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Drug screening and genome editing in human pancreatic cancer organoids identifies drug-gene interactions and candidates for off-label treatment.
Hirt CK, Booij TH, Grob L, Simmler P, Toussaint NC, Keller D, Taube D, Ludwig V, Goryachkin A, Pauli C, Lenggenhager D, Stekhoven DJ, Stirnimann CU, Endhardt K, Ringnalda F, Villiger L, Siebenhüner A, Karkampouna S, De Menna M, Beshay J, Klett H, Kruithof-de Julio M, Schüler J, Schwank G. Hirt CK, et al. Among authors: stekhoven dj. Cell Genom. 2022 Feb;2(2):100095. doi: 10.1016/j.xgen.2022.100095. Cell Genom. 2022. PMID: 35187519 Free PMC article.
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.
Singer J, Ruscheweyh HJ, Hofmann AL, Thurnherr T, Singer F, Toussaint NC, Ng CKY, Piscuoglio S, Beisel C, Christofori G, Dummer R, Hall MN, Krek W, Levesque MP, Manz MG, Moch H, Papassotiropoulos A, Stekhoven DJ, Wild P, Wüst T, Rinn B, Beerenwinkel N. Singer J, et al. Among authors: stekhoven dj. Bioinformatics. 2018 Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540. Bioinformatics. 2018. PMID: 28968639 Free PMC article.
Bioinformatics for precision oncology.
Singer J, Irmisch A, Ruscheweyh HJ, Singer F, Toussaint NC, Levesque MP, Stekhoven DJ, Beerenwinkel N. Singer J, et al. Among authors: stekhoven dj. Brief Bioinform. 2019 May 21;20(3):778-788. doi: 10.1093/bib/bbx143. Brief Bioinform. 2019. PMID: 29272324 Free PMC article. Review.
SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics.
Singer F, Irmisch A, Toussaint NC, Grob L, Singer J, Thurnherr T, Beerenwinkel N, Levesque MP, Dummer R, Quagliata L, Rothschild SI, Wicki A, Beisel C, Stekhoven DJ. Singer F, et al. Among authors: stekhoven dj. BMC Med Inform Decis Mak. 2018 Oct 29;18(1):89. doi: 10.1186/s12911-018-0680-0. BMC Med Inform Decis Mak. 2018. PMID: 30373609 Free PMC article.
The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support.
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. Irmisch A, et al. Among authors: stekhoven dj. Cancer Cell. 2021 Mar 8;39(3):288-293. doi: 10.1016/j.ccell.2021.01.004. Epub 2021 Jan 21. Cancer Cell. 2021. PMID: 33482122 Free article.
scROSHI: robust supervised hierarchical identification of single cells.
Prummer M, Bertolini A, Bosshard L, Barkmann F, Yates J, Boeva V; Tumor Profiler Consortium; Stekhoven D, Singer F. Prummer M, et al. NAR Genom Bioinform. 2023 Jun 16;5(2):lqad058. doi: 10.1093/nargab/lqad058. eCollection 2023 Jun. NAR Genom Bioinform. 2023. PMID: 37332656 Free PMC article.
SCIM: universal single-cell matching with unpaired feature sets.
Stark SG, Ficek J, Locatello F, Bonilla X, Chevrier S, Singer F; Tumor Profiler Consortium; Rätsch G, Lehmann KV. Stark SG, et al. Bioinformatics. 2020 Dec 30;36(Suppl_2):i919-i927. doi: 10.1093/bioinformatics/btaa843. Bioinformatics. 2020. PMID: 33381818 Free PMC article.
34 results