Jakob Skou Pedersen

Jakob Skou Pedersen

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Jakob Skou Pedersen

Jakob Skou Pedersen

Publications by authors named "Jakob Skou Pedersen"

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33Publications

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Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.

Genome Res 2019 07 20;29(7):1067-1077. Epub 2019 Jun 20.

Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands.

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http://dx.doi.org/10.1101/gr.246223.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6633256PMC
July 2019

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Bioinformatics 2019 01;35(2):189-199

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bty511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330011PMC
January 2019

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.

Algorithms Mol Biol 2018 8;13:17. Epub 2018 Dec 8.

1Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1186/s13015-018-0135-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286601PMC
December 2018

A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data.

BMC Bioinformatics 2018 04 19;19(1):147. Epub 2018 Apr 19.

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, DK-8200, Denmark.

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http://dx.doi.org/10.1186/s12859-018-2141-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909259PMC
April 2018

Significance evaluation in factor graphs.

BMC Bioinformatics 2017 Mar 31;18(1):199. Epub 2017 Mar 31.

Department of Molecular Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus, Denmark.

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http://dx.doi.org/10.1186/s12859-017-1614-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374669PMC
March 2017

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

Mol Biol Evol 2016 12 13;33(12):3284-3298. Epub 2016 Sep 13.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

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http://dx.doi.org/10.1093/molbev/msw184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100044PMC
December 2016

ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

Bioinformatics 2016 09 21;32(17):2626-35. Epub 2016 Apr 21.

Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark Bioinformatics Research Centre, Aarhus University, Aarhus C DK-8000, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btw175DOI Listing
September 2016

Widespread DNA hypomethylation and differential gene expression in Turner syndrome.

Sci Rep 2016 Sep 30;6:34220. Epub 2016 Sep 30.

Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043230PMC
http://dx.doi.org/10.1038/srep34220DOI Listing
September 2016

SNPest: a probabilistic graphical model for estimating genotypes.

BMC Res Notes 2014 Oct 7;7:698. Epub 2014 Oct 7.

Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej, 2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1756-0500-7-698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203901PMC
October 2014

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

Genome Res 2011 Nov 12;21(11):1929-43. Epub 2011 Oct 12.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1101/gr.112516.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205577PMC
November 2011

Editing modifies the GABA(A) receptor subunit alpha3.

RNA 2007 May 16;13(5):698-703. Epub 2007 Mar 16.

Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden.

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http://www.rnajournal.org/cgi/doi/10.1261/rna.349107
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http://dx.doi.org/10.1261/rna.349107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852825PMC
May 2007

Identification and classification of conserved RNA secondary structures in the human genome.

PLoS Comput Biol 2006 Apr 21;2(4):e33. Epub 2006 Apr 21.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0020033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440920PMC
April 2006

An evolutionary model for protein-coding regions with conserved RNA structure.

Mol Biol Evol 2004 Oct 30;21(10):1913-22. Epub 2004 Jun 30.

Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark.

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http://dx.doi.org/10.1093/molbev/msh199DOI Listing
October 2004

A comparative method for finding and folding RNA secondary structures within protein-coding regions.

Nucleic Acids Res 2004 24;32(16):4925-36. Epub 2004 Sep 24.

Bioinformatics Research Center, Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 550, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1093/nar/gkh839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC519121PMC
October 2004

Gene finding with a hidden Markov model of genome structure and evolution.

Bioinformatics 2003 Jan;19(2):219-27

Bioinformatics Research Center, Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 550, Ny Munkegade, 8000 Aarhus C, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/19.2.219DOI Listing
January 2003