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Marinucci M, Ercan C, Taha-Mehlitz S, Fourie L, Panebianco F, Bianco G, Gallon J, Staubli S, Soysal SD, Zettl A, Rauthe S, Vosbeck J, Droeser RA, Bolli M, Peterli R, von Flüe M, Ng CKY, Kollmar O, Coto-Llerena M, Piscuoglio S. Standardizing Patient-Derived Organoid Generation Workflow to Avoid Microbial Contamination From Colorectal Cancer Tissues. Front Oncol. 2022 Jan 10;11:781833. doi: 10.3389/fonc.2021.781833. PMID: 35083141.

Coto-Llerena M, Benjak A, Gallon J, Meier MA, Boldanova T, Terracciano LM, Ng CKY, Piscuoglio S. Circulating Cell-Free DNA Captures the Intratumor Heterogeneity in Multinodular Hepatocellular Carcinoma. JCO Precis Oncol. 2022 Mar;6:e2100335. PMID: 35263170.

Bianco G, Coto-Llerena M, Gallon J, Kancherla V, Taha-Mehlitz S, Marinucci M, Konantz M, Srivatsa S, Montazeri H, Panebianco F, Tirunagaru VG, De Menna M, Paradiso V, Ercan C, Dahmani A, Montaudon E, Beerenwinkel N, Kruithof-de Julio M, Terracciano LM, Lengerke C, Jeselsohn RM, Doebele RC, Bidard FC, Marangoni E, Ng CKY, Piscuoglio S. GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Commun Biol. 2022 Apr 19;5(1):373.. Erratum in: Commun Biol. 2022 Jul 4;5(1):658. PMID: 3544067.

Rodriguez-Calero A, Gallon J, Akhoundova D, Maletti S, Ferguson A, Cyrta J, Amstutz U, Garofoli A, Paradiso V, Tomlins SA, Hewer E, Genitsch V, Fleischmann A, Vassella E, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Ng CKY, Gillessen S, Piscuoglio S, Rubin MA. Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nat Commun. 2022 May 3;13(1):2400. PMID: 35504881.

Ng CKY, Dazert E, Boldanova T, Coto-Llerena M, Nuciforo S, Ercan C, Suslov A, Meier MA, Bock T, Schmidt A, Ketterer S, Wang X, Wieland S, Matter MS, Colombi M, Piscuoglio S, Terracciano LM, Hall MN, Heim MH. Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Nat Commun. 2022 May 4;13(1):2436. PMID: 35508466.

Ercan C, Coto-Llerena M, Gallon J, Fourie L, Marinucci M, Hess GF, Vosbeck J, Taha-Mehlitz S, Boldanova T, Meier MA, Tzankov A, Matter MS, Hoffmann MHK, Di Tommaso L, von Flüe M, Ng CKY, Heim MH, Soysal SD, Terracciano LM, Kollmar O, Piscuoglio S. Genomic analysis of focal nodular hyperplasia with associated hepatocellular carcinoma unveils its malignant potential: a case report. Commun Med (Lond). 2022 Feb 3;2:11. PMID: 35603298.

Suter P, Dazert E, Kuipers J, Ng CKY, Boldanova T, Hall MN, Heim MH, Beerenwinkel N. Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. PLoS Comput Biol. 2022 Sep 6;18(9):e1009767. doi: 10.1371/journal.pcbi.1009767. PMID: 36067230.

Selenica P, Marra A, Choudhury NJ, Gazzo A, Falcon CJ, Patel J, Pei X, Zhu Y, Ng CKY, Curry M, Heller G, Zhang YK, Berger MF, Ladanyi M, Rudin CM, Chandarlapaty S, Lovly CM, Reis-Filho JS, Yu HA. APOBEC mutagenesis, kataegis, chromothripsis in EGFR-mutant osimertinib-resistant lung adenocarcinomas. Ann Oncol. 2022 Dec;33(12):1284-1295. Epub 2022 Sep 9. PMID: 36089134.

Kashani E, Schnidrig D, Hashemi Gheinani A, Ninck MS, Zens P, Maragkou T, Baumgartner U, Schucht P, Rätsch G, Rubin MA, Berezowska S, Ng CKY, Vassella E; SOCIBP consortium. Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. Neuro Oncol. 2022 Sep 17:noac220. Epub ahead of print. Erratum in: Neuro Oncol. 2023 Feb 14;25(2):430. PMID: 36124685.

Haas Q, Markov N, Muerner L, Rubino V, Benjak A, Haubitz M, Baerlocher GM, Ng CKY, Münz C, Riether C, Ochsenbein AF, Simon HU, von Gunten S. Siglec-7 represents a glyco-immune checkpoint for non-exhausted effector memory CD8+ T cells with high functional and metabolic capacities. Front Immunol. 2022 Sep 23;13:996746. doi: 10.3389/fimmu.2022.996746. PMID: 36211376.

Park S, Mossmann D, Chen Q, Wang X, Dazert E, Colombi M, Schmidt A, Ryback B, Ng CKY, Terracciano LM, Heim MH, Hall MN. Transcription factors TEAD2 and E2A globally repress acetyl-CoA synthesis to promote tumorigenesis. Mol Cell. 2022 Nov 17;82(22):4246-4261.e11. PMID: 36400009.

Srivatsa S, Montazeri H, Bianco G, Coto-Llerena M, Marinucci M, Ng CKY, Piscuoglio S, Beerenwinkel N. Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens. Nat Commun. 2022 Dec 14;13(1):7748. doi: 10.1038/s41467-022-35378-z. PMID: 36517508.

Garofoli A, Schnidrig D, Ng CKY. PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. Methods Mol Biol. 2022;2493:195-204. doi: 10.1007/978-1-0716-2293-3_12. PMID: 35751816.

Zanotti S, Boot GF, Coto-Llerena M, Gallon J, Hess GF, Soysal SD, Kollmar O, Ng CKY, Piscuoglio S. The Role of Chronic Liver Diseases in the Emergence and Recurrence of Hepatocellular Carcinoma: An Omics Perspective. Front Med (Lausanne). 2022 Jun 24;9:888850. doi: 10.3389/fmed.2022.888850. PMID: 35814741.

Garofoli A, Schnidrig D, Ng CKY. PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. Methods Mol Biol. 2022;2493:195-204. PMID: 35751816.


Coto-Llerena M, Tosti N, Taha-Mehlitz S, Kancherla V, Paradiso V, Gallon J, Bianco G, Garofoli A, Ghosh S, Tang F, Ercan C, Christofori GM, Matter MS, Droeser RA, Zavolan M, Soysal SD, von Flüe M, Kollmar O, Terracciano LM, Ng CKY, Piscuoglio S. 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. Hepatol Commun. 2021 Jan 20;5(4):661-674. doi: 10.1002/hep4.1656. PMID: 33860124; PMCID: PMC8034568.

Taha-Mehlitz S, Bianco G, Coto-Llerena M, Kancherla V, Bantug GR, Gallon J, Ercan C, Panebianco F, Eppenberger-Castori S, von Strauss M, Staubli S, Bolli M, Peterli R, Matter MS, Terracciano LM, von Flüe M, Ng CKY, Soysal SD, Kollmar O, Piscuoglio S. Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis. Theranostics. 2021 Feb 15;11(9):4011-4029. doi: 10.7150/thno.50051. PMID: 33754045; PMCID: PMC7977451.

Tampakis A, Weixler B, Rast S, Tampaki EC, Cremonesi E, Kancherla V, Tosti N, Kettelhack C, Ng CKY, Delko T, Soysal SD, von Holzen U, Felekouras E, Nikiteas N, Bolli M, Tornillo L, Terracciano L, Eppenberger-Castori S, Spagnoli GC, Piscuoglio S, von Flüe M, Däster S, Droeser RA. Nestin and CD34 expression in colorectal cancer predicts improved overall survival. Acta Oncol. 2021 Mar 18:1-8. doi: 10.1080/0284186X.2021.1891280. Epub ahead of print. PMID: 33734917.

Karkampouna S, La Manna F, Benjak A, Kiener M, De Menna M, Zoni E, Grosjean J, Klima I, Garofoli A, Bolis M, Vallerga A, Theurillat JP, De Filippo MR, Genitsch V, Keller D, Booij TH, Stirnimann CU, Eng K, Sboner A, Ng CKY, Piscuoglio S, Gray PC, Spahn M, Rubin MA, Thalmann GN, Kruithof-de Julio M. Patient-derived xenografts and organoids model therapy response in prostate cancer. Nat Commun. 2021 Feb 18;12(1):1117. doi: 10.1038/s41467-021-21300-6. PMID: 33602919; PMCID: PMC7892572.

Irmisch A, Bonilla X, Chevrier S, Lehmann KV, Singer F, Toussaint NC, Esposito C, Mena J, Milani ES, Casanova R, Stekhoven DJ, Wegmann R, Jacob F, Sobottka B, Goetze S, Kuipers J, Sarabia Del Castillo J, Prummer M, Tuncel MA, Menzel U, Jacobs A, Engler S, Sivapatham S, Frei AL, Gut G, Ficek J, Miglino N; Tumor Profiler Consortium, Aebersold R, Bacac M, Beerenwinkel N, Beisel C, Bodenmiller B, Dummer R, Heinzelmann-Schwarz V, Koelzer VH, Manz MG, Moch H, Pelkmans L, Snijder B, Theocharides APA, Tolnay M, Wicki A, Wollscheid B, Rätsch G, Levesque MP. The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell. 2021 Mar 8;39(3):288-293. doi: 10.1016/j.ccell.2021.01.004. Epub 2021 Jan 21. PMID: 33482122.


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Krause A, Roma L, Lorber T, Habicht J, Lardinois D, De Filippo MR, Prince SS, Piscuoglio S, Ng C, Bubendorf L. Deciphering the clonal relationship between glandular and squamous components in adenosquamous carcinoma of the lung using whole exome sequencing. Lung Cancer. 2020 Dec;150:132-138. doi: 10.1016/j.lungcan.2020.10.013. Epub 2020 Oct 29. PMID: 33137577.

Tosti N, Cremonesi E, Governa V, Basso C, Kancherla V, Coto-Llerena M, Amicarella F, Weixler B, Däster S, Sconocchia G, Majno PE, Christoforidis D, Tornillo L, Terracciano L, Ng CKY, Piscuoglio S, von Flüe M, Spagnoli G, Eppenberger-Castori S, Iezzi G, Droeser RA. Infiltration by IL22-Producing T Cells Promotes Neutrophil Recruitment and Predicts Favorable Clinical Outcome in Human Colorectal Cancer. Cancer Immunol Res. 2020 Nov;8(11):1452-1462. doi: 10.1158/2326-6066.CIR-19-0934. Epub 2020 Aug 24. PMID: 32839156.

Coto-Llerena M, Ercan C, Kancherla V, Taha-Mehlitz S, Eppenberger-Castori S, Soysal SD, Ng CKY, Bolli M, von Flüe M, Nicolas GP, Terracciano LM, Fani M, Piscuoglio S. High Expression of FAP in Colorectal Cancer Is Associated With Angiogenesis and Immunoregulation Processes. Front Oncol. 2020 Jul 8;10:979. doi: 10.3389/fonc.2020.00979. PMID: 32733792; PMCID: PMC7362758.

Ritter M, Paradiso V, Widmer P, Garofoli A, Quagliata L, Eppenberger-Castori S, Soysal SD, Muenst S, Ng CKY, Piscuoglio S, Weber W, Weber WP. Identification of Somatic Mutations in Thirty-year-old Serum Cell-free DNA From Patients With Breast Cancer: A Feasibility Study. Clin Breast Cancer. 2020 Oct;20(5):413-421.e1. doi: 10.1016/j.clbc.2020.04.005. Epub 2020 May 6. PMID: 32650988.

De Mattos-Arruda L, Vazquez M, Finotello F, Lepore R, Porta E, Hundal J, Amengual-Rigo P, Ng CKY, Valencia A, Carrillo J, Chan TA, Guallar V, McGranahan N, Blanco J, Griffith M. Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group. Ann Oncol. 2020 Aug;31(8):978-990. doi: 10.1016/j.annonc.2020.05.008. Epub 2020 Jun 28. PMID: 32610166; PMCID: PMC7885309.

Burger B, Ghosh A, Ng CKY, Piscuoglio S, Spoerri I, Itin PH, Greer K, Elbaum D. Discovery of heterozygous KRT10 alterations in MAUIE cases underlines the importance of regular skin cancer screening in ichthyosis with confetti. Br J Dermatol. 2020 Nov;183(5):954-955. doi: 10.1111/bjd.19218. Epub 2020 Jun 29. PMID: 32407542.


Tang F, Gao R, Jeevan-Raj B, Wyss CB, Kalathur RKR, Piscuoglio S, Ng CKY, Hindupur SK, Nuciforo S, Dazert E, Bock T, Song S, Buechel D, Morini MF, Hergovich A, Matthias P, Lim DS, Terracciano LM, Heim MH, Hall MN, Christofori G. LATS1 but not LATS2 represses autophagy by a kinase-independent scaffold function. Nat Commun. 2019 Dec 17;10(1):5755. doi: 10.1038/s41467-019-13591-7. PMID: 31848340; PMCID: PMC6917744.

Zoni E, Minoli M, Bovet C, Wehrhan A, Piscuoglio S, Ng CKY, Gray PC, Spahn M, Thalmann GN, Kruithof-de Julio M. Preoperative plasma fatty acid metabolites inform risk of prostate cancer progression and may be used for personalized patient stratification. BMC Cancer. 2019 Dec 16;19(1):1216. doi: 10.1186/s12885-019-6418-2. PMID: 31842810; PMCID: PMC6916032.

Zeindler J, Soysal SD, Piscuoglio S, Ng CKY, Mechera R, Isaak A, Weber WP, Muenst S, Kurzeder C. Nectin-4 Expression Is an Independent Prognostic Biomarker and Associated With Better Survival in Triple-Negative Breast Cancer. Front Med (Lausanne). 2019 Sep 13;6:200. doi: 10.3389/fmed.2019.00200. PMID: 31572728; PMCID: PMC6753375.

Soysal SD, Ng CKY, Costa L, Weber WP, Paradiso V, Piscuoglio S, Muenst S. Genetic Alterations in Benign Breast Biopsies of Subsequent Breast Cancer Patients. Front Med (Lausanne). 2019 Jul 24;6:166. doi: 10.3389/fmed.2019.00166. PMID: 31396514; PMCID: PMC6667637.

Blumer T, Fofana I, Matter MS, Wang X, Montazeri H, Calabrese D, Coto-Llerena M, Boldanova T, Nuciforo S, Kancherla V, Tornillo L, Piscuoglio S, Wieland S, Terracciano LM, Ng CKY, Heim MH. Hepatocellular Carcinoma Xenografts Established From Needle Biopsies Preserve the Characteristics of the Originating Tumors. Hepatol Commun. 2019 May 6;3(7):971-986. doi: 10.1002/hep4.1365. PMID: 31334445; PMCID: PMC6601318.

Zeindler J, Angehrn F, Droeser R, Däster S, Piscuoglio S, Ng CKY, Kilic E, Mechera R, Meili S, Isaak A, Weber WP, Muenst S, Soysal SD. Infiltration by myeloperoxidase-positive neutrophils is an independent prognostic factor in breast cancer. Breast Cancer Res Treat. 2019 Oct;177(3):581-589. doi: 10.1007/s10549-019-05336-3. Epub 2019 Jul 2. PMID: 31267330.

Garofoli A, Paradiso V, Montazeri H, Jermann PM, Roma G, Tornillo L, Terracciano LM, Piscuoglio S, Ng CKY. PipeIT: A Singularity Container for Molecular Diagnostic Somatic Variant Calling on the Ion Torrent Next-Generation Sequencing Platform. J Mol Diagn. 2019 Sep;21(5):884-894. doi: 10.1016/j.jmoldx.2019.05.001. Epub 2019 Jun 21. PMID: 31229654.

Weigelt B, Vargas HA, Selenica P, Geyer FC, Mazaheri Y, Blecua P, Conlon N, Hoang LN, Jungbluth AA, Snyder A, Ng CKY, Papanastasiou AD, Sosa RE, Soslow RA, Chi DS, Gardner GJ, Shen R, Reis-Filho JS, Sala E. Radiogenomics Analysis of Intratumor Heterogeneity in a Patient With High-Grade Serous Ovarian Cancer. JCO Precis Oncol. 2019 Jun 6;3:PO.18.00410. doi: 10.1200/PO.18.00410. PMID: 32914032; PMCID: PMC7446483.

Bertucci F, Ng CKY, Patsouris A, Droin N, Piscuoglio S, Carbuccia N, Soria JC, Dien AT, Adnani Y, Kamal M, Garnier S, Meurice G, Jimenez M, Dogan S, Verret B, Chaffanet M, Bachelot T, Campone M, Lefeuvre C, Bonnefoi H, Dalenc F, Jacquet A, De Filippo MR, Babbar N, Birnbaum D, Filleron T, Le Tourneau C, André F. Genomic characterization of metastatic breast cancers. Nature. 2019 May;569(7757):560-564. doi: 10.1038/s41586-019-1056-z. Epub 2019 May 22. Erratum in: Nature. 2019 Aug;572(7767):E7. PMID: 31118521.

Dogan S, Ng CKY, Xu B, Kumar R, Wang L, Edelweiss M, Scott SN, Zehir A, Drilon A, Morris LGT, Lee NY, Antonescu CR, Ho AL, Katabi N, Berger MF, Reis-Filho JS. The repertoire of genetic alterations in salivary duct carcinoma including a novel HNRNPH3-ALK rearrangement. Hum Pathol. 2019 Jun;88:66-77. doi: 10.1016/j.humpath.2019.03.004. Epub 2019 Apr 1. PMID: 30946933; PMCID: PMC7388159.

Zoni E, Astrologo L, Ng CKY, Piscuoglio S, Melsen J, Grosjean J, Klima I, Chen L, Snaar-Jagalska EB, Flanagan K, van der Pluijm G, Kloen P, Cecchini MG, Kruithof-de Julio M, Thalmann GN. Therapeutic Targeting of CD146/MCAM Reduces Bone Metastasis in Prostate Cancer. Mol Cancer Res. 2019 May;17(5):1049-1062. doi: 10.1158/1541-7786.MCR-18-1220. Epub 2019 Feb 11. PMID: 30745464.

Pareja F, Lee JY, Brown DN, Piscuoglio S, Gularte-Mérida R, Selenica P, Da Cruz Paula A, Arunachalam S, Kumar R, Geyer FC, Silveira C, da Silva EM, Li A, Marchiò C, Ng CKY, Mariani O, Fuhrmann L, Wen HY, Norton L, Vincent-Salomon A, Brogi E, Reis-Filho JS, Weigelt B. The Genomic Landscape of Mucinous Breast Cancer. J Natl Cancer Inst. 2019 Jul 1;111(7):737-741. doi: 10.1093/jnci/djy216. PMID: 30649385; PMCID: PMC6624163.

Mechera R, Soysal SD, Piscuoglio S, Ng CKY, Zeindler J, Mujagic E, Däster S, Glauser P, Hoffmann H, Kilic E, Droeser RA, Weber WP, Muenst S. Expression of RET is associated with Oestrogen receptor expression but lacks prognostic significance in breast cancer. BMC Cancer. 2019 Jan 8;19(1):41. doi: 10.1186/s12885-018-5262-0. PMID: 30621641; PMCID: PMC6325785.


Montagna G, Ng CKY, Vlajnic T, Paradiso V, Dellas S, Reina H, Kind A, Weber WP, Piscuoglio S, Kurzeder C. Fibroepithelial Breast Lesion: When Sequencing Can Help to Make a Clinical Decision. A Case Report. Clin Breast Cancer. 2019 Feb;19(1):e1-e6. doi: 10.1016/j.clbc.2018.10.007. Epub 2018 Nov 1. PMID: 30470624.

Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C. Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity. Cell Rep. 2018 Nov 6;25(6):1446-1457. doi: 10.1016/j.celrep.2018.10.046. PMID: 30404001; PMCID: PMC6261536.

Lee JY, Schizas M, Geyer FC, Selenica P, Piscuoglio S, Sakr RA, Ng CKY, Carniello JVS, Towers R, Giri DD, de Andrade VP, Papanastasiou AD, Viale A, Harris RS, Solit DB, Weigelt B, Reis-Filho JS, King TA. Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma. Clin Cancer Res. 2019 Jan 15;25(2):674-686. doi: 10.1158/1078-0432.CCR-18-1103. Epub 2018 Sep 5. PMID: 30185420; PMCID: PMC6726436.

Paradiso V, Garofoli A, Tosti N, Lanzafame M, Perrina V, Quagliata L, Matter MS, Wieland S, Heim MH, Piscuoglio S, Ng CKY, Terracciano LM. Diagnostic Targeted Sequencing Panel for Hepatocellular Carcinoma Genomic Screening. J Mol Diagn. 2018 Nov;20(6):836-848. doi: 10.1016/j.jmoldx.2018.07.003. Epub 2018 Aug 22. PMID: 30142445.

Nuciforo S, Fofana I, Matter MS, Blumer T, Calabrese D, Boldanova T, Piscuoglio S, Wieland S, Ringnalda F, Schwank G, Terracciano LM, Ng CKY, Heim MH. Organoid Models of Human Liver Cancers Derived from Tumor Needle Biopsies. Cell Rep. 2018 Jul 31;24(5):1363-1376. doi: 10.1016/j.celrep.2018.07.001. PMID: 30067989; PMCID: PMC6088153.