TREMSUCS-TCGA – an integrated workflow for the identification of biomarkers for treatment success

Authors: Balogh Gabor, Jorge Natasha, Dupain Célia, Kamal Maud, Servant Nicolas, Le Tourneau Christophe, Stadler Peter F., Bernhart Stephan H.

Source: Journal of Integrative Bioinformatics, Vol 21, Iss 4, Pp 993-8 (2024)

Subject Terms: tcga, scc, biomarker, precision medicine, differential expression, differentially methylated regions, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/95572e2bae4447ca90547ed0200ee842

Deciphering molecular relapse and intra-tumor heterogeneity in non-metastatic resectable head and neck squamous cell carcinoma using circulating tumor DNA

Authors: Marret, Grégoire ^a, Lamy, Constance ^a, Vacher, Sophie ^b, Cabel, Luc ^c, Séné, Mathieu ^b, Ahmanache, Ladidi ^b, Courtois, Laura ^b, El Beaino, Zakhia ^d, Klijanienko, Jerzy ^d, Martinat, Charlotte ^d, Servant, Nicolas ^e, Kamoun, Choumouss ^e, Halladjian, Maral ^a, Bronzini, Thierry ^f, Balsat, Cédric ^g, Laes, Jean-François ^g, Prévot, Aubray ^g, Sauvage, Sébastien ^g, Lienard, Maxime ^g, Martin, Emmanuel ^g, Genin, Bérengère ^g, Badois, Nathalie ^h, Lesnik, Maria ^h, Dubray-Vautrin, Antoine ^h, Choussy, Olivier ^h, Ghanem, Wahib ^h, Taouachi, Rabah ^h, Planchon, Julien Masliah ^b, Bièche, Ivan ^{b, 1}, Le Tourneau, Christophe ^{a, i, ⁎, 1}, Kamal, Maud ^{a, 1}

Source: In Oral Oncology January 2025 160

Intratumoral microbiome is driven by metastatic site and associated with immune histopathological parameters: An ancillary study of the SHIVA clinical trial

Authors: Hilmi, Marc, Kamal, Maud, Vacher, Sophie, Dupain, Célia, Ibadioune, Sabrina, Halladjian, Maral, Sablin, Marie Paule, Marret, Grégoire, Ajgal, Zahra Castel, Nijnikoff, Michèle, Salomon, Anne, El Beaino, Zakhia, Servant, Nicolas, Dureau, Sylvain, Sokol, Harry, Nicolle, Remy, Le Tourneau, Christophe, Bieche, Ivan, Neuzillet, Cindy

Source: European journal of cancer. 183:152-161

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190699234.0x000001&indx=1&recIds=ETOCvdc_100190699234.0x000001

Molecular underpinnings and environmental drivers of loss of heterozygosity in Drosophila intestinal stem cells

Authors: Al Zouabi, Lara, Stefanutti, Marine, Roumeliotis, Spyridon, Le Meur, Gwenn, Boumard, Benjamin, Riddiford, Nick, Rubanova, Natalia, Bohec, Mylène, Gervais, Louis, Servant, Nicolas, Bardin, Allison J.

Source: In Cell Reports 26 December 2023 42(12)

Chromatin state transitions in the Drosophila intestinal lineage identify principles of cell-type specification

Authors: Josserand, Manon, Rubanova, Natalia, Stefanutti, Marine, Roumeliotis, Spyridon, Espenel, Marion, Marshall, Owen J., Servant, Nicolas, Gervais, Louis, Bardin, Allison J.

Source: In Developmental Cell 18 December 2023 58(24):3048-3063

Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

Authors: Gentien, David, Saberi-Ansari, Elnaz, Servant, Nicolas, Jolly, Ariane, de la Grange, Pierre, Némati, Fariba, Liot, Géraldine, Saule, Simon, Teissandier, Aurélie, Bourc’his, Deborah, Girard, Elodie, Wong, Jennifer, Masliah-Planchon, Julien, Narmanli, Erkan, Liu, Yuanlong, Torun, Emma, Goulancourt, Rebecca, Rodrigues, Manuel, Gaudé, Laure Villoing, Reyes, Cécile, Bazire, Matéo, Chenegros, Thomas, Henry, Emilie, Rapinat, Audrey, Bohec, Mylene, Baulande, Sylvain, M’kacher, Radhia, Jeandidier, Eric, Nicolas, André, Ciriello, Giovanni, Margueron, Raphael, Decaudin, Didier, Cassoux, Nathalie, Piperno-Neumann, Sophie, Stern, Marc-Henri, Gibcus, Johan Harmen, Dekker, Job, Heard, Edith, Roman-Roman, Sergio, Waterfall, Joshua J.

Source: In Cell Reports 26 September 2023 42(9)

Robust Seriation and Applications to Cancer Genomics

Authors: Recanati, Antoine, Servant, Nicolas, Vert, Jean-Philippe, d'Aspremont, Alexandre

Subject Terms: Mathematics - Optimization and Control

Access URL: http://arxiv.org/abs/1806.00664

Human papilloma virus integration sites and genomic signatures in head and neck squamous cell carcinoma

Authors: Mainguené, Juliette, Vacher, Sophie, Kamal, Maud, Hamza, Abderaouf, Masliah‐Planchon, Julien, Baulande, Sylvain, Ibadioune, Sabrina, Borcoman, Edith, Cacheux, Wulfran, Calugaru, Valentin, Courtois, Laura, Crozes, Carole, Deloger, Marc, Girard, Elodie, Delord, Jean‐Pierre, Dubray‐Vautrin, Antoine, Larbi Chérif, Linda, Dupain, Celia, Jeannot, Emmanuelle, Klijanienko, Jerzy, Lameiras, Sonia, Lecerf, Charlotte, Modesto, Anouchka, Nicolas, Alain, Rouzier, Roman, Saada‐Bouzid, Esma, Saintigny, Pierre, Sudaka, Anne, Servant, Nicolas, Le Tourneau, Christophe, Bièche, Ivan

Source: Molecular oncology. 16(16):3001-3016

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100158343725.0x000001&indx=1&recIds=ETOCvdc_100158343725.0x000001

Bioinformatics Methods for ChIP-seq Histone Analysis

Authors: Servant, Nicolas

Source: Methods in molecular biology. 2529:267-296

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629710691&indx=1&recIds=ETOCRN629710691

Methylation, Gene Expression, and Risk Genotypes at the TERT‐CLPTM1L Locus in Cervical Cancer.

Authors: Ramachandran, Dhanya, Mao, Qianqian, Liao, Dandan, Kamal, Maud, Schürmann, Peter, Eisenblätter, Rieke, Geffers, Robert, Balint, Balazs, Lecompte, Lolita, Servant, Nicolas, Chérif, Linda Larbi, Lamy, Constance, Baulande, Sylvain, Legoix, Patricia, Le Tourneau, Christophe, Latouche, Aurélien, Hillemanns, Peter, Scholl, Suzy, Dörk, Thilo

Source: Molecular Carcinogenesis; Jan2025, Vol. 64 Issue 1, p14-24, 11p

SMARCA4‐deficient rhabdoid tumours show intermediate molecular features between SMARCB1‐deficient rhabdoid tumours and small cell carcinomas of the ovary, hypercalcaemic type

Authors: Andrianteranagna, Mamy, Cyrta, Joanna, Masliah‐Planchon, Julien, Nemes, Karolina, Corsia, Alice, Leruste, Amaury, Holdhof, Dörthe, Kordes, Uwe, Orbach, Daniel, Corradini, Nadège, Entz‐Werle, Natacha, Pierron, Gaëlle, Castex, Marie‐Pierre, Brouchet, Anne, Weingertner, Noëlle, Ranchère, Dominique, Fréneaux, Paul, Delattre, Olivier, Bush, Jonathan, Leary, Alexandra, Frühwald, Michael C, Schüller, Ulrich, Servant, Nicolas, Bourdeaut, Franck

Source: Journal of pathology. 255(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125633005.0x000001&indx=1&recIds=ETOCvdc_100125633005.0x000001

Bioinformatic Analysis of Single-Cell Hi-C Data from Early Mouse Embryo

Authors: Collombet, Samuel, Pérez-Rico, Yuvia A., Ancelin, Katia, Servant, Nicolas, Heard, Edith

Source: Methods in molecular biology. 2214:295-316

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624905610&indx=1&recIds=ETOCRN624905610

Copy number alterations in metastatic and early breast tumours: prognostic and acquired biomarkers of resistance to CDK4/6 inhibitors.

Authors: Sablin, Marie-Paule, Gestraud, Pierre, Jonas, Sarah Flora, Lamy, Constance, Lacroix-Triki, Magali, Bachelot, Thomas, Filleron, Thomas, Lacroix, Ludovic, Tran-Dien, Alicia, Jézéquel, Pascal, Mauduit, Marjorie, Barros Monteiro, Janice, Jimenez, Marta, Michiels, Stefan, Attignon, Valery, Soubeyran, Isabelle, Driouch, Keltouma, Servant, Nicolas, Le Tourneau, Christophe, Kamal, Maud

Source: British Journal of Cancer; Oct2024, Vol. 131 Issue 6, p1060-1067, 8p

Post‐transcriptional polyadenylation site cleavage maintains 3′‐end processing upon DNA damage

Authors: Sfaxi, Rym, Biswas, Biswendu, Boldina, Galina, Cadix, Mandy, Servant, Nicolas, Chen, Huimin, Larson, Daniel R, Dutertre, Martin, Robert, Caroline, Vagner, Stéphan

Source: EMBO journal. 42(7)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100194162160.0x000001&indx=1&recIds=ETOCvdc_100194162160.0x000001

Improving breast cancer sensitivity to paclitaxel by increasing aneuploidy

Authors: Rodrigues-Ferreira, Sylvie, Nehlig, Anne, Moindjie, Hadia, Monchecourt, Clarisse, Seiler, Cynthia, Marangoni, Elisabetta, Chateau-Joubert, Sophie, Dujaric, Marie-Eglantine, Servant, Nicolas, Asselain, Bernard, deCremoux, Patricia, Lacroix-Triki, Magali, Arnedos, Monica, Pierga, Jean-Yves, André, Fabrice, Nahmias, Clara

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Nov . 116(47), 23691-23697.

Access URL: https://www.jstor.org/stable/26861956

A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

Authors: Galupa, Rafael, Nora, Elphège Pierre, Worsley-Hunt, Rebecca, Picard, Christel, Gard, Chris, van Bemmel, Joke Gerarda, Servant, Nicolas, Zhan, Yinxiu, El Marjou, Fatima, Johanneau, Colin, Diabangouaya, Patricia, Le Saux, Agnès, Lameiras, Sonia, Pipoli da Fonseca, Juliana, Loos, Friedemann, Gribnau, Joost, Baulande, Sylvain, Ohler, Uwe, Giorgetti, Luca, Heard, Edith

Source: In Molecular Cell 16 January 2020 77(2):352-367

Clinical and genetic landscape of treatment naive cervical cancer: Alterations in PIK3CA and in epigenetic modulators associated with sub-optimal outcome

Authors: Scholl, Suzy, Popovic, Marina, de la Rochefordiere, Anne, Girard, Elodie, Dureau, Sylvain, Mandic, Aljosa, Koprivsek, Katarina, Samet, Nina, Craina, Marius, Margan, Madalin, Samuels, Sanne, Zijlmans, Henry, Kenter, Gemma, Hillemanns, Peter, Dema, Sorin, Dema, Alis, Malenkovic, Goran, Djuran, Branislav, Floquet, Anne, Garbay, Delphine, Guyon, Frédéric, Colombo, Pierre Emmanuel, Fabbro, Michel, Kerr, Christine, Ngo, Charlotte, Lecuru, Fabrice, Campo, Eleonor Rivin del, Coutant, Charles, Marchal, Frédéric, Mesgouez-Nebout, Nathalie, Fourchotte, Virginie, Feron, Jean Guillaume, Morice, Philippe, Deutsch, Eric, Wimberger, Pauline, Classe, Jean-Marc, Gleeson, Noreen, von der Leyen, Heiko, Minsat, Mathieu, Dubot, Coraline, Gestraud, Pierre, Kereszt, Attila, Nagy, Istvan, Balint, Balazs, Berns, Els, Jordanova, Ekaterina, Saint-Jorre, Nicolas de, Savignoni, Alexia, Servant, Nicolas, Hupe, Philippe, de Koning, Leanne, Fumoleau, Pierre, Rouzier, Roman, Kamal, Maud

Source: In EBioMedicine May 2019 43:253-260

EZH1/2 function mostly within canonical PRC2 and exhibit proliferation-dependent redundancy that shapes mutational signatures in cancer

Authors: Wassef, Michel, Luscan, Armelle, Aflaki, Setareh, Zielinski, Dina, Jansen, Pascal W. T. C., Baymaz, H. Irem, Battistella, Aude, Kersouani, Carole, Servant, Nicolas, Wallace, Margaret R., Romero, Pierre, Kosmider, Olivier, Just, Pierre-Alexandre, Hivelin, Mikaël, Jacques, Sébastien, Vincent-Salomon, Anne, Vermeulen, Michiel, Vidaud, Michel, Pasmant, Eric, Margueron, Raphaël

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Mar . 116(13), 6075-6080.

Access URL: https://www.jstor.org/stable/26696667

Metastatic renal cell carcinoma with occult primary: a multicenter prospective cohort.

Authors: Jacquin, Nicolas, Flippot, Ronan, Masliah-Planchon, Julien, Grisay, Guillaume, Brillet, Riwan, Dupain, Célia, Kamal, Maud, Guillou, Isabelle, Gruel, Nadège, Servant, Nicolas, Gestraud, Pierre, Wong, Jennifer, Cockenpot, Vincent, Goncalves, Andreia, Selves, Janick, Blons, Hélène, Rouleau, Etienne, Delattre, Olivier, Gervais, Claire, Le Tourneau, Christophe

Source: NPJ Precision Oncology; 7/19/2024, Vol. 8 Issue 1, p1-6, 6p

Subject Terms: TREATMENT effectiveness, CANCER of unknown primary origin, RENAL cell carcinoma, OCCULTISM, METASTASIS

BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation

Authors: Campagne, Antoine, Lee, Ming-Kang, Zielinski, Dina, Michaud, Audrey, Corre, Stéphanie, Dingli, Florent, Chen, Hong, Shahidian, Lara, Vassilev, Ivaylo, Servant, Nicolas, Loew, Damarys, Pasmant, Eric, Postel-Vinay, Sophie, Wassef, Michel, Margueron, Raphaël

Source: Nature communications. 10(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100111627058.0x000001&indx=1&recIds=ETOCvdc_100111627058.0x000001