Publications

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Preprints and articles awaiting peer review

  • Gudipati, R. K.; Gaidatzis, D.; Seebacher, J.; Muehlhaeusser, S.; Kempf, G.; Cavadini, S.; Hess, D.; Soneson, C.; Grosshans, H.: Massively parallel mapping of substrate cleavage sites defines dipeptidyl peptidase four subsite cooperativity. bioRxiv doi: https://doi.org/10.1101/2023.11.17.567387. Posted November 17, 2023.

  • Hutchison, W. J.; Keyes, T. J.; Crowell, H. L.; Soneson, C.; Mu, W.; Park, J.-E.; Davis, E. S.; Nahid, A. A.; Tang, M.; Yuan, V.; Axisa, P.-P.; Kitt, J. W.; Poon, C.-L.; Sato, N.; Kosmac, M.; Serizay, J.; Gottardo, R.; Morgan, M.; Lee, S.; Lawrence, M.; Hicks, S. C.; Nolan, G. P.; Davis, K. L.; Papenfuss, A. T.; Love, M. I.; Mangiola, S.: The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv doi: https://doi.org/10.1101/2023.09.10.557072. Posted October 10, 2023.

  • Tiberi, S.; Meili, J.; Cai, P.; Soneson, C.; He, D.; Sarkar, H.; Avalos-Pacheco, A.; Patro, R.; Robinson, M. D.: DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes. bioRxiv doi: https://doi.org/10.1101/2023.08.17.553679. Posted August 17, 2023.

  • Kocere, A.; Chiavacci, E.; Soneson, C.; Wells, H. H.; Mendez-Acevedo, K. M.; Macgowan, J. S.; Jacobson, S. T.; Hiltabidle, M. S.; Raghunath, A.; Shavit, J. A.; Panakova, D.; Williams, M. L. K.; Robinson, M. D.; Mosimann, C.; Burger, A.: Rbm8a deficiency causes hematopoietic defects by modulating Wnt/PCP signaling. bioRxiv doi: https://doi.org/10.1101/2023.04.12.536513. Posted February 01, 2024.

  • He, D.; Soneson, C.; Patro, R.: Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing. bioRxiv doi: https://doi.org/10.1101/2023.01.04.522742. Posted January 04, 2023. GitHub repo.

  • Srivastava, A.; Zakeri, M.; Sarkar, H.; Soneson, C.; Kingsford, C.; Patro, R.: Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism. bioRxiv doi: https://doi.org/10.1101/2021.01.17.426996. Posted January 19, 2021.

  • Paulo Czarnewski, Ahmed Mahfouz, Raffaele A. Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez-Uriarte, Charlotte Soneson, Tony Burdett, Barbara Szomolay, Pavankumar Videm, Hans-Rudolf Hotz, Irene Papatheodorou, John M. Hancock, Björn Grüning, Wilfried Haerty, Roland Krause, Salvador Capella-Gutierrez, Brane Leskošek, Luca Alessandri, Maddalena Arigoni, Tadeja Rezen, Alexander Botzki, Polonca Ferk, Jessica Lindvall, Katharina F Heil, Naveed Ishaque, Eija Korpelainen: Community-driven ELIXIR activities in single-cell omics. F1000Research doi: https://doi.org/10.12688/f1000research.122312.1. Posted July 29, 2022.

2023

2022

  • Prummel KD, Crowell HL, Nieuwenhuize S, Brombacher EC, Daetwyler S, Soneson C, Kresoja-Rakic J, Kocere A, Ronner M, Ernst A, Labbaf Z, Clouthier DE, Firulli AB, Sánchez-Iranzo H, Naganathan SR, O’Rourke R, Raz E, Mercader N, Burger A, Felley-Bosco E, Huisken J, Robinson MD, Mosimann C: Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nat Commun 13(1):1677 (2022). DOI: 10.1038/s41467-022-29311-7. PMID 35354817. Preprint.

  • He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R: Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19(3):316-322 (2022). DOI: 10.1038/s41592-022-01408-3. PMID 35277707. Preprint.

  • Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB: monaLisa: an R/Bioconductor package for identifying regulatory motifs. Bioinformatics 38(9):2624-2625 (2022). DOI: 10.1093/bioinformatics/btac102. PMID 35199152. Software/Resources. Preprint.

  • Wagner J, Masek M, Jacobs A, Soneson C, Sivapatham S, Damond N, de Souza N, Robinson MD, Bodenmiller B: Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Sci Data 9(1):44 (2022). DOI: 10.1038/s41597-022-01137-4. PMID 35140234. GitHub repo. Preprint.

2021

2020

2019

2018

2017

  • Van den Berge K, Soneson C, Robinson MD, Clement L: stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol 18(1):151 (2017). DOI: 10.1186/s13059-017-1277-0. PMID 28784146. Software/Resources. Preprint.

  • Gille D, Zangger N, Soneson C, Bütikofer U, Delorenzi M, Schwander F, Kopf-Bolanz KA, Chollet M, Walther B, Laederach K, Vergères G: Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men. J Nutr Biochem 43:156-165 (2017). DOI: 10.1016/j.jnutbio.2017.02.012. PMID 28319853.

  • Neubert NJ, Tillé L, Barras D, Soneson C, Baumgaertner P, Rimoldi D, Gfeller D, Delorenzi M, Fuertes Marraco SA, Speiser DE: Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells. Cancer Res 77(7):1623-1636 (2017). DOI: 10.1158/0008-5472.CAN-16-2680. PMID 28104684.

  • Sauerwald J, Soneson C, Robinson MD, Luschnig S: Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila. Development 144(4):657-663 (2017). DOI: 10.1242/dev.144535. PMID 28087625.

  • Zanini IM, Soneson C, Lorenzi LE, Azzalin CM: Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. J Cell Sci 130(4):767-778 (2017). DOI: 10.1242/jcs.194068. PMID 28062851.

  • Mathias A, Perriard G, Canales M, Soneson C, Delorenzi M, Schluep M, Du Pasquier RA: Increased ex vivo antigen presentation profile of B cells in multiple sclerosis. Mult Scler 23(6):802-809 (2017). DOI: 10.1177/1352458516664210. PMID 27503907.

2016

  • Neubert NJ, Soneson C, Barras D, Baumgaertner P, Rimoldi D, Delorenzi M, Fuertes Marraco SA, Speiser DE: A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells. Front Immunol 7:326 (2016). DOI: 10.3389/fimmu.2016.00326. PMID 27625650.

  • Soneson C, Robinson MD: iCOBRA: open, reproducible, standardized and live method benchmarking. Nat Methods 13(4):283 (2016). DOI: 10.1038/nmeth.3805. PMID 27027585. Software/Resources. Preprint.

  • Scholz G, Jandus C, Zhang L, Grandclément C, Lopez-Mejia IC, Soneson C, Delorenzi M, Fajas L, Held W, Dormond O, Romero P: Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells. EBioMedicine 4:50-61 (2016). DOI: 10.1016/j.ebiom.2016.01.019. PMID 26981571.

  • Soneson C, Matthes KL, Nowicka M, Law CW, Robinson MD: Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biol 17:12 (2016). DOI: 10.1186/s13059-015-0862-3. PMID 26813113. GitHub repo. Preprint.

  • Kuhle J, Barro C, Disanto G, Mathias A, Soneson C, Bonnier G, Yaldizli Ö, Regeniter A, Derfuss T, Canales M, Schluep M, Du Pasquier R, Krueger G, Granziera C: Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity. Mult Scler 22(12):1550-1559 (2016). DOI: 10.1177/1352458515623365. PMID 26754800.

  • Schell MJ, Yang M, Missiaglia E, Delorenzi M, Soneson C, Yue B, Nebozhyn MV, Loboda A, Bloom G, Yeatman TJ: A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome. Clin Cancer Res 22(3):734-45 (2016). DOI: 10.1158/1078-0432.CCR-15-0143. PMID 26446941.

  • Schiffthaler B, Kostadima M, NGS Trainer Consortium, Delhomme N, Rustici G: Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability. PLoS Comput Biol 12(6):e1004937 (2016). DOI: 10.1371/journal.pcbi.1004937. PMID 27309738.

  • SIB Swiss Institute of Bioinformatics Members: The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Res 44(D1):D27-37 (2016). DOI: 10.1093/nar/gkv1310. PMID 26615188.

2015

  • Soneson C, Love MI, Robinson MD: Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res 4:1521 (2015). DOI: 10.12688/f1000research.7563.2. PMID 26925227. Software/Resources.

  • Fuertes Marraco SA, Soneson C, Delorenzi M, Speiser DE: Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans. Genom Data 5:297-301 (2015). DOI: 10.1016/j.gdata.2015.06.024. PMID 26484272.

  • Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S: The consensus molecular subtypes of colorectal cancer. Nat Med 21(11):1350-6 (2015). DOI: 10.1038/nm.3967. PMID 26457759.

  • Johnsson K, Soneson C, Fontes M: Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness. IEEE Trans Pattern Anal Mach Intell 37(1):196-202 (2015). DOI: 10.1109/TPAMI.2014.2343220. PMID 26353219.

  • Shchepachev V, Wischnewski H, Soneson C, Arnold AW, Azzalin CM: Human Mpn1 promotes post-transcriptional processing and stability of U6atac. FEBS Lett 589(18):2417-23 (2015). DOI: 10.1016/j.febslet.2015.06.046. PMID 26213367.

  • Fuertes Marraco SA, Soneson C, Cagnon L, Gannon PO, Allard M, Abed Maillard S, Montandon N, Rufer N, Waldvogel S, Delorenzi M, Speiser DE: Long-lasting stem cell-like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination. Sci Transl Med 7(282):282ra48 (2015). DOI: 10.1126/scitranslmed.aaa3700. PMID 25855494.

  • Lorenzi LE, Bah A, Wischnewski H, Shchepachev V, Soneson C, Santagostino M, Azzalin CM: Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels. EMBO J 34(1):115-29 (2015). DOI: 10.15252/embj.201489559. PMID 25398909.

2014

  • Soneson C, Gerster S, Delorenzi M: Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PLoS One 9(6):e100335 (2014). DOI: 10.1371/journal.pone.0100335. PMID 24967636.

  • Soneson C: compcodeR–an R package for benchmarking differential expression methods for RNA-seq data. Bioinformatics 30(17):2517-8 (2014). DOI: 10.1093/bioinformatics/btu324. PMID 24813215. Software/Resources.

  • Sun Y, Zhang W, Chen D, Lv Y, Zheng J, Lilljebjörn H, Ran L, Bao Z, Soneson C, Sjögren HO, Salford LG, Ji J, French PJ, Fioretos T, Jiang T, Fan X: A glioma classification scheme based on coexpression modules of EGFR and PDGFRA. Proc Natl Acad Sci U S A 111(9):3538-43 (2014). DOI: 10.1073/pnas.1313814111. PMID 24550449.

  • Duffy D, Mamdouh R, Laird M, Soneson C, Le Fouler L, El-Daly M, Casrouge A, Decalf J, Abbas A, Eldin NS, Fontes M, Abdel-Hamid M, Mohamed MK, Rafik M, Fontanet A, Albert ML: The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis. Hepatology 59(4):1273-82 (2014). DOI: 10.1002/hep.26901. PMID 24500966.

  • Missiaglia E, Jacobs B, D’Ario G, Di Narzo AF, Soneson C, Budinska E, Popovici V, Vecchione L, Gerster S, Yan P, Roth AD, Klingbiel D, Bosman FT, Delorenzi M, Tejpar S: Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features. Ann Oncol 25(10):1995-2001 (2014). DOI: 10.1093/annonc/mdu275. PMID 25057166.

  • Soneson C, Fontes M: Incorporation of gene exchangeabilities improves the reproducibility of gene set rankings. Computational Statistics & Data Analysis 71:588-598 (2014). DOI: 10.1016/j.csda.2012.07.026.

2013

  • Soneson C, Delorenzi M: A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14:91 (2013). DOI: 10.1186/1471-2105-14-91. PMID 23497356.

  • Soneson C, Torstensson A: Manliga och kvinnliga teknologers självbilder och deras stereotypbilder av teknologer. Högre Utbildning 3(1):3-14 (2013). .

2012

  • Shchepachev V, Wischnewski H, Missiaglia E, Soneson C, Azzalin CM: Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3’-to-5’ RNA exonuclease processing U6 small nuclear RNA. Cell Rep 2(4):855-65 (2012). DOI: 10.1016/j.celrep.2012.08.031. PMID 23022480.

  • Soneson C, Fontes M: A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities. Biostatistics 13(1):129-41 (2012). DOI: 10.1093/biostatistics/kxr023. PMID 21908866.

2011

  • Fontes M, Soneson C: The projection score–an evaluation criterion for variable subset selection in PCA visualization. BMC Bioinformatics 12:307 (2011). DOI: 10.1186/1471-2105-12-307. PMID 21798031.

  • Soneson C, Fontes M: A method for visual identification of small sample subgroups and potential biomarkers. Annals of Applied Statistics 5(3):2131-2149 (2011). DOI: 10.1214/11-AOAS460.

2010

  • Soneson C, Fontes M, Zhou Y, Denisov V, Paulsen JS, Kirik D, Petersén A, Huntington Study Group PREDICT-HD investigators: Early changes in the hypothalamic region in prodromal Huntington disease revealed by MRI analysis. Neurobiol Dis 40(3):531-43 (2010). DOI: 10.1016/j.nbd.2010.07.013. PMID 20682340.

  • Lilljebjörn H, Soneson C, Andersson A, Heldrup J, Behrendtz M, Kawamata N, Ogawa S, Koeffler HP, Mitelman F, Johansson B, Fontes M, Fioretos T: The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. Hum Mol Genet 19(16):3150-8 (2010). DOI: 10.1093/hmg/ddq224. PMID 20513752.

  • Soneson C, Lilljebjörn H, Fioretos T, Fontes M: Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. BMC Bioinformatics 11:191 (2010). DOI: 10.1186/1471-2105-11-191. PMID 20398334.

2009

  • Björklund T, Hall H, Breysse N, Soneson C, Carlsson T, Mandel RJ, Carta M, Kirik D: Optimization of continuous in vivo DOPA production and studies on ectopic DA synthesis using rAAV5 vectors in Parkinsonian rats. J Neurochem 111(2):355-67 (2009). DOI: 10.1111/j.1471-4159.2009.06340.x. PMID 19686242.