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Items: 41


A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.

Soneson C, Love MI, Patro R, Hussain S, Malhotra D, Robinson MD.

Life Sci Alliance. 2019 Jan 17;2(1). pii: e201800175. doi: 10.26508/lsa.201800175. Print 2019 Feb.


Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Love MI, Soneson C, Patro R.

Version 3. F1000Res. 2018 Jun 27 [revised 2018 Jan 1];7:952. doi: 10.12688/f1000research.15398.3. eCollection 2018.


A systematic performance evaluation of clustering methods for single-cell RNA-seq data.

Duò A, Robinson MD, Soneson C.

Version 2. F1000Res. 2018 Jul 26 [revised 2018 Jan 1];7:1141. doi: 10.12688/f1000research.15666.2. eCollection 2018.


Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity.

Perez-Shibayama C, Gil-Cruz C, Cheng HW, Onder L, Printz A, Mörbe U, Novkovic M, Li C, Lopez-Macias C, Buechler MB, Turley SJ, Mack M, Soneson C, Robinson MD, Scandella E, Gommerman J, Ludewig B.

Sci Immunol. 2018 Aug 10;3(26). pii: eaar4539. doi: 10.1126/sciimmunol.aar4539.


iSEE: Interactive SummarizedExperiment Explorer.

Rue-Albrecht K, Marini F, Soneson C, Lun ATL.

F1000Res. 2018 Jun 14;7:741. doi: 10.12688/f1000research.14966.1. eCollection 2018.


Bias, robustness and scalability in single-cell differential expression analysis.

Soneson C, Robinson MD.

Nat Methods. 2018 Apr;15(4):255-261. doi: 10.1038/nmeth.4612. Epub 2018 Feb 26.


Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L.

Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4.


Towards unified quality verification of synthetic count data with countsimQC.

Soneson C, Robinson MD.

Bioinformatics. 2018 Feb 15;34(4):691-692. doi: 10.1093/bioinformatics/btx631.


stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage.

Van den Berge K, Soneson C, Robinson MD, Clement L.

Genome Biol. 2017 Aug 7;18(1):151. doi: 10.1186/s13059-017-1277-0.


Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men.

Gille D, Zangger N, Soneson C, Bütikofer U, Delorenzi M, Schwander F, Kopf-Bolanz KA, Chollet M, Walther B, Laederach K, Vergères G.

J Nutr Biochem. 2017 May;43:156-165. doi: 10.1016/j.jnutbio.2017.02.012. Epub 2017 Mar 4.


Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells.

Neubert NJ, Tillé L, Barras D, Soneson C, Baumgaertner P, Rimoldi D, Gfeller D, Delorenzi M, Fuertes Marraco SA, Speiser DE.

Cancer Res. 2017 Apr 1;77(7):1623-1636. doi: 10.1158/0008-5472.CAN-16-2680. Epub 2017 Jan 19.


Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila.

Sauerwald J, Soneson C, Robinson MD, Luschnig S.

Development. 2017 Feb 15;144(4):657-663. doi: 10.1242/dev.144535. Epub 2017 Jan 13.


Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.

Zanini IM, Soneson C, Lorenzi LE, Azzalin CM.

J Cell Sci. 2017 Feb 15;130(4):767-778. doi: 10.1242/jcs.194068. Epub 2017 Jan 6.


A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells.

Neubert NJ, Soneson C, Barras D, Baumgaertner P, Rimoldi D, Delorenzi M, Fuertes Marraco SA, Speiser DE.

Front Immunol. 2016 Aug 30;7:326. doi: 10.3389/fimmu.2016.00326. eCollection 2016.


Increased ex vivo antigen presentation profile of B cells in multiple sclerosis.

Mathias A, Perriard G, Canales M, Soneson C, Delorenzi M, Schluep M, Du Pasquier RA.

Mult Scler. 2017 May;23(6):802-809. doi: 10.1177/1352458516664210. Epub 2016 Aug 8.


iCOBRA: open, reproducible, standardized and live method benchmarking.

Soneson C, Robinson MD.

Nat Methods. 2016 Apr;13(4):283. doi: 10.1038/nmeth.3805. No abstract available.


Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells.

Scholz G, Jandus C, Zhang L, Grandclément C, Lopez-Mejia IC, Soneson C, Delorenzi M, Fajas L, Held W, Dormond O, Romero P.

EBioMedicine. 2016 Jan 16;4:50-61. doi: 10.1016/j.ebiom.2016.01.019. eCollection 2016 Feb.


Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.

Soneson C, Love MI, Robinson MD.

Version 2. F1000Res. 2015 Dec 30 [revised 2016 Jan 1];4:1521. doi: 10.12688/f1000research.7563.2. eCollection 2015.


Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

Soneson C, Matthes KL, Nowicka M, Law CW, Robinson MD.

Genome Biol. 2016 Jan 26;17:12. doi: 10.1186/s13059-015-0862-3.


Serum neurofilament light chain in early relapsing remitting MS is increased and correlates with CSF levels and with MRI measures of disease severity.

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.

Mult Scler. 2016 Oct;22(12):1550-1559. Epub 2016 Jan 11.


Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans.

Fuertes Marraco SA, Soneson C, Delorenzi M, Speiser DE.

Genom Data. 2015 Jul 2;5:297-301. doi: 10.1016/j.gdata.2015.06.024. eCollection 2015 Sep.


The consensus molecular subtypes of colorectal cancer.

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.

Nat Med. 2015 Nov;21(11):1350-6. doi: 10.1038/nm.3967. Epub 2015 Oct 12.


A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome.

Schell MJ, Yang M, Missiaglia E, Delorenzi M, Soneson C, Yue B, Nebozhyn MV, Loboda A, Bloom G, Yeatman TJ.

Clin Cancer Res. 2016 Feb 1;22(3):734-45. doi: 10.1158/1078-0432.CCR-15-0143. Epub 2015 Oct 7.


Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness.

Johnsson K, Soneson C, Fontes M.

IEEE Trans Pattern Anal Mach Intell. 2015 Jan;37(1):196-202. doi: 10.1109/TPAMI.2014.2343220.


Human Mpn1 promotes post-transcriptional processing and stability of U6atac.

Shchepachev V, Wischnewski H, Soneson C, Arnold AW, Azzalin CM.

FEBS Lett. 2015 Aug 19;589(18):2417-23. doi: 10.1016/j.febslet.2015.06.046. Epub 2015 Jul 23.


Long-lasting stem cell-like memory CD8+ T cells with a naïve-like profile upon yellow fever vaccination.

Fuertes Marraco SA, Soneson C, Cagnon L, Gannon PO, Allard M, Abed Maillard S, Montandon N, Rufer N, Waldvogel S, Delorenzi M, Speiser DE.

Sci Transl Med. 2015 Apr 8;7(282):282ra48. doi: 10.1126/scitranslmed.aaa3700.


Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels.

Lorenzi LE, Bah A, Wischnewski H, Shchepachev V, Soneson C, Santagostino M, Azzalin CM.

EMBO J. 2015 Jan 2;34(1):115-29. doi: 10.15252/embj.201489559. Epub 2014 Nov 14.


Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features.

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.

Ann Oncol. 2014 Oct;25(10):1995-2001. doi: 10.1093/annonc/mdu275. Epub 2014 Jul 23.


Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

Soneson C, Gerster S, Delorenzi M.

PLoS One. 2014 Jun 26;9(6):e100335. doi: 10.1371/journal.pone.0100335. eCollection 2014.


compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.

Soneson C.

Bioinformatics. 2014 Sep 1;30(17):2517-8. doi: 10.1093/bioinformatics/btu324. Epub 2014 May 9.


A glioma classification scheme based on coexpression modules of EGFR and PDGFRA.

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.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3538-43. doi: 10.1073/pnas.1313814111. Epub 2014 Feb 18.


[Investigate the effects of abolishing internship].

Morell M, Andreasson M, Soneson CJ, Weiman E, Jansson H, Larsson F, Vahlberg P, Frank S, Karlsson O, Leivik M, Sandström N, Wendt A.

Lakartidningen. 2013 Dec 13-2014 Jan 7;110(51-52):2316. Swedish. No abstract available.


The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis.

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.

Hepatology. 2014 Apr;59(4):1273-82. doi: 10.1002/hep.26901. Epub 2014 Feb 18.


A comparison of methods for differential expression analysis of RNA-seq data.

Soneson C, Delorenzi M.

BMC Bioinformatics. 2013 Mar 9;14:91. doi: 10.1186/1471-2105-14-91.


Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA.

Shchepachev V, Wischnewski H, Missiaglia E, Soneson C, Azzalin CM.

Cell Rep. 2012 Oct 25;2(4):855-65. doi: 10.1016/j.celrep.2012.08.031. Epub 2012 Sep 27.


A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities.

Soneson C, Fontes M.

Biostatistics. 2012 Jan;13(1):129-41. doi: 10.1093/biostatistics/kxr023. Epub 2011 Sep 10.


The projection score--an evaluation criterion for variable subset selection in PCA visualization.

Fontes M, Soneson C.

BMC Bioinformatics. 2011 Jul 28;12:307. doi: 10.1186/1471-2105-12-307.


Early changes in the hypothalamic region in prodromal Huntington disease revealed by MRI analysis.

Soneson C, Fontes M, Zhou Y, Denisov V, Paulsen JS, Kirik D, Petersén A; Huntington Study Group PREDICT-HD investigators.

Neurobiol Dis. 2010 Dec;40(3):531-43. doi: 10.1016/j.nbd.2010.07.013. Epub 2010 Aug 2.


The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias.

Lilljebjörn H, Soneson C, Andersson A, Heldrup J, Behrendtz M, Kawamata N, Ogawa S, Koeffler HP, Mitelman F, Johansson B, Fontes M, Fioretos T.

Hum Mol Genet. 2010 Aug 15;19(16):3150-8. doi: 10.1093/hmg/ddq224. Epub 2010 May 31.


Integrative analysis of gene expression and copy number alterations using canonical correlation analysis.

Soneson C, Lilljebjörn H, Fioretos T, Fontes M.

BMC Bioinformatics. 2010 Apr 15;11:191. doi: 10.1186/1471-2105-11-191.


Optimization of continuous in vivo DOPA production and studies on ectopic DA synthesis using rAAV5 vectors in Parkinsonian rats.

Björklund T, Hall H, Breysse N, Soneson C, Carlsson T, Mandel RJ, Carta M, Kirik D.

J Neurochem. 2009 Oct;111(2):355-67. doi: 10.1111/j.1471-4159.2009.06340.x. Epub 2009 Aug 17.

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