CYANUS - a web platform for analyzing drug response markers in cytometry data

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CYANUS - a web platform for analyzing drug response markers in cytometry data

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proceedings-article

Author(s): Lis Arend ¹ , Judith Bernett ¹ , Quirin Manz ¹ ^, , Melissa Klug ¹ , Olga Lazareva ¹ , Jan Baumbach ² , Dario Bongiovanni ³ , Markus List ¹

Publication date (Electronic preprint): 26 August 2022

Publisher: ScienceOpen

Conference name: RExPO22

Conference date: 2-3 September, 2022

Keywords: cytometry, CyTOF, differential expression analysis, benchmark, drug response

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Abstract

Content

Author and article information

Conference

Publisher: ScienceOpen

Publication date (Electronic preprint): 26 August 2022

Affiliations

[1 ] Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany

[2 ] Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany

[3 ] Department of Internal Medicine I, School of Medicine, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany

Author notes

[* ]Email: quirin.manz@ 123456tum.de .

Author information

Lis Arend https://orcid.org/0000-0001-7990-8385

Judith Bernett https://orcid.org/0000-0001-5812-8013

Quirin Manz https://orcid.org/0000-0002-5706-2718

Melissa Klug https://orcid.org/0000-0001-5193-2770

Olga Lazareva https://orcid.org/0000-0001-9546-7807

Jan Baumbach https://orcid.org/0000-0002-0282-0462

Dario Bongiovanni https://orcid.org/0000-0002-4162-1482

Markus List https://orcid.org/0000-0002-0941-4168

Article

DOI: 10.14293/S2199-1006.1.SOR-.PPP5QEXA.v1

SO-VID: 72f48977-cba5-4687-995b-4111ad9e7096

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This work has been published open access under Creative Commons Attribution License CC BY 4.0 , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Conditions, terms of use and publishing policy can be found at www.scienceopen.com .

Conference name: RExPO22

Conference location: Maastricht, Netherlands

Conference date: 2-3 September, 2022

History

Date received : 26 August 2022

Data availability: The datasets generated during and/or analysed during the current study are available in the repository: https://flowrepository.org/id/FR-FCM-Z4AE, https://exbio.wzw.tum.de/cyanus/

Keywords: drug response,differential expression analysis,CyTOF,cytometry,benchmark

References

Fernandez Dawn M., Giannarelli Chiara. Immune cell profiling in atherosclerosis: role in research and precision medicine. Nature Reviews Cardiology. Vol. 19(1):43–58. 2022. Springer Science and Business Media LLC. [Cross Ref]
Georgopoulou Dimitra, Callari Maurizio, Rueda Oscar M., Shea Abigail, Martin Alistair, Giovannetti Agnese, Qosaj Fatime, Dariush Ali, Chin Suet-Feung, Carnevalli Larissa S., Provenzano Elena, Greenwood Wendy, Lerda Giulia, Esmaeilishirazifard Elham, O’Reilly Martin, Serra Violeta, Bressan Dario, Mills Gordon B., Ali H. Raza, Cosulich Sabina S., Hannon Gregory J., Bruna Alejandra, Caldas Carlos. Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response. Nature Communications. Vol. 12(1)2021. Springer Science and Business Media LLC. [Cross Ref]
Bongiovanni Dario, Klug Melissa, Lazareva Olga, Weidlich Simon, Biasi Marina, Ursu Simona, Warth Sarah, Buske Christian, Lukas Marina, Spinner Christoph D., Scheidt Moritz von, Condorelli Gianluigi, Baumbach Jan, Laugwitz Karl-Ludwig, List Markus, Bernlochner Isabell. SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype. Cell Death & Disease. Vol. 12(1)2021. Springer Science and Business Media LLC. [Cross Ref]
Arend Lis, Bernett Judith, Manz Quirin, Klug Melissa, Lazareva Olga, Baumbach Jan, Bongiovanni Dario, List Markus. A systematic comparison of novel and existing differential analysis methods for CyTOF data. Briefings in Bioinformatics. Vol. 23(1)2022. Oxford University Press (OUP). [Cross Ref]

Comments

Comment on this article

[1] Fernandez Dawn M., Giannarelli Chiara. Immune cell profiling in atherosclerosis: role in research and precision medicine. Nature Reviews Cardiology. Vol. 19(1):43–58. 2022. Springer Science and Business Media LLC. [Cross Ref]

[2] Georgopoulou Dimitra, Callari Maurizio, Rueda Oscar M., Shea Abigail, Martin Alistair, Giovannetti Agnese, Qosaj Fatime, Dariush Ali, Chin Suet-Feung, Carnevalli Larissa S., Provenzano Elena, Greenwood Wendy, Lerda Giulia, Esmaeilishirazifard Elham, O’Reilly Martin, Serra Violeta, Bressan Dario, Mills Gordon B., Ali H. Raza, Cosulich Sabina S., Hannon Gregory J., Bruna Alejandra, Caldas Carlos. Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response. Nature Communications. Vol. 12(1)2021. Springer Science and Business Media LLC. [Cross Ref]

[3] Bongiovanni Dario, Klug Melissa, Lazareva Olga, Weidlich Simon, Biasi Marina, Ursu Simona, Warth Sarah, Buske Christian, Lukas Marina, Spinner Christoph D., Scheidt Moritz von, Condorelli Gianluigi, Baumbach Jan, Laugwitz Karl-Ludwig, List Markus, Bernlochner Isabell. SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype. Cell Death & Disease. Vol. 12(1)2021. Springer Science and Business Media LLC. [Cross Ref]

[4] Arend Lis, Bernett Judith, Manz Quirin, Klug Melissa, Lazareva Olga, Baumbach Jan, Bongiovanni Dario, List Markus. A systematic comparison of novel and existing differential analysis methods for CyTOF data. Briefings in Bioinformatics. Vol. 23(1)2022. Oxford University Press (OUP). [Cross Ref]