List of works by Jakob Skou Pedersen

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

scientific article published on 24 September 2004

A dual program for translation regulation in cellular proliferation and differentiation

scientific article published on September 2014

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

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

scientific article published on 19 April 2018

Abstract 3153: Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer

An RNA gene expressed during cortical development evolved rapidly in humans

scientific article

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

scientific article published on 30 June 2004

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery.

scientific article published on 4 February 2015

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

scientific article published on 05 February 2020

Cellular disposal of miR23b by RAB27-dependent exosome release is linked to acquisition of metastatic properties

scientific article published on 26 September 2014

Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer.

scientific article published on 28 November 2017

Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma.

scientific article

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome

scientific article published in Scientific Reports

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

EBADIMEX: An empirical Bayes approach to detect joint differential expression and methylation and to classify samples

Editing modifies the GABA(A) receptor subunit alpha3

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

scientific article

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

scientific article

Forces shaping the fastest evolving regions in the human genome

scientific article

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

scientific article published in January 2003

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

scientific article (publication date: March 2014)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

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

scientific article

Identification of expressed and conserved human noncoding RNAs

scientific article published on 16 December 2013

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

scientific article

Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis

scientific article published on 25 September 2020

Mutational context and diverse clonal development in early and late bladder cancer.

scientific article published on 15 May 2014

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

scientific article

Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue

scientific article

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

scientific article published on 31 March 2017

Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients.

scientific article

PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification

scientific article

Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.

scientific article published on 3 August 2016

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

scientific article published on 11 January 2018

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

Posttranscriptional crossregulation between Drosha and DGCR8.

scientific article published on January 2009

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

scientific article

RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy

scientific article published on 30 December 2016

Regmex, Motif analysis in ranked lists of sequences

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

scientific article published on 08 December 2018

SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism

scientific article published on 26 June 2016

SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

scientific article published on 22 December 2016

SNPest: a probabilistic graphical model for estimating genotypes

scientific article

Significance evaluation in factor graphs

scientific article

Structured RNAs in the ENCODE selected regions of the human genome

scientific article

The UCSC Genome Browser Database: 2008 update

scientific article (publication date: 2008)

The UCSC Genome Browser Database: update 2006

scientific article

The UCSC genome browser database: update 2007.

scientific article

The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence

scientific article published on 24 April 2015

The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer

scientific article published on 25 January 2022

Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis

scientific article

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

Widespread DNA hypomethylation and differential gene expression in Turner syndrome

scientific article published on 30 September 2016

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

scientific article

miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells

scientific article

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

scientific article published on 01 January 2019

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