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Kueng, Nicholas; Sidler, Daniel; Banz, Vanessa; Largiadèr, Carlo R; Ng, Charlotte K Y; Amstutz, Ursula (2023). Investigation of Different Library Preparation and Tissue of Origin Deconvolution Methods for Urine and Plasma cfDNA Methylome Analysis. Diagnostics, 13(15) MDPI 10.3390/diagnostics13152505
Amante, Romain J; Jehanno, Charly; De Silva, Duvini; Coissieux, Marie-May; Ackerknecht, Markus; Romanet, Vincent; Sethi, Atul; Hamelin, Baptiste; Preca, Bogdan-Tiberius; Piscuoglio, Salvatore; Ng, Charlotte K Y; Mohseni, Morvarid; Bentires-Alj, Mohamed (2023). PI3K inhibition circumvents resistance to SHP2 blockade in metastatic triple-negative breast cancer. Journal of mammary gland biology and neoplasia, 28(1), p. 13. Springer 10.1007/s10911-023-09539-9
Gallon, John; Rodríguez-Calero, Antonio; Benjak, Andrej; Akhoundova, Dilara; Maletti, Sina; Amstutz, Ursula; Hewer, Ekkehard; Genitsch, Vera; Fleischmann, Achim; Rushing, Elisabeth J; Grobholz, Rainer; Fischer, Ingeborg; Jochum, Wolfram; Cathomas, Gieri; Osunkoya, Adeboye O; Bubendorf, Lukas; Moch, Holger; Thalmann, George; Feng, Felix Y; Gillessen, Silke; ... (2023). DNA methylation landscapes of prostate cancer brain metastasis are shaped by early driver genetic alterations. Cancer research, 83(8), pp. 1203-1213. American Association for Cancer Research AACR 10.1158/0008-5472.CAN-22-2236
Kashani, Elham; Schnidrig, Désirée; Hashemi Gheinani, Ali; Ninck, Martina Selina; Zens, Philipp; Maragkou, Theoni; Baumgartner, Ulrich; Schucht, Philippe; Rätsch, Gunnar; Rubin, Mark A; Berezowska, Sabina; Ng, Charlotte K Y; Vassella, Erik (2023). Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. Neuro-Oncology, 25(4), pp. 662-673. Oxford University Press 10.1093/neuonc/noac220
Schnidrig, Desiree; Garofoli, Andrea; Benjak, Andrej; Rätsch, Gunnar; Rubin, Mark A; Piscuoglio, Salvatore; Ng, Charlotte K Y (2023). PipeIT2: A tumor-only somatic variant calling workflow for molecular diagnostic ion torrent sequencing data. Genomics, 115(2), p. 110587. Elsevier 10.1016/j.ygeno.2023.110587
Srivatsa, Sumana; Montazeri, Hesam; Bianco, Gaia; Coto-Llerena, Mairene; Marinucci, Mattia; Ng, Charlotte K Y; Piscuoglio, Salvatore; Beerenwinkel, Niko (2022). Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nature communications, 13(1), p. 7748. Nature Publishing Group 10.1038/s41467-022-35378-z
Selenica, P; Marra, A; Choudhury, N J; Gazzo, A; Falcon, C J; Patel, J; Pei, X; Zhu, Y; Ng, C K Y; Curry, M; Heller, G; Zhang, Y-K; Berger, M F; Ladanyi, M; Rudin, C M; Chandarlapaty, S; Lovly, C M; Reis-Filho, J S; Yu, H A (2022). APOBEC mutagenesis, kataegis, chromothripsis in EGFR-mutant osimertinib-resistant lung adenocarcinomas. Annals of oncology, 33(12), pp. 1284-1295. Oxford University Press 10.1016/j.annonc.2022.09.151
Park, Sujin; Mossmann, Dirk; Chen, Qian; Wang, Xueya; Dazert, Eva; Colombi, Marco; Schmidt, Alexander; Ryback, Brendan; Ng, Charlotte K Y; Terracciano, Luigi M; Heim, Markus H; Hall, Michael N (2022). Transcription factors TEAD2 and E2A globally repress acetyl-CoA synthesis to promote tumorigenesis. Molecular cell, 82(22), pp. 4246-4261. Cell Press 10.1016/j.molcel.2022.10.027
Suter, Polina; Dazert, Eva; Kuipers, Jack; Ng, Charlotte K Y; Boldanova, Tuyana; Hall, Michael N; Heim, Markus H; Beerenwinkel, Niko (2022). Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS computational biology, 18(9), e1009767. Public Library of Science 10.1371/journal.pcbi.1009767
Zanotti, Sofia; Boot, Gina F; Coto-Llerena, Mairene; Gallon, John; Hess, Gabriel F; Soysal, Savas D; Kollmar, Otto; Ng, Charlotte K Y; Piscuoglio, Salvatore (2022). The Role of Chronic Liver Diseases in the Emergence and Recurrence of Hepatocellular Carcinoma: An Omics Perspective. Frontiers in medicine, 9, p. 888850. Frontiers 10.3389/fmed.2022.888850
Ng, Charlotte K Y; Dazert, Eva; Boldanova, Tuyana; Coto-Llerena, Mairene; Nuciforo, Sandro; Ercan, Caner; Suslov, Aleksei; Meier, Marie-Anne; Bock, Thomas; Schmidt, Alexander; Ketterer, Sylvia; Wang, Xueya; Wieland, Stefan; Matter, Matthias S; Colombi, Marco; Piscuoglio, Salvatore; Terracciano, Luigi M; Hall, Michael N; Heim, Markus H (2022). Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Nature Communications, 13(1), p. 2436. Springer Nature 10.1038/s41467-022-29960-8
Rodriguez-Calero, Antonio; Gallon, John; Akhoundova, Dilara; Maletti, Sina; Ferguson, Alison; Cyrta, Joanna; Amstutz, Ursula; Garofoli, Andrea; Paradiso, Viola; Tomlins, Scott A; Hewer, Ekkehard; Genitsch, Vera; Fleischmann, Achim; Vassella, Erik; Rushing, Elisabeth J; Grobholz, Rainer; Fischer, Ingeborg; Jochum, Wolfram; Cathomas, Gieri; Osunkoya, Adeboye O; ... (2022). Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nature Communications, 13(1), p. 2400. Springer Nature 10.1038/s41467-022-30003-5
Bianco, Gaia; Coto-Llerena, Mairene; Gallon, John; Kancherla, Venkatesh; Taha-Mehlitz, Stephanie; Marinucci, Mattia; Konantz, Martina; Srivatsa, Sumana; Montazeri, Hesam; Panebianco, Federica; Tirunagaru, Vijaya G; De Menna, Marta; Paradiso, Viola; Ercan, Caner; Dahmani, Ahmed; Montaudon, Elodie; Beerenwinkel, Niko; Kruithof-de Julio, Marianna; Terracciano, Luigi M; Lengerke, Claudia; ... (2022). GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Communications biology, 5(1), p. 373. Springer Nature 10.1038/s42003-022-03296-x
Coto-Llerena, Mairene; Benjak, Andrej; Gallon, John; Meier, Marie-Anne; Boldanova, Tuyana; Terracciano, Luigi M; Ng, Charlotte K Y; Piscuoglio, Salvatore (2022). Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma. JCO precision oncology, 6, e2100335. American Society of Clinical Oncology 10.1200/PO.21.00335
Gallon, John; Coto-Llerena, Mairene; Ercan, Caner; Bianco, Gaia; Paradiso, Viola; Nuciforo, Sandro; Taha-Melitz, Stephanie; Meier, Marie-Anne; Boldanova, Tujana; Pérez-Del-Pulgar, Sofía; Rodríguez-Tajes, Sergio; von Flüe, Markus; Soysal, Savas D; Kollmar, Otto; Llovet, Josep M; Villanueva, Augusto; Terracciano, Luigi M; Heim, Markus H; Ng, Charlotte K. Y. and Piscuoglio, Salvatore (2022). Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma. Molecular oncology, 16(3), pp. 665-682. Wiley 10.1002/1878-0261.13154
Marinucci, Mattia; Ercan, Caner; Taha-Mehlitz, Stephanie; Fourie, Lana; Panebianco, Federica; Bianco, Gaia; Gallon, John; Staubli, Sebastian; Soysal, Savas D; Zettl, Andreas; Rauthe, Stephan; Vosbeck, Jürg; Droeser, Raoul A; Bolli, Martin; Peterli, Ralph; von Flüe, Markus; Ng, Charlotte K Y; Kollmar, Otto; Coto-Llerena, Mairene and Piscuoglio, Salvatore (2022). Standardizing Patient-Derived Organoid Generation Workflow to Avoid Microbial Contamination From Colorectal Cancer Tissues. Frontiers in oncology, 11, p. 781833. Frontiers Research Foundation 10.3389/fonc.2021.781833
Ercan, Caner; Coto-Llerena, Mairene; Gallon, John; Fourie, Lana; Marinucci, Mattia; Hess, Gabriel F; Vosbeck, Jürg; Taha-Mehlitz, Stephanie; Boldanova, Tuyana; Meier, Marie-Anne; Tzankov, Alexandar; Matter, Matthias S; Hoffmann, Martin H K; Di Tommaso, Luca; von Flüe, Markus; Ng, Charlotte K. Y.; Heim, Markus H; Soysal, Savas D; Terracciano, Luigi M; Kollmar, Otto; ... (2022). Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report. Communications medicine, 2, p. 11. Springer Nature 10.1038/s43856-022-00074-y
Garofoli, Andrea; Schnidrig, Désirée; Ng, Charlotte K Y (2022). PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. Methods in molecular biology, 2493, pp. 195-204. Springer 10.1007/978-1-0716-2293-3_12
Haas, Quentin; Markov, Nikita; Muerner, Lukas; Rubino, Viviana; Benjak, Andrej; Haubitz, Monika; Baerlocher, Gabriela M; Ng, Charlotte K Y; Münz, Christian; Riether, Carsten; Ochsenbein, Adrian F; Simon, Hans-Uwe; von Gunten, Stephan (2022). Siglec-7 represents a glyco-immune checkpoint for non-exhausted effector memory CD8+ T cells with high functional and metabolic capacities. Frontiers in immunology, 13, p. 996746. Frontiers Research Foundation 10.3389/fimmu.2022.996746
Montazeri, Hesam; Coto-Llerena, Mairene; Bianco, Gaia; Zangene, Ehsan; Taha-Mehlitz, Stephanie; Paradiso, Viola; Srivatsa, Sumana; de Weck, Antoine; Roma, Guglielmo; Lanzafame, Manuela; Bolli, Martin; Beerenwinkel, Niko; von Flüe, Markus; Terracciano, Luigi M; Piscuoglio, Salvatore; Ng, Charlotte K Y (2021). Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens. Nucleic acids research, 49(15), pp. 8488-8504. Oxford University Press 10.1093/nar/gkab627
Chen, Qian; Coto-Llerena, Mairene; Suslov, Aleksei; Teixeira, Raphael Dias; Fofana, Isabel; Nuciforo, Sandro; Hofmann, Maike; Thimme, Robert; Hensel, Nina; Lohmann, Volker; Ng, Charlotte K Y; Rosenberger, George; Wieland, Stefan; Heim, Markus H (2021). Interferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses. Nature Communications, 12(1), p. 4882. Springer Nature 10.1038/s41467-021-25218-x
Dimitrakopoulos, Christos; Hindupur, Sravanth Kumar; Colombi, Marco; Liko, Dritan; Ng, Charlotte K Y; Piscuoglio, Salvatore; Behr, Jonas; Moore, Ariane L; Singer, Jochen; Ruscheweyh, Hans-Joachim; Matter, Matthias S; Mossmann, Dirk; Terracciano, Luigi M; Hall, Michael N; Beerenwinkel, Niko (2021). Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma. BMC Genomics, 22(1), p. 592. BioMed Central 10.1186/s12864-021-07876-9
Tampakis, Athanasios; Weixler, Benjamin; Rast, Silvan; Tampaki, Ekaterini-Christina; Cremonesi, Eleonora; Kancherla, Venkatesh; Tosti, Nadia; Kettelhack, Christoph; Ng, Charlotte K Y; Delko, Tarik; Soysal, Savas D; von Holzen, Urs; Felekouras, Evangelos; Nikiteas, Nikolaos; Bolli, Martin; Tornillo, Luigi; Terracciano, Luigi; Eppenberger-Castori, Serenella; Spagnoli, Giulio C; Piscuoglio, Salvatore; ... (2021). Nestin and CD34 expression in colorectal cancer predicts improved overall survival. Acta oncologica, 60(6), pp. 727-734. Taylor & Francis 10.1080/0284186X.2021.1891280
Coto-Llerena, Mairene; Tosti, Nadia; Taha-Mehlitz, Stephanie; Kancherla, Venkatesh; Paradiso, Viola; Gallon, John; Bianco, Gaia; Garofoli, Andrea; Ghosh, Souvik; Tang, Fengyuan; Ercan, Caner; Christofori, Gerhard M; Matter, Matthias S; Droeser, Raoul A; Zavolan, Mihaela; Soysal, Savas D; von Flüe, Markus; Kollmar, Otto; Terracciano, Luigi M; Ng, Charlotte K. Y.; ... (2021). Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members. Hepatology communications, 5(4), pp. 661-674. Wiley 10.1002/hep4.1656
Krause, Arthur; Roma, Luca; Lorber, Thomas; Dietsche, Tanja; Perrina, Valeria; Müller, David C; Lardinois, Didier; Ruiz, Christian; Savic Prince, Spasenija; Piscuoglio, Salvatore; Ng, Charlotte K. Y.; Bubendorf, Lukas (2021). Genomic evolutionary trajectory of metastatic squamous cell carcinoma of the lung. Translational lung cancer research, 10(4), pp. 1792-1803. AME Publishing 10.21037/tlcr-21-48
Karkampouna, Sofia; La Manna, Federico; Benjak, Andrej; Kiener, Mirjam; De Menna, Marta; Zoni, Eugenio; Grosjean, Joël; Klima, Irena; Garofoli, Andrea; Bolis, Marco; Vallerga, Arianna; Theurillat, Jean-Philippe; De Filippo, Maria R.; Genitsch, Vera; Keller, David; Booij, Tijmen H; Stirnimann, Christian U; Eng, Kenneth; Sboner, Andrea; Ng, Kiu Yan Charlotte; ... (2021). Patient-derived xenografts and organoids model therapy response in prostate cancer. Nature communications, 12(1), p. 1117. 10.1038/s41467-021-21300-6
Tornillo, Luigi; Lehmann, Frank Serge; Garofoli, Andrea; Paradiso, Viola; Ng, Charlotte K. Y.; Piscuoglio, Salvatore (2021). The Genomic Landscape of Serrated Lesion of the Colorectum: Similarities and Differences With Tubular and Tubulovillous Adenomas. Frontiers in oncology, 11, p. 668466. Frontiers Research Foundation 10.3389/fonc.2021.668466
Taha-Mehlitz, Stephanie; Bianco, Gaia; Coto-Llerena, Mairene; Kancherla, Venkatesh; Bantug, Glenn R; Gallon, John; Ercan, Caner; Panebianco, Federica; Eppenberger-Castori, Serenella; von Strauss, Marco; Staubli, Sebastian; Bolli, Martin; Peterli, Ralph; Matter, Matthias S; Terracciano, Luigi M; von Flüe, Markus; Ng, Charlotte K. Y.; Soysal, Savas D; Kollmar, Otto and Piscuoglio, Salvatore (2021). Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis. Theranostics, 11(9), pp. 4011-4029. Ivyspring International 10.7150/thno.50051
Karkampouna, Sofia; De Filippo, Maria R.; Ng, Charlotte K. Y.; Klima, Irena; Zoni, Eugenio; Spahn, Martin; Stein, Frank; Haberkant, Per; Thalmann, George; Kruithof-de Julio, Marianna (2020). Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures. Cancers, 12(12) MDPI AG 10.3390/cancers12123786
Tosti, Nadia; Cremonesi, Eleonora; Governa, Valeria; Basso, Camilla; Kancherla, Venkatesh; Coto-Llerena, Mairene; Amicarella, Francesca; Weixler, Benjamin; Däster, Silvio; Sconocchia, Giuseppe; Majno, Pietro Edoardo; Christoforidis, Dimitri; Tornillo, Luigi; Terracciano, Luigi; Ng, Charlotte K. Y.; Piscuoglio, Salvatore; von Flüe, Markus; Spagnoli, Giulio; Eppenberger-Castori, Serenella; Iezzi, Giandomenica; ... (2020). Infiltration by IL22-Producing T Cells Promotes Neutrophil Recruitment and Predicts Favorable Clinical Outcome in Human Colorectal Cancer. Cancer immunology research, 8(11), pp. 1452-1462. American Association for Cancer Research 10.1158/2326-6066.CIR-19-0934
Burger, B; Ghosh, A; Ng, C K Y; Piscuoglio, S; Spoerri, I; Itin, P H; Greer, K; Elbaum, D (2020). Discovery of heterozygous KRT10 alterations in MAUIE cases underlines the importance of regular skin cancer screening in ichthyosis with confetti. The British journal of dermatology, 183(5), pp. 954-955. Wiley 10.1111/bjd.19218
Ritter, Mathilde; Paradiso, Viola; Widmer, Patrik; Garofoli, Andrea; Quagliata, Luca; Eppenberger-Castori, Serenella; Soysal, Savas D; Muenst, Simone; Ng, Charlotte K Y; Piscuoglio, Salvatore; Weber, Walter; Weber, Walter P (2020). Identification of Somatic Mutations in Thirty-year-old Serum Cell-free DNA From Patients With Breast Cancer: A Feasibility Study. Clinical breast cancer, 20(5), 413-421.e1. Elsevier 10.1016/j.clbc.2020.04.005
De Mattos-Arruda, L; Vazquez, M; Finotello, F; Lepore, R; Porta, E; Hundal, J; Amengual-Rigo, P; Ng, C K Y; Valencia, A; Carrillo, J; Chan, T A; Guallar, V; McGranahan, N; Blanco, J; Griffith, M (2020). Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group. Annals of oncology, 31(8), pp. 978-990. Elsevier 10.1016/j.annonc.2020.05.008
Coto-Llerena, Mairene; Ercan, Caner; Kancherla, Venkatesh; Taha-Mehlitz, Stephanie; Eppenberger-Castori, Serenella; Soysal, Savas D; Ng, Charlotte K. Y.; Bolli, Martin; von Flüe, Markus; Nicolas, Guillaume P; Terracciano, Luigi M; Fani, Melpomeni; Piscuoglio, Salvatore (2020). High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes. Frontiers in oncology, 10(979), p. 979. Frontiers Research Foundation 10.3389/fonc.2020.00979
Krause, Arthur; Roma, Luca; Lorber, Thomas; Habicht, James; Lardinois, Didier; De Filippo, Maria Rosaria; Prince, Spasenija Savic; Piscuoglio, Salvatore; Ng, Charlotte K Y; Bubendorf, Lukas (2020). Deciphering the clonal relationship between glandular and squamous components in adenosquamous carcinoma of the lung using whole exome sequencing. Lung cancer, 150, pp. 132-138. Elsevier 10.1016/j.lungcan.2020.10.013
Garofoli, Andrea; Paradiso, Viola; Montazeri, Hesam; Jermann, Philip M; Roma, Guglielmo; Tornillo, Luigi; Terracciano, Luigi M; Piscuoglio, Salvatore; Ng, Kiu Yan Charlotte (2019). PipeIT: A Singularity Container for Molecular Diagnostic Somatic Variant Calling on the Ion Torrent Next-Generation Sequencing Platform. The journal of molecular diagnostics, 21(5), pp. 884-894. Elsevier 10.1016/j.jmoldx.2019.05.001
Blumer, Tanja; Fofana, Isabel; Matter, Matthias S; Wang, Xueya; Montazeri, Hesam; Calabrese, Diego; Coto-Llerena, Mairene; Boldanova, Tujana; Nuciforo, Sandro; Kancherla, Venkatesh; Tornillo, Luigi; Piscuoglio, Salvatore; Wieland, Stefan; Terracciano, Luigi M; Ng, Kiu Yan Charlotte; Heim, Markus H (2019). Hepatocellular Carcinoma Xenografts Established From Needle Biopsies Preserve the Characteristics of the Originating Tumors. Hepatology communications, 3(7), pp. 971-986. Wiley 10.1002/hep4.1365
Bertucci, François; Ng, Kiu Yan Charlotte; Patsouris, Anne; Droin, Nathalie; Piscuoglio, Salvatore; Carbuccia, Nadine; Soria, Jean Charles; Dien, Alicia Tran; Adnani, Yahia; Kamal, Maud; Garnier, Séverine; Meurice, Guillaume; Jimenez, Marta; Dogan, Semih; Verret, Benjamin; Chaffanet, Max; Bachelot, Thomas; Campone, Mario; Lefeuvre, Claudia; Bonnefoi, Herve; ... (2019). Genomic characterization of metastatic breast cancers. Nature, 569(7757), pp. 560-564. Springer Nature 10.1038/s41586-019-1056-z
Soysal, Savas D; Ng, Charlotte K. Y.; Costa, Luigi; Weber, Walter P; Paradiso, Viola; Piscuoglio, Salvatore; Muenst, Simone (2019). Genetic Alterations in Benign Breast Biopsies of Subsequent Breast Cancer Patients. Frontiers in medicine, 6, p. 166. Frontiers 10.3389/fmed.2019.00166
Zoni, Eugenio; Minoli, Martina; Bovet, Cédric; Wehrhan, Anne; Piscuoglio, Salvatore; Ng, Kiu Yan; Gray, Peter C.; Spahn, Martin; Thalmann, George N.; Kruithof-de Julio, Marianna (2019). Preoperative plasma fatty acid metabolites inform risk of prostate cancer progression and may be used for personalized patient stratification. BMC cancer, 19(1), p. 1216. BioMed Central 10.1186/s12885-019-6418-2
