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Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.
NPJ Genom Med. 2018 Jan 11;3:1. doi: 10.1038/s41525-017-0040-5. eCollection 2018.
NPJ Genom Med. 2018.
PMID: 29354286
Free PMC article.
Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate.
Juul M, Bertl J, Guo Q, Nielsen MM, Świtnicki M, Hornshøj H, Madsen T, Hobolth A, Pedersen JS.
Juul M, et al.
Elife. 2017 Mar 31;6:e21778. doi: 10.7554/eLife.21778.
Elife. 2017.
PMID: 28362259
Free PMC article.
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EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples.
Madsen T, Świtnicki M, Juul M, Pedersen JS.
Madsen T, et al.
Stat Appl Genet Mol Biol. 2019 Nov 16;18(6):/j/sagmb.2019.18.issue-6/sagmb-2018-0050/sagmb-2018-0050.xml. doi: 10.1515/sagmb-2018-0050.
Stat Appl Genet Mol Biol. 2019.
PMID: 31734658
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PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification.
Świtnicki MP, Juul M, Madsen T, Sørensen KD, Pedersen JS.
Świtnicki MP, et al.
Bioinformatics. 2016 May 1;32(9):1353-65. doi: 10.1093/bioinformatics/btv758. Epub 2016 Jan 6.
Bioinformatics. 2016.
PMID: 26740525
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ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.
Sahoo S, Świtnicki MP, Pedersen JS.
Sahoo S, et al. Among authors: switnicki mp.
Bioinformatics. 2016 Sep 1;32(17):2626-35. doi: 10.1093/bioinformatics/btw175. Epub 2016 Apr 21.
Bioinformatics. 2016.
PMID: 27153612
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RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy.
Strand SH, Switnicki M, Moller M, Haldrup C, Storebjerg TM, Hedegaard J, Nordentoft I, Hoyer S, Borre M, Pedersen JS, Wild PJ, Park JY, Orntoft TF, Sorensen KD.
Strand SH, et al.
Oncotarget. 2017 Jan 24;8(4):5774-5788. doi: 10.18632/oncotarget.14391.
Oncotarget. 2017.
PMID: 28052017
Free PMC article.
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Genome-wide binding patterns of thyroid hormone receptor beta.
Ayers S, Switnicki MP, Angajala A, Lammel J, Arumanayagam AS, Webb P.
Ayers S, et al. Among authors: switnicki mp.
PLoS One. 2014 Feb 18;9(2):e81186. doi: 10.1371/journal.pone.0081186. eCollection 2014.
PLoS One. 2014.
PMID: 24558356
Free PMC article.
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