Zobrazeno 1 - 10
of 146
pro vyhledávání: '"Charlotte, Soneson"'
Autor:
Rajani Kanth Gudipati, Dimos Gaidatzis, Jan Seebacher, Sandra Muehlhaeusser, Georg Kempf, Simone Cavadini, Daniel Hess, Charlotte Soneson, Helge Großhans
Publikováno v:
Molecular Systems Biology, Vol 20, Iss 12, Pp 1303-1328 (2024)
Abstract Substrate specificity determines protease functions in physiology and in clinical and biotechnological applications, yet quantitative cleavage information is often unavailable, biased, or limited to a small number of events. Here, we develop
Externí odkaz:
https://doaj.org/article/90d17309994f44198ecc68e8695d20d8
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-3 (2024)
Externí odkaz:
https://doaj.org/article/dc0cc4d6c6d0430e81aa43079643851b
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-22 (2023)
Abstract Multiplexed assays of variant effect (MAVE) experimentally measure the effect of large numbers of sequence variants by selective enrichment of sequences with desirable properties followed by quantification by sequencing. mutscan is an R pack
Externí odkaz:
https://doaj.org/article/ea9c0ea77f814529833d13b0967dfccf
Autor:
Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schmeing, Stefan Milosavljevic, Yvan Saeys, Serghei Mangul, Mark D. Robinson
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-11 (2023)
Abstract Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines,
Externí odkaz:
https://doaj.org/article/21cd2e92fd404c0081d6e6fad0fc21dd
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-19 (2023)
Abstract Background With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq) datasets, the number of computational tools to analyze aspects of the generated data has grown rapidly. As a result, there is a recurring need to demonstrate
Externí odkaz:
https://doaj.org/article/e08713a7e5c143ad956a8f8efad3ef4a
Autor:
Karin D. Prummel, Helena L. Crowell, Susan Nieuwenhuize, Eline C. Brombacher, Stephan Daetwyler, Charlotte Soneson, Jelena Kresoja-Rakic, Agnese Kocere, Manuel Ronner, Alexander Ernst, Zahra Labbaf, David E. Clouthier, Anthony B. Firulli, Héctor Sánchez-Iranzo, Sundar R. Naganathan, Rebecca O’Rourke, Erez Raz, Nadia Mercader, Alexa Burger, Emanuela Felley-Bosco, Jan Huisken, Mark D. Robinson, Christian Mosimann
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-21 (2022)
The mesothelium supports homeostasis and regeneration, yet its development origins remain unclear. Here, the authors uncovered the earliest mesothelium progenitor cells in zebrafish, linking Hand2 gene function to mesothelium formation and its re-act
Externí odkaz:
https://doaj.org/article/445f40166b9345a1905f77ae35cd17f3
Autor:
Johanna Wagner, Markus Masek, Andrea Jacobs, Charlotte Soneson, Sujana Sivapatham, Nicolas Damond, Natalie de Souza, Mark D. Robinson, Bernd Bodenmiller
Publikováno v:
Scientific Data, Vol 9, Iss 1, Pp 1-16 (2022)
Measurement(s) RNA-seq gene expression profiling assay • cell surface proteins • protein expression at the single-cell level • Epithelial-to-Mesenchymal Transition • breast cancer cell • mammary gland epithelial cell Technology Type(s) mRNA
Externí odkaz:
https://doaj.org/article/81a2b53781e4443a83618d3a2b4f6b3d
Autor:
Ruizhu Huang, Charlotte Soneson, Pierre-Luc Germain, Thomas S.B. Schmidt, Christian Von Mering, Mark D. Robinson
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-21 (2021)
Abstract treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or leaves that contain features of
Externí odkaz:
https://doaj.org/article/b1d8cc0b3f064bf1a238e2055b34cbd8
Autor:
Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, Daniela Calini, Ludovic Collin, Catarina Raposo, Dheeraj Malhotra, Mark D. Robinson
Publikováno v:
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
Single-cell transcriptomics enhanced our ability to profile heterogeneous cell populations. It is not known which statistical frameworks are performant to detect subpopulation-level responses. Here, the authors developed a simulation framework to eva
Externí odkaz:
https://doaj.org/article/ca630df4491c4fa29d160b6e84f04cc4
Autor:
Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-29 (2020)
Abstract Background The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been
Externí odkaz:
https://doaj.org/article/78912e03065e4f5e8d496ea17a6e5ae8