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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
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
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
Servant, Raphaëlle; Garioni, Michele; Vlajnic, Tatjana; Blind, Melanie; Pueschel, Heike; Müller, David C; Zellweger, Tobias; Templeton, Arnoud J; Garofoli, Andrea; Maletti, Sina Laura; Piscuoglio, Salvatore; Rubin, Mark A.; Seifert, Helge; Rentsch, Cyrill A; Bubendorf, Lukas; Le Magnen, Clémentine (2021). Prostate cancer patient-derived organoids: detailed outcome from a prospective cohort of 81 clinical specimens. The journal of pathology, 254(5), pp. 543-555. Wiley 10.1002/path.5698
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
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
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
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
