Charlotte Soneson

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 33

Top Topics

Radiofrequency Ablation

Immune Response

Top Venues

bioRxiv : the preprint server for biology

Molecular biology and evolution

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
William J Hutchison, Timothy J Keyes, null null, Helena Lucia Crowell, Jacques Serizay, Charlotte Soneson, Eric S Davis, Noriaki Sato, Lambda Moses, Boyd Tarlinton, Abdullah Al Nahid, Miha Kosmac, Quentin Clayssen, Victor Yuan, Wancen Mu, Ji-Eun Park, Izabela Mamede, Min Hyung Ryu, Pierre-Paul Axisa, Paulina Paiz, Chi-Lam Poon, Ming Tang, Raphaël Gottardo, Martin Morgan, Stuart Lee, Michael Lawrence, Stephanie C Hicks, Garry P Nolan, Kara L Davis, Anthony T Papenfuss, Michael I Love, Stefano Mangiola
The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology (2024)
Paul Bastide, Charlotte Soneson, David Ben Stern, Olivier Lespinet, Mélina Gallopin
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Molecular biology and evolution 40 (1) (2023)
Agnese Kocere, Elena Chiavacci, Kevin Manuel Méndez-Acevedo, Charlotte Soneson, Max S Hiltabidle, Ekambaram Perumal, Jacalyn S MacGowan, Jordan A Shavit, Daniela Panakova, Margot Kossmann Williams, Mark D Robinson, Christian Mosimann, Alexa Burger
TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling. bioRxiv : the preprint server for biology (2023)
Agnese Kocere, Elena Chiavacci, Kevin Manuel Méndez-Acevedo, Charlotte Soneson, Max S Hiltabidle, Ekambaram Perumal, Jacalyn S MacGowan, Jordan A Shavit, Daniela Panakova, Margot Kossmann Williams, Mark D Robinson, Christian Mosimann, Alexa Burger
TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling. bioRxiv : the preprint server for biology (2023)
Charlotte Soneson, Alexandra M Bendel, Guillaume Diss, Michael B Stadler
mutscan-a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data. Genome biology 24 (1) (2023)
Paul Bastide, Charlotte Soneson, David Ben Stern, Olivier Lespinet, Mélina Gallopin
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Molecular biology and evolution 40 (1) (2023)
Paul Bastide, Charlotte Soneson, David Ben Stern, Olivier Lespinet, Mélina Gallopin
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Molecular biology and evolution 40 (1) (2023)
Agnese Kocere, Elena Chiavacci, Kevin Manuel Méndez-Acevedo, Charlotte Soneson, Max S Hiltabidle, Ekambaram Perumal, Jacalyn S MacGowan, Jordan A Shavit, Daniela Panakova, Margot Kossmann Williams, Mark D Robinson, Christian Mosimann, Alexa Burger
TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling. bioRxiv : the preprint server for biology (2023)
Agnese Kocere, Elena Chiavacci, Kevin Manuel Méndez-Acevedo, Charlotte Soneson, Max S Hiltabidle, Ekambaram Perumal, Jacalyn S MacGowan, Jordan A Shavit, Daniela Panakova, Margot Kossmann Williams, Mark D Robinson, Christian Mosimann, Alexa Burger
TAR Syndrome-associated Rbm8a deficiency causes hematopoietic defects and attenuates Wnt/PCP signaling. bioRxiv : the preprint server for biology (2023)
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M Rijli, Dirk Schübeler, Michael B Stadler
monaLisa: an R/Bioconductor package for identifying regulatory motifs. Bioinformatics (Oxford, England) 38 (9) (2022)
Charlotte Soneson, Avi Srivastava, Rob Patro, Michael B Stadler
Preprocessing choices affect RNA velocity results for droplet scRNA-seq data. PLoS computational biology 17 (1) (2021)
Almut Lütge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D Robinson
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life science alliance 4 (6) (2021)
Ruizhu Huang, Charlotte Soneson, Felix G M Ernst, Kevin C Rue-Albrecht, Guangchuang Yu, Stephanie C Hicks, Mark D Robinson
TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research 9 (2020)
Michael I Love, Charlotte Soneson, Peter F Hickey, Lisa K Johnson, N Tessa Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Tximeta: Reference sequence checksums for provenance identification in RNA-seq. PLoS computational biology 16 (2) (2020)
Charlotte Soneson, Federico Marini, Florian Geier, Michael I Love, Michael B Stadler
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Research (2020)
Charlotte Soneson, Federico Marini, Florian Geier, Michael I Love, Michael B Stadler
ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R. F1000Research 9 (2020)
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, Kevin Christophe Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike L Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C Hicks
Orchestrating single-cell analysis with Bioconductor. Nature methods 17 (2) (2019)
Hung-Wei Cheng, Lucas Onder, Mario Novkovic, Charlotte Soneson, Mechthild Lütge, Natalia Pikor, Elke Scandella, Mark D Robinson, Jun-Ichi Miyazaki, Anne Tersteegen, Ursula Sorg, Klaus Pfeffer, Thomas Rülicke, Thomas Hehlgans, Burkhard Ludewig
Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp. Nature communications 10 (1) (2019)
Charlotte Soneson, Yao Yao, Anna Bratus-Neuenschwander, Andrea Patrignani, Mark D Robinson, Shobbir Hussain
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nature communications 10 (1) (2019)
Stephany Orjuela, Ruizhu Huang, Katharina M Hembach, Mark D Robinson, Charlotte Soneson
ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data. G3 (Bethesda, Md.) 9 (7) (2019)
Christian Perez-Shibayama, Cristina Gil-Cruz, Hung-Wei Cheng, Lucas Onder, Andrea Printz, Urs M Mörbe, Mario Novkovic, Conglei Li, Constantino Lopez-Macias, Matthew B Buechler, Shannon J Turley, Matthias Mack, Charlotte Soneson, Mark D Robinson, Elke Scandella, Jennifer L Gommerman, Burkhard Ludewig
Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity. Science immunology 3 (26) (2019)
Lukas M Weber, Malgorzata Nowicka, Charlotte Soneson, Mark D Robinson
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. Communications biology 2 (2019)
Charlotte Soneson, Michael I Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D Robinson
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life science alliance 2 (1) (2019)
Lukas M Weber, Charlotte Soneson
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. F1000Research 8 (2019)
Charlotte Soneson, Mark D Robinson
Bias, robustness and scalability in single-cell differential expression analysis. Nature methods 15 (4) (2018)
Angelo Duò, Mark D Robinson, Charlotte Soneson
A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Research (2018)
Angelo Duò, Mark D Robinson, Charlotte Soneson
A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Research (2018)
Angelo Duò, Mark D Robinson, Charlotte Soneson
A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Research 7 (2018)
Isabella M Y Zanini, Charlotte Soneson, Luca E Lorenzi, Claus M Azzalin
Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. Journal of cell science 130 (4) (2017)