Author details

Full Name

Jakob Skou Pedersen

Affiliation

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37745562	circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.	bioRxiv	2024
36980716	Epigenetic Silencing of Is Associated with Dedifferentiation and Poor Survival in Multiple Solid Tumor Types.		2023
37592287	Sequence dependencies and mutation rates of localized mutational processes in cancer.		2023
37554968	Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer.		2023
36883553	Pan-cancer association of DNA repair deficiencies with whole-genome mutational patterns.		2023
36697832	Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.	Nature	2023
37121998	DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection.		2023
35078526	The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer.	Genome Medicine	2022
35379819	Author Correction: Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis.	Nature Communications	2022
36482178	Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.	Commun Biol	2022
35030248	Error Characterization and Statistical Modeling Improves Circulating Tumor DNA Detection by Droplet Digital PCR.	Clinical Chemistry	2022
33986299	The landscape and driver potential of site-specific hotspots across cancer genomes.	NPJ Genom Med	2021
33911110	miRNA activity inferred from single cell mRNA expression.	Scientific Reports	2021
33287884	Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.	Genome Med	2020
32489015	Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females.	American Journal of Medical Genetics, Part C: Seminars in Medical Genetics	2020
32084333	Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.	Cell	2020
32978382	Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis.	Nature Communications	2020
31221724	Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.	Genome Res	2019
31734658	EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples.	Statistical Applications in Genetics and Molecular Biology	2019
29945188	ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.	Bioinformatics	2019
29382943	Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients.	Scientific Reports	2018
30122371	APD-Containing Cyclolipodepsipeptides Target Mitochondrial Function in Hypoxic Cancer Cells.	Cell Chemical Biology	2018
30555524	Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.	Algorithms for Molecular Biology	2018
30213969	DNA hypermethylation and differential gene expression associated with Klinefelter syndrome.	Scientific Reports	2018
29673314	A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data.	BMC Bioinformatics	2018
29354286	Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.	NPJ Genom Med	2018
28052017	RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy.	Oncotarget	2017
28362259	Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate.	eLife	2017
28359297	Significance evaluation in factor graphs.	BMC Bioinformatics	2017
29263845	Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer.	npj Genomic Medicine	2017
28222791	epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data.		2017
27488526	Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma.	Cancer Research	2016
25654990	Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery.	Gut	2016
27396952	SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism.	Mol Oncol	2016
27153612	ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.		2016
26740525	PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification.		2016
27321955	Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma.	Cancer Cell	2016
27526785	miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells.	Nature Communications	2016
28004750	SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization.	Nat Commun	2016
27687697	Widespread DNA hypomethylation and differential gene expression in Turner syndrome.	Scientific Reports	2016
27624717	Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.	Molecular Biology and Evolution	2016
25908244	The lncRNA MIR31HG regulates p16(INK4A) expression to modulate senescence.	Nat Commun	2015
24878701	Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue.	PLoS ONE	2014
25261234	Cellular disposal of miR23b by RAB27-dependent exosome release is linked to acquisition of metastatic properties.	Cancer Res	2014
25294605	SNPest: a probabilistic graphical model for estimating genotypes.	BMC Research Notes	2014
24344320	Identification of expressed and conserved human noncoding RNAs.	RNA	2014
24299735	Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.	Genome Res	2014
25215487	A dual program for translation regulation in cellular proliferation and differentiation.	Cell	2014
24835989	Mutational context and diverse clonal development in early and late bladder cancer.	Cell Rep	2014
21993624	A high-resolution map of human evolutionary constraint using 29 mammals.	Nature	2011