi M, Kakegawa T, Lacroix L, Saulnier P, Job B, Deloger M, Jimenez M, Mahier C, Baris V, Laplante P, Kannouche P, Marty V, Lacroix-Triki M, Diéras V, André F.
Trastuzumab deruxtecan in metastatic breast cancer with variable HER2 expression: the phase 2 DAISY trial
Nat Med. 2023 Aug;29(8):2110-2120. doi: 10.1038/s41591-023-02478-2. Epub 2023 Jul 24.
36.
Tarantino P, Viale G, Press MF, Hu X, Penault-Llorca F, Bardia A, Batistatou A, Burstein HJ, Carey LA, Cortes J, Denkert C, Diéras V, Jacot W, Koutras AK, Lebeau A, Loibl S, Modi S, Mosele MF, Provenzano E, Pruneri G, Reis-Filho JS, Rojo F, Salgado R, Schmid P, Schnitt SJ, Tolaney SM, Trapani D, Vincent-Salomon A, Wolff AC, Pentheroudakis G, André F, Curigliano G.
ESMO expert consensus statements (ECS) on the definition, diagnosis, and management of HER2-low breast cancer
Ann Oncol. 2023 Aug;34(8):645-659.
35.
Benkirane, Hakim; Pradat, Yoann; Michiels, Stefan; Cournède Paul-Henry.
CustOmics: A versatile deep-learning based strategy for multi-omics integration.
PLoS Comput Biol
Available online 2023 Mar 6
Abstract
The availability of patient cohorts with several types of omics data opens new perspectives for exploring the disease’s underlying biological processes and developing predictive models. It also comes with new challenges in computational biology in terms of integrating high-dimensional and heterogeneous data in a fashion that captures the interrelationships between multiple genes and their functions. Deep learning methods offer promising perspectives for integrating multi-omics data. In this paper, we review the existing integration strategies based on autoencoders and propose a new customizable one whose principle relies on a two-phase approach. In the first phase, we adapt the training to each data source independently before learning cross-modality interactions in the second phase. By taking into account each source’s singularity, we show that this approach succeeds at taking advantage of all the sources more efficiently than other strategies. Moreover, by adapting our architecture to the computation of Shapley additive explanations, our model can provide interpretable results in a multi-source setting. Using multiple omics sources from different TCGA cohorts, we demonstrate the performance of the proposed method for cancer on test cases for several tasks, such as the classification of tumor types and breast cancer subtypes, as well as survival outcome prediction. We show through our experiments the great performances of our architecture on seven different datasets with various sizes and provide some interpretations of the results obtained. Our code is available on (https://github.com/HakimBenkirane/CustOmics).
34.
Pradat, Yoann; Viot, Julien; Gunbin, Konstantin; Yurchenko, Andrey; Cerbone, Luigi; Deloger, Marc; Grisay, Guillaume; Verlingue, Loic; Scott, Véronique; Padioleau, Ismael; Panunzi, Leonardo; Michiels, Stefan; Hollebecque, Antoine; Jules-Clément, Gér^ome; Mezquita, Laura; Lainé, Antoine; Loriot, Yohann; Besse, Benjamin; Friboulet, Luc; André, Fabrice; Cournède, Paul-Henry; Gautheret, Daniel; Nikolaev, Sergey
Integrative pan-cancer genomic and transcriptomic analyses of refractory metastatic cancer
Cancer Discov.
Available online 2023 Mar 2
Abstract
Metastatic relapse after treatment is the leading cause of cancer mortality, and known resistance mechanisms are missing for most treatments administered to patients. To bridge this gap, we analyze a pan-cancer cohort (META-PRISM) of 1,031 refractory metastatic tumors profiled via whole-exome and transcriptome sequencing. META-PRISM tumors, particularly prostate, bladder, and pancreatic types, displayed the most transformed genomes compared to primary untreated tumors. Standard-of-care resistance biomarkers were identified only in lung and colon cancers – 9.6% of META-PRISM tumors, indicating that too few resistance mechanisms have received clinical validation. In contrast, we verified the enrichment of multiple investigational and hypothetical resistance mechanisms in treated compared to non-treated patients, thereby confirming their putative role in treatment resistance. Additionally, we demonstrated that molecular markers improve six-month survival prediction, particularly in patients with advanced breast cancer. Our analysis establishes the utility of META-PRISM cohort for investigating resistance mechanisms and performing predictive analyses in cancer.
33.
A. Bayle, L. Belcaid, M. Aldea, D. Vasseur, F. Peyraud, C. Nicotra, A. Geraud, M. Sakkal, L. Seknazi, L. Cerbone, F. Blanc-Durand, J. Hadoux, F. Mosele, M. Tagliamento, A. Bernard-Tessier, B. Verret, C. Smolenschi, R. Clodion, N. Auger, P. Martin Romano, A. Gazzah, M. Ngo Camus, J. Micol, O. Caron, A. Hollebecque, Y. Loriot, B. Besse, L. Lacroix, E. Rouleau, S. Ponce, J.C. Soria, F. Barlesi, F. Andre, A. Italiano,
Clinical utility of circulating tumor DNA sequencing with a large panel: a National Center for Precision Medicine (PRISM) study
Annals of Oncology
Available online 25 January 2023
32.
Guido Kroemer, Jennifer L. McQuade, Miriam Merad, Fabrice André, Laurence Zitvogel
Bodywide ecological interventions on cancer
Nat Med 29, 59–74 (2023).
2022
31.
Anne-Gaëlle Goubet; Leonardo Lordello; Carolina Alves Costa Silva; Isabelle Peguillet; Marianne Gazzano; Maxime Descartes Mbogning-Fonkou; Cassandra Thelemaque; Cédric Lebacle; Constance Thibault; François Audenet; Géraldine Pignot; Gwenaelle Gravis; Carole Helissey; Luca Campedel; Morgan Roupret; Evanguelos Xylinas; Idir Ouzaid; Agathe Dubuisson; Marine Mazzenga; Caroline Flament; Pierre Ly; Virginie Marty; Nicolas Signolle; Allan Sauvat; Thomas Sbarrato; Mounia Filahi; Caroline Davin; Gabriel Haddad; Jacques Bou Khalil; Camille Bleriot; François-Xavier Danlos; Garett Dunsmore; Kevin Mulder; Aymeric Silvin; Thibault Raoult; Baptiste Archambaud; Shaima Belhechmi; Ivo Gomperts Boneca; Nadège Cayet; Maryse Moya-Nilges; Adeline Mallet; Romain Daillere; Etienne Rouleau; Camelia Radulescu; Yves Allory; Jacques Fieschi; Mathieu Rouanne; Florent Ginhoux; Gwénaël Le Teuff; Lisa Derosa; Aurélien Marabelle; Jeroen Van Dorp; Nick Van Dijk; Michiel S. Van Der Heijden; Benjamin Besse; Fabrice Andre; Miriam Merad; Guido Kroemer; Jean-Yves Scoazec; Laurence Zitvogel; Yohann Loriot.
Escherichia coli-Specific CXCL13-Producing TFH Are Associated with Clinical
Efficacy of Neoadjuvant PD-1 Blockade against Muscle-Invasive Bladder Cancer.
Cancer discovery, 2022 Oct 5;12(10):2280-2307.
Andre, Fabrice; Filleron, Thomas; Kamal, Maud; Mosele, Fernanda; Arnedos, Monica; Dalenc, Florence; Sablin, Marie-Paule; Campone, Mario; Bonnefoi, Hervé; Lefeuvre-Plesse, Claudia; Jacot, William; Coussy, Florence; Ferrero, Jean-Marc; Emile, George; Mouret-Reynier, Marie-Ange; Thery, Jean-Christophe; Isambert, Nicolas; Mege, Alice; Barthelemy, Philippe; You, Benoit; Hajjaji, Nawale; Lacroix, Ludovic; Rouleau, Etienne; Tran-Dien, Alicia; Boyault, Sandrine; Attignon, Valery; Gestraud, Pierre; Servant, Nicolas; Tourneau, Christophe Le; Cherif, Linda Larbi; Soubeyran, Isabelle; Montemurro, Filippo; Morel, Alain; Lusque, Amelie; Jimenez, Marta; Jacquet, Alexandra; Gonçalves, Anthony; Bachelot, Thomas; Bieche, Ivan
Genomics to select treatment for patients with metastatic breast cancer
Nature, 2022, ISSN: 1476-4687.
Hermange, Gurvan; Rakotonirainy, Alicia; Bentriou, Mahmoud; Tisserand, Amandine; El-Khoury, Mira; Girodon, François; Marzac, Christophe; Vainchenker, William; Plo, Isabelle; Cournède, Paul-Henry
Inferring the initiation and development of myeloproliferative neoplasms
Proc Natl Acad Sci U S A, vol. 119, no. 37, p. e2120374119, 2022, ISSN: 1091-6490.
Bayle, A; Peyraud, F; Belcaid, L; Brunet, M; Aldea, M; Clodion, R; Dubos, P; Vasseur, D; Nicotra, C; Geraud, A; Sakkal, M; Cerbone, L; Blanc-Durand, F; Mosele, F; Romano, P Martin; Camus, M Ngo; Soubeyran, I; Khalifa, E; Alame, M; Blouin, L; Dinart, D; Bellera, C; Hollebecque, A; Ponce, S; Loriot, Y; Besse, B; Lacroix, Ludovic; Rouleau, E; Barlesi, F; Andre, F; Italiano, A
Liquid versus tissue biopsy for detecting actionable alterations according to ESCAT in patients with advanced cancer: A study from the French National Center for Precision Medicine (PRISM)
Annals of Oncology. Volume 33, Issue 12, December 2022, Pages 1328-1331
Le Bescond, Loic; Lerousseau, Marvin; Garberis, Ingrid; André, Fabrice; Christodoulidis, Stergios; Vakalopoulou, Maria; Talbot, Hugues
Unsupervised Nuclei Segmentation using Spatial Organization Priors Inproceedings
MICCAI 2022 – 25th International Conference on Medical Image Computing and Computer Assisted Intervention, Singapore, Singapore, 2022.
Trapani, D; Franzoi, M A; Burstein, H J; Carey, L A; Delaloge, S; Harbeck, N; Hayes, D F; Kalinsky, K; Pusztai, L; Regan, M M; Sestak, I; Spanic, T; Sparano, J; Jezdic, S; Cherny, N; Curigliano, G; Andre, F
Risk-adapted modulation through de-intensification of cancer treatments: an ESMO classification
Ann Oncol, vol. 33, no. 7, p. 702–712, 2022, ISSN: 1569-8041.
John, Ashley L St; Rathore, Abhay P S; Ginhoux, Florent
New perspectives on the origins and heterogeneity of mast cells
Nat Rev Immunol, 2022, ISSN: 1474-1741.
Mateo, Joaquin; Steuten, Lotte; Aftimos, Philippe; André, Fabrice; Davies, Mark; Garralda, Elena; Geissler, Jan; Husereau, Don; Martinez-Lopez, Iciar; Normanno, Nicola; Reis-Filho, Jorge S; Stefani, Stephen; Thomas, David M; Westphalen, C Benedikt; Voest, Emile
Delivering precision oncology to patients with cancer
Nat Med, vol. 28, no. 4, p. 658–665, 2022, ISSN: 1546-170X.
Meglio, Antonio Di; Havas, Julie; Soldato, Davide; Presti, Daniele; Martin, Elise; Pistilli, Barbara; Menvielle, Gwenn; Dumas, Agnes; Charles, Cecile; Everhard, Sibille; Martin, Anne-Laure; Coutant, Charles; Tarpin, Carole; Vanlemmens, Laurence; Levy, Christelle; Rigal, Olivier; Delaloge, Suzette; Lin, Nancy U; Ganz, Patricia A; Partridge, Ann H; André, Fabrice; Michiels, Stefan; Vaz-Luis, Ines
Development and Validation of a Predictive Model of Severe Fatigue After Breast Cancer Diagnosis: Toward a Personalized Framework in Survivorship Care
J Clin Oncol, vol. 40, no. 10, p. 1111–1123, 2022, ISSN: 1527-7755.
Meglio, Antonio Di; Havas, Julie; Gbenou, Arnauld S; Martin, Elise; El-Mouhebb, Mayssam; Pistilli, Barbara; Menvielle, Gwenn; Dumas, Agnes; Everhard, Sibille; Martin, Anne-Laure; Cottu, Paul H; Lerebours, Florence; Coutant, Charles; Lesur, Anne; Tredan, Olivier; Soulie, Patrick; Vanlemmens, Laurence; Joly, Florence; Delaloge, Suzette; Ganz, Patricia A; André, Fabrice; Partridge, Ann H; Jones, Lee W; Michiels, Stefan; Vaz-Luis, Ines
Dynamics of Long-Term Patient-Reported Quality of Life and Health Behaviors After Adjuvant Breast Cancer Chemotherapy
J Clin Oncol, p. JCO2100277, 2022, ISSN: 1527-7755.
Vaz-Luis, Ines; Meglio, Antonio Di; Havas, Julie; El-Mouhebb, Mayssam; Lapidari, Pietro; Presti, Daniele; Soldato, Davide; Pistilli, Barbara; Dumas, Agnes; Menvielle, Gwenn; Charles, Cecile; Everhard, Sibille; Martin, Anne-Laure; Cottu, Paul H; Lerebours, Florence; Coutant, Charles; Dauchy, Sarah; Delaloge, Suzette; Lin, Nancy U; Ganz, Patricia A; Partridge, Ann H; André, Fabrice; Michiels, Stefan
Long-Term Longitudinal Patterns of Patient-Reported Fatigue After Breast Cancer: A Group-Based Trajectory Analysis
J Clin Oncol, p. JCO2101958, 2022, ISSN: 1527-7755.
Middleton, G; Robbins, H; Andre, F; Swanton, C
A state-of-the-art review of stratified medicine in cancer: towards a future precision medicine strategy in cancer
Ann Oncol, vol. 33, no. 2, p. 143–157, 2022, ISSN: 1569-8041.
Chakravarty, Debyani; Johnson, Amber; Sklar, Jeffrey; Lindeman, Neal I; Moore, Kathleen; Ganesan, Shridar; Lovly, Christine M; Perlmutter, Jane; Gray, Stacy W; Hwang, Jimmy; Lieu, Christopher; André, Fabrice; Azad, Nilofer; Borad, Mitesh; Tafe, Laura; Messersmith, Hans; Robson, Mark; Meric-Bernstam, Funda
Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion
J Clin Oncol, vol. 40, no. 11, p. 1231–1258, 2022, ISSN: 1527-7755.
Chen, J; Facchinetti, F; Braye, F; Yurchenko, A A; Bigot, L; Ponce, S; Planchard, D; Gazzah, A; Nikolaev, S; Michiels, S; Vasseur, D; Lacroix, L; Tselikas, L; Nobre, C; Olaussen, K A; Andre, F; Scoazec, J Y; Barlesi, F; Soria, J C; Loriot, Y; Besse, B; Friboulet, L
Single-cell DNA-seq depicts clonal evolution of multiple driver alterations in osimertinib-resistant patients
Ann Oncol, vol. 33, no. 4, p. 434–444, 2022, ISSN: 1569-8041.
Zhang, Jingwei; Zhang, Xin; Ma, Ke; Gupta, Rajarsi; Saltz, Joel; Vakalopoulou, Maria; Samaras, Dimitris
Gigapixel Whole-Slide Images Classification Using Locally Supervised Learning
Medical Image Computing and Computer Assisted Intervention — MICCAI 2022, p. 192–201, Springer Nature Switzerland, Cham, 2022, ISBN: 978-3-031-16434-7.
Scalbert, Marin; Vakalopoulou, Maria; Couzinié-Devy, Florent
Test-Time Image-to-Image Translation Ensembling Improves Out-of-Distribution Generalization in Histopathology
Medical Image Computing and Computer Assisted Intervention — MICCAI 2022, p. 120–129, Springer Nature Switzerland, Cham, 2022, ISBN: 978-3-031-16434-7.
Derosa, Lisa; Routy, Bertrand; Thomas, Andrew Maltez; Iebba, Valerio; Zalcman, Gerard; Friard, Sylvie; Mazieres, Julien; Audigier-Valette, Clarisse; Moro-Sibilot, Denis; Goldwasser, François; Silva, Carolina Alves Costa; Terrisse, Safae; Bonvalet, Melodie; Scherpereel, Arnaud; Pegliasco, Hervé; Richard, Corentin; Ghiringhelli, François; Elkrief, Arielle; Desilets, Antoine; Blanc-Durand, Felix; Cumbo, Fabio; Blanco, Aitor; Boidot, Romain; Chevrier, Sandy; Daillère, Romain; Kroemer, Guido; Alla, Laurie; Pons, Nicolas; Chatelier, Emmanuelle Le; Galleron, Nathalie; Roume, Hugo; Dubuisson, Agathe; Bouchard, Nicole; Messaoudene, Meriem; Drubay, Damien; Deutsch, Eric; Barlesi, Fabrice; Planchard, David; Segata, Nicola; Martinez, Stéphanie; Zitvogel, Laurence; Soria, Jean-Charles; Besse, Benjamin
Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer
Nat Med, vol. 28, no. 2, p. 315–324, 2022, ISSN: 1546-170X.
2021
Lerousseau, Marvin; Vakalopoulou, Maria; Deutsch, Eric; Paragios, Nikos
SparseConvMIL: Sparse Convolutional Context-Aware Multiple Instance Learning for Whole Slide Image Classification
Proceedings of the MICCAI Workshop on Computational Pathology, p. 129–139, PMLR, 2021.
Chassagnon, Guillaume; Vakalopoulou, Maria; Battistella, Enzo; Christodoulidis, Stergios; Hoang-Thi, Trieu-Nghi; Dangeard, Severine; Deutsch, Eric; Andre, Fabrice; Guillo, Enora; Halm, Nara; Hajj, Stefany El; Bompard, Florian; Neveu, Sophie; Hani, Chahinez; Saab, Ines; Campredon, Aliénor; Koulakian, Hasmik; Bennani, Souhail; Freche, Gael; Barat, Maxime; Lombard, Aurelien; Fournier, Laure; Monnier, Hippolyte; Grand, Téodor; Gregory, Jules; Nguyen, Yann; Khalil, Antoine; Mahdjoub, Elyas; Brillet, Pierre-Yves; Ba, Stéphane Tran; Bousson, Valérie; Mekki, Ahmed; Carlier, Robert-Yves; Revel, Marie-Pierre; Paragios, Nikos
AI-driven quantification, staging and outcome prediction of COVID-19 pneumonia
Medical Image Analysis, vol. 67, p. 101860, 2021.
Mosca, Matthieu; Hermange, Gurvan; Tisserand, Amandine; Noble, Robert John; Marzac, Christophe; Marty, Caroline; Sueur, Cécile Le; Campario, Hugo; Vertenoeil, Gaëlle; El-Khoury, Mira; Catelain, Cyril; Rameau, Philippe; Gella, Cyril; Lenglet, Julien; Casadevall, Nicole; Favier, Remi; Solary, Eric; Cassinat, Bruno; Kiladjian, Jean-Jacques; Constantinescu, Stefan N; Pasquier, Florence; Hochberg, Michael E; Raslova, Hana; Villeval, Jean-Luc J -L; Girodon, François; Vainchenker, William; Cournède, Paul-Henry; Plo, Isabelle
Inferring the dynamic of mutated hematopoietic stem and progenitor cells induced by IFNα in myeloproliferative neoplasms
Blood, 2021, ISSN: 0006-4971.
Aldea, Mihaela; Andre, Fabrice; Marabelle, Aurelien; Dogan, Semih; Barlesi, Fabrice; Soria, Jean-Charles
Overcoming Resistance to Tumor-Targeted and Immune-Targeted Therapies
Cancer Discov, vol. 11, no. 4, p. 874–899, 2021, ISSN: 2159-8290.
Kuksin, Maria; Morel, Daphné; Aglave, Marine; Danlos, François-Xavier; Marabelle, Aurélien; Zinovyev, Andrei; Gautheret, Daniel; Verlingue, Loïc
Applications of single-cell and bulk RNA sequencing in onco-immunology
Eur J Cancer, vol. 149, p. 193–210, 2021, ISSN: 1879-0852.
Terrisse, Safae; Derosa, Lisa; Iebba, Valerio; Ghiringhelli, François; Vaz-Luis, Ines; Kroemer, Guido; Fidelle, Marine; Christodoulidis, Stergios; Segata, Nicola; Thomas, Andrew Maltez; Martin, Anne-Laure; Sirven, Aude; Everhard, Sibille; Aprahamian, Fanny; Nirmalathasan, Nitharsshini; Aarnoutse, Romy; Smidt, Marjolein; Ziemons, Janine; Caldas, Carlos; Loibl, Sibylle; Denkert, Carsten; Durand, Sylvere; Iglesias, Claudia; Pietrantonio, Filippo; Routy, Bertrand; André, Fabrice; Pasolli, Edoardo; Delaloge, Suzette; Zitvogel, Laurence
Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
Cell Death Differ, vol. 28, no. 9, p. 2778–2796, 2021, ISSN: 1476-5403.
Gennari, A; André, F; Barrios, C H; Cortés, J; de Azambuja, E; DeMichele, A; Dent, R; Fenlon, D; Gligorov, J; Hurvitz, S A; Im, S-A; Krug, D; Kunz, W G; Loi, S; Penault-Llorca, F; Ricke, J; Robson, M; Rugo, H S; Saura, C; Schmid, P; Singer, C F; Spanic, T; Tolaney, S M; Turner, N C; Curigliano, G; Loibl, S; Paluch-Shimon, S; and, N Harbeck
ESMO Clinical Practice Guideline for the diagnosis, staging and treatment of patients with metastatic breast cancer
Annals of Oncology, Volume 32, Issue 12, December 2021, Pages 1475-1495
Gennari, A; André, F; Barrios, C H; Cortés, J; de Azambuja, E; DeMichele, A; Dent, R; Fenlon, D; Gligorov, J; Hurvitz, S A; Im, S-A; Krug, D; Kunz, W G; Loi, S; Penault-Llorca, F; Ricke, J; Robson, M; Rugo, H S; Saura, C; Schmid, P; Singer, C F; Spanic, T; Tolaney, S M; Turner, N C; Curigliano, G; Loibl, S; Paluch-Shimon, S; and, N Harbeck
ESMO Clinical Practice Guideline for the diagnosis, staging and treatment of patients with metastatic breast cancer
Annals of Oncology, Volume 32, Issue 12, 2021, Pages 1475-1495, ISSN 0923-7534.
Lerousseau, Marvin; Classe, Marion; Battistella, Enzo; Estienne, Théo; Henry, Théophraste; Leroy, Amaury; Sun, Roger; Vakalopoulou, Maria; Scoazec, Jean-Yves; Deutsch, Eric; Paragios, Nikos
Weakly Supervised Pan-Cancer Segmentation Tool
Medical Image Computing and Computer Assisted Intervention — MICCAI 2021, p. 248–256, Springer International Publishing, Cham, 2021, ISBN: 978-3-030-87237-3.
2020
Watkins, Thomas B K; Lim, Emilia L; Petkovic, Marina; Elizalde, Sergi; Birkbak, Nicolai J; Wilson, Gareth A; Moore, David A; Gronroos, Eva; Rowan, Andrew; Dewhurst, Sally M; Demeulemeester, Jonas; Dentro, Stefan C; Horswell, Stuart; Au, Lewis; Haase, Kerstin; Escudero, Mickael; Rosenthal, Rachel; Bakir, Maise Al; Xu, Hang; Litchfield, Kevin; Lu, Wei Ting; Mourikis, Thanos P; Dietzen, Michelle; Spain, Lavinia; Cresswell, George D; Biswas, Dhruva; Lamy, Philippe; Nordentoft, Iver; Harbst, Katja; Castro-Giner, Francesc; Yates, Lucy R; Caramia, Franco; Jaulin, Fanny; Vicier, Cecile; Tomlinson, Ian P M; Brastianos, Priscilla K; Cho, Raymond J; Bastian, Boris C; Dyrskjot, Lars; Jonsson, Goran B; Savas, Peter; Loi, Sherene; Campbell, Peter J; Andre, Fabrice; Luscombe, Nicholas M; Steeghs, Neeltje; Tjan-Heijnen, Vivianne C G; Szallasi, Zoltan; Turajlic, Samra; Jamal-Hanjani, Mariam; Loo, Peter Van; Bakhoum, Samuel F; Schwarz, Roland F; McGranahan, Nicholas; Swanton, Charles.
Pervasive chromosomal instability and karyotype order in tumour evolution
Nature, vol. 587, no. 7832, p. 126+, 2020, ISSN: 0028-0836.
Silvin, Aymeric; Chapuis, Nicolas; Dunsmore, Garett; Goubet, Anne-Gaëlle; Dubuisson, Agathe; Derosa, Lisa; Almire, Carole; Hénon, Clémence; Kosmider, Olivier; Droin, Nathalie; Rameau, Philippe; Catelain, Cyril; Alfaro, Alexia; Dussiau, Charles; Friedrich, Chloé; Sourdeau, Elise; Marin, Nathalie; Szwebel, Tali-Anne; Cantin, Delphine; Mouthon, Luc; Borderie, Didier; Deloger, Marc; Bredel, Delphine; Mouraud, Severine; Drubay, Damien; Andrieu, Muriel; Lhonneur, Anne-Sophie; Saada, Véronique; Stoclin, Annabelle; Willekens, Christophe; Pommeret, Fanny; Griscelli, Frank; Ng, Lai Guan; Zhang, Zheng; Bost, Pierre; Amit, Ido; Barlesi, Fabrice; Marabelle, Aurélien; Pène, Frédéric; Gachot, Bertrand; André, Fabrice; Zitvogel, Laurence; Ginhoux, Florent; Fontenay, Michaela; Solary, Eric.
Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19
Cell, vol. 182, no. 6, p. 1401–1418.e18, 2020.
2.
Sahasrabudhe, Mihir; Christodoulidis, Stergios; Salgado, Roberto; Michiels, Stefan; Loi, Sherene; André, Fabrice; Paragios, Nikos; Vakalopoulou, Maria
Self-supervised Nuclei Segmentation in Histopathological Images Using Attention
MICCAI 2020, p. 393–402, Springer International Publishing, Cham, 2020, ISBN: 978-3-030-59722-1.
1.
Lerousseau, Marvin; Vakalopoulou, Maria; Classe, Marion; Adam, Julien; Battistella, Enzo; Carré, Alexandre; Estienne, Théo; Henry, Théophraste; Deutsch, Eric; Paragios, Nikos.
Weakly Supervised Multiple Instance Learning Histopathological Tumor Segmentation
MICCAI 2020, p. 470–479, Springer International Publishing, Cham, 2020, ISBN: 978-3-030-59722-1.