28 Result(s)
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Jakob Skou Pedersen
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Open AccessSequence dependencies and mutation rates of localized mutational processes in cancer
Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a resu...
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Open AccessDREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and di...
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Open AccessAuthor Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Open AccessAuthor Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
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Open AccessAuthor Correction: Pathway and network analysis of more than 2500 whole cancer genomes
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Open AccessAuthor Correction: Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis
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Open AccessThe transcriptional landscape and biomarker potential of circular RNAs in prostate cancer
Circular RNAs (circRNAs) constitute a largely unexplored source for biomarker discovery in prostate cancer (PC). Here, we characterize the biomarker potential of circRNAs in PC, where the need for novel diagno...
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Open AccessThe landscape and driver potential of site-specific hotspots across cancer genomes
Large sets of whole cancer genomes make it possible to study mutation hotspots genome-wide. Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Canc...
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Open AccessmiRNA activity inferred from single cell mRNA expression
High throughput single-cell RNA sequencing (scRNAseq) can provide mRNA expression profiles for thousands of cells. However, miRNAs cannot currently be studied at the same scale. By exploiting that miRNAs bind ...
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Open AccessTranscriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little...
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Open AccessMolecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis
Overtreatment with cisplatin-based chemotherapy is a major issue in the management of muscle-invasive bladder cancer (MIBC), and currently none of the reported biomarkers for predicting response have been impl...
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Open AccessPathway and network analysis of more than 2500 whole cancer genomes
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent n...
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Open AccessCancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs c...
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Open AccessAnalyses of non-coding somatic drivers in 2,658 cancer whole genomes
The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from ...
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Open AccessRegmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments
Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by ...
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Open AccessDNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Klinefelter syndrome (KS) has a prevalence ranging from 85 to 250 per 100.000 newborn boys making it the most frequent sex chromosome aneuploidy in the general population. The molecular basis for the phenotypi...
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Open AccessA site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data
Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral muta...
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Open AccessOptimized targeted sequencing of cell-free plasma DNA from bladder cancer patients
Analysis of plasma cell-free DNA (cfDNA) may provide important information in cancer research, though the often small fraction of DNA originating from tumor cells makes the analysis technically challenging. Di...
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Open AccessPan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival
Cancer develops by accumulation of somatic driver mutations, which impact cellular function. Mutations in non-coding regulatory regions can now be studied genome-wide and further characterized by correlation w...
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Open AccessCircular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer
The functions and biomarker potential of circular RNAs (circRNAs) in various cancer types are a rising field of study, as emerging evidence relates circRNAs to tumorigenesis. Here, we profiled the expression o...
