Charlotte Soneson

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Mark D. RobinsonFull Professor of Statistical Genomics, University of ZurichVerified email at mls.uzh.ch
Mauro DelorenziSIB Swiss Institute of BioinformaticsVerified email at unil.ch
Michael I. LoveAssociate Professor, Biostatistics & Genetics, UNC-Chapel HillVerified email at email.unc.edu
Rob PatroAssociate Professor, Department of Computer Science, University of MarylandVerified email at cs.umd.edu
Magnus FontesGeneral Manager Institut Roche, Professor of Mathematics, Lund UniversityVerified email at roche.com
Helena L. CrowellPostdoc - CNAG, Barcelona, SpainVerified email at cnag.eu
Davide RissoDepartment of Statistical Sciences, University of Padova, ItalyVerified email at unipd.it
Koen Van den BergeJ&J Innovative MedicineVerified email at berkeley.edu
Lieven ClementAssociate Professor in Statistical Genomics, Ghent UniversityVerified email at ugent.be
Michael B. StadlerHead of Computational Biology, Friedrich Miescher Institute for Biomedical Research, SwitzerlandVerified email at fmi.ch
Kevin RUE-ALBRECHTOxford UniversityVerified email at imm.ox.ac.uk
Stephanie C. HicksAssociate Professor, Johns Hopkins Bloomberg School of Public HealthVerified email at jhu.edu
Federico MariniBioinformatics Group Leader@Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)Verified email at uni-mainz.de
Aaron LunGenentech, Inc.Verified email at gene.com
Raphael GottardoLausanne University Hospital and University of LausanneVerified email at chuv.ch
Wolfgang HuberEMBL - European Molecular Biology LaboratoryVerified email at embl.org
Robert A. Amezquita, PhDSr Computational ImmunologistVerified email at pfizer.com
Levi WaldronCity University of New York Graduate School of Public Health and Health PolicyVerified email at sph.cuny.edu
Ludwig GeistlingerCenter for Computational Biomedicine, Harvard Medical SchoolVerified email at hms.harvard.edu
Lindsay N. CarppFred Hutchinson Cancer Research CenterVerified email at fredhutch.org

Charlotte Soneson

Research Associate, FMI, Basel

Verified email at fmi.ch - Homepage


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The consensus molecular subtypes of colorectal cancer J Guinney, R Dienstmann, X Wang, A De Reynies, A Schlicker, ... Nature medicine 21 (11), 1350-1356, 2015	4838	2015
Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences C Soneson, MI Love, MD Robinson F1000Research 4, 2015	3844	2015
A comparison of methods for differential expression analysis of RNA-seq data C Soneson, M Delorenzi BMC bioinformatics 14, 1-18, 2013	1130	2013
Bias, robustness and scalability in single-cell differential expression analysis C Soneson, MD Robinson Nature methods 15 (4), 255-261, 2018	721	2018
Orchestrating single-cell analysis with Bioconductor RA Amezquita, ATL Lun, E Becht, VJ Carey, LN Carpp, L Geistlinger, ... Nature methods 17 (2), 137-145, 2020	701	2020
Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features E Missiaglia, B Jacobs, G D'ario, AF Di Narzo, C Soneson, E Budinska, ... Annals of oncology 25 (10), 1995-2001, 2014	686	2014
A systematic performance evaluation of clustering methods for single-cell RNA-seq data A Duò, MD Robinson, C Soneson F1000Research 7, 2018	360	2018
Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity J Kuhle, C Barro, G Disanto, A Mathias, C Soneson, G Bonnier, Ö Yaldizli, ... Multiple Sclerosis Journal 22 (12), 1550-1559, 2016	282	2016
Tximeta: Reference sequence checksums for provenance identification in RNA-seq MI Love, C Soneson, PF Hickey, LK Johnson, NT Pierce, L Shepherd, ... PLoS computational biology 16 (2), e1007664, 2020	234	2020
A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes C Soneson, Y Yao, A Bratus-Neuenschwander, A Patrignani, ... Nature communications 10 (1), 3359, 2019	229	2019
muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data HL Crowell, C Soneson, PL Germain, D Calini, L Collin, C Raposo, ... Nature communications 11 (1), 6077, 2020	222	2020
Long-lasting stem cell–like memory CD8⁺ T cells with a naïve-like profile upon yellow fever vaccination SA Fuertes Marraco, C Soneson, L Cagnon, PO Gannon, M Allard, ... Science translational medicine 7 (282), 282ra48-282ra48, 2015	212	2015
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications K Van den Berge, F Perraudeau, C Soneson, MI Love, D Risso, JP Vert, ... Genome biology 19, 1-17, 2018	209	2018
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering LM Weber, M Nowicka, C Soneson, MD Robinson Communications biology 2 (1), 183, 2019	201	2019
Alignment and mapping methodology influence transcript abundance estimation A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ... Genome biology 21, 1-29, 2020	157	2020
Essential guidelines for computational method benchmarking LM Weber, W Saelens, R Cannoodt, C Soneson, A Hapfelmeier, ... Genome biology 20, 1-12, 2019	150	2019
Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage C Soneson, KL Matthes, M Nowicka, CW Law, MD Robinson Genome biology 17, 1-15, 2016	148	2016
RNA sequencing data: hitchhiker's guide to expression analysis K Van den Berge, KM Hembach, C Soneson, S Tiberi, L Clement, MI Love, ... Annual Review of Biomedical Data Science 2 (1), 139-173, 2019	144	2019
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification MI Love, C Soneson, R Patro F1000Research 7, 2018	134	2018
Modulation of mTOR signalling triggers the formation of stem cell-like memory T cells G Scholz, C Jandus, L Zhang, C Grandclément, IC Lopez-Mejia, ... EBioMedicine 4, 50-61, 2016	118	2016

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