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Charlotte Soneson

Friedrich Miescher Institute for Biomedical Research

47H-index
219Paper Count
2.1WCitation Count
Published Papers 52
Publication Date
An in vitro menstrual cycle using organoids captures epithelial cell transitions during menstruation and regeneration of the human endometrium
err2026-04-28
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errKonstantina Nikolakopoulou; Weand Ybañez; Lhéanna Klaeylé; Lisa Frugoli; Tereza Cindrova-Davies; Hans-Rudolf Hotz; Charlotte Soneson; Margherita Yayoi Turco
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Rbm8a deficiency causes hematopoietic defects by modulating Wnt/PCP signaling
err2025-09-02
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errAgnese Kocere; Elena Chiavacci; Charlotte Soneson; Seth T. Jacobson; Emma N. Harrison; Kevin Manuel Méndez-Acevedo; Jacalyn S. MacGowan; Harrison H. Wells; Max S. Hiltabidle; Azhwar Raghunath; Jordan A. Shavit; Daniela Panáková; Margot L.K. Williams; Mark D. Robinson; Christian Mosimann; Alexa Burger
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A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin
err2025-02-01
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errSkribbe, Merle; Soneson, Charlotte; Stadler, Michael B.; Schwaiger, Michaela; Sreechakram, Vishnu N. Suma; Iesmantavicius, Vytautas; Hess, Daniel; Moreno, Eliza Pandini Figueiredo; Braun, Sigurd; Seebacher, Jan; Smallwood, Sebastien A.; Buhler, Marc
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Deep quantification of substrate turnover defines protease subsite cooperativity
err2024-10-28
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errGudipati, Rajani Kanth; Gaidatzis, Dimos; Seebacher, Jan; Muehlhaeusser, Sandra; Kempf, Georg; Cavadini, Simone; Hess, Daniel; Soneson, Charlotte; Grosshans, Helge
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The tidyomics ecosystem: enhancing omic data analyses
err2024-06-14
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PREAI
errHutchison, William J.; Keyes, Timothy J.; Crowell, Helena L.; Serizay, Jacques; Soneson, Charlotte; Davis, Eric S.; Sato, Noriaki; Moses, Lambda; Tarlinton, Boyd; Nahid, Abdullah A.; Kosmac, Miha; Clayssen, Quentin; Yuan, Victor; Mu, Wancen; Park, Ji-Eun; Mamede, Izabela; Ryu, Min Hyung; Axisa, Pierre-Paul; Paiz, Paulina; Poon, Chi-Lam; Tang, Ming; Gottardo, Raphael; Morgan, Martin; Lee, Stuart; Lawrence, Michael; Hicks, Stephanie C.; Nolan, Garry P.; Davis, Kara L.; Papenfuss, Anthony T.; Love, Michael I.; Mangiola, Stefano
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Convergence of multiple RNA-silencing pathways on GW182/TNRC6
err2023-07-01
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errWelte, Thomas; Goulois, Alison; Stadler, Michael B.; Hess, Daniel; Soneson, Charlotte; Neagu, Anca; Azzi, Chiara; Wisser, Marlena J.; Seebacher, Jan; Schmidt, Isabel; Estoppey, David; Nigsch, Florian; Reece-Hoyes, John; Hoepfner, Dominic; Grosshans, Helge
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mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data
err2023-06-01
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errSoneson, Charlotte; Bendel, Alexandra M. M.; Diss, Guillaume; Stadler, Michael B. B.
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Conserved stromal-immune cell circuits secure B cell homeostasis and function
err2023-05-18
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errLutge, Mechthild; De Martin, Angelina; Gil-Cruz, Cristina; Perez-Shibayama, Christian; Stanossek, Yves; Onder, Lucas; Cheng, Hung-Wei; Kurz, Lisa; Cadosch, Nadine; Soneson, Charlotte; Robinson, Mark D.; Stoeckli, Sandro J.; Ludewig, Burkhard; Pikor, Natalia B.
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Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability
err2023-05-17
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errSonrel, Anthony; Luetge, Almut; Soneson, Charlotte; Mallona, Izaskun; Germain, Pierre-Luc; Knyazev, Sergey; Gilis, Jeroen; Gerber, Reto; Seurinck, Ruth; Paul, Dominique; Sonder, Emanuel; Crowell, Helena L. L.; Fanaswala, Imran; Al-Ajami, Ahmad; Heidari, Elyas; Schmeing, Stephan; Milosavljevic, Stefan; Saeys, Yvan; Mangul, Serghei; Robinson, Mark D.
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The shaky foundations of simulating single-cell RNA sequencing data
err2023-03-29
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errCrowell, Helena L.; Leonardo, Sarah X. Morillo X.; Soneson, Charlotte; Robinson, Mark D.
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A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data
err2022-12-12
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errBastide, Paul; Soneson, Charlotte; Stern, David B.; Lespinet, Olivier; Gallopin, Melina
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Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma
err2022-03-30
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errPrummel, Karin D.; Crowell, Helena L.; Nieuwenhuize, Susan; Brombacher, Eline C.; Daetwyler, Stephan; Soneson, Charlotte; Kresoja-Rakic, Jelena; Ronner, Manuel; Kocere, Agnese; Ernst, Alexander; Labbaf, Zahra; Clouthier, David E.; Firulli, Anthony B.; Sanchez-Iranzo, Hector; Naganathan, Sundar R.; O'Rourke, Rebecca; Raz, Erez; Mercader, Nadia; Burger, Alexa; Felley-Bosco, Emanuela; Huisken, Jan; Robinson, Mark D.; Mosimann, Christian
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Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
err2022-03-11
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errHe, Dongze; Zakeri, Mohsen; Sarkar, Hirak; Soneson, Charlotte; Srivastava, Avi; Patro, Rob
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treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
err2021-05-17
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errHuang, Ruizhu; Soneson, Charlotte; Germain, Pierre-Luc; Schmidt, Thomas S. B.; Von Mering, Christian; Robinson, Mark D.
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CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
err2021-03-23
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errLuetge, Almut; Zyprych-Walczak, Joanna; Kunzmann, Urszula Brykczynska; Crowell, Helena L.; Calini, Daniela; Malhotra, Dheeraj; Soneson, Charlotte; Robinson, Mark D.
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A unique bipartite Polycomb signature regulates stimulus-response transcription during development
err2021-02-18
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errKitazawa, Taro; Machlab, Dania; Joshi, Onkar; Maiorano, Nicola; Kohler, Hubertus; Ducret, Sebastien; Kessler, Sandra; Gezelius, Henrik; Soneson, Charlotte; Papasaikas, Panagiotis; Lopez-Bendito, Guillermina; Stadler, Michael B.; Rijli, Filippo M.
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Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
err2021-01-11
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errSoneson, Charlotte; Srivastava, Avi; Patro, Rob; Stadler, Michael B.
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MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome
err2020-12-09
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errWang, Yuluan; Soneson, Charlotte; Malinowska, Anna L.; Laski, Artur; Ghosh, Souvik; Kanitz, Alexander; Gebert, Luca F. R.; Robinson, Mark D.; Hall, Jonathan
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muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
err2020-11-30
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errCrowell, Helena L.; Soneson, Charlotte; Germain, Pierre-Luc; Calini, Daniela; Collin, Ludovic; Raposo, Catarina; Malhotra, Dheeraj; Robinson, Mark D.
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Alignment and mapping methodology influence transcript abundance estimation
err2020-09-07
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errSrivastava, Avi; Malik, Laraib; Sarkar, Hirak; Zakeri, Mohsen; Almodaresi, Fatemeh; Soneson, Charlotte; Love, Michael I.; Kingsford, Carl; Patro, Rob
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