A5058438834- Cancer-related molecular mechanisms research
- Neuroblastoma Research and Treatments
- MicroRNA in disease regulation
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Protein Degradation and Inhibitors
- Circular RNAs in diseases
- Cytokine Signaling Pathways and Interactions
- RNA and protein synthesis mechanisms
- Signaling Pathways in Disease
- Genomics and Phylogenetic Studies
- Extracellular vesicles in disease
- interferon and immune responses
- RNA Interference and Gene Delivery
- Cancer Genomics and Diagnostics
- Mycobacterium research and diagnosis
- Single-cell and spatial transcriptomics
- Cancer, Hypoxia, and Metabolism
- Chromatin Remodeling and Cancer
- Ocular Oncology and Treatments
- Epigenetics and DNA Methylation
- Estrogen and related hormone effects
- CRISPR and Genetic Engineering
- Ubiquitin and proteasome pathways
Ghent University Hospital
2016-2025
Cancer Research Institute Ghent
2016-2025
Ghent University
2016-2025
VIB-UGent Center for Medical Biotechnology
2019-2024
VIB-UGent Center for Inflammation Research
2017
University of Southampton
2017
George Washington University
2017
Children's Cancer Center
2011
Baylor College of Medicine
2011
Royal College of Surgeons in Ireland
2010-2011
Abstract Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use mean value all expressed microRNAs in a given sample as normalization factor for real-time quantitative PCR data and compare its performance to currently adopted approach. We demonstrate that outperforms current strategy terms better reduction technical variation more accurate appreciation biological changes.
Despite an enormous interest in the role of extracellular vesicles, including exosomes, cancer and their use as biomarkers for diagnosis, prognosis, drug response recurrence, there is no consensus on dependable isolation protocols. We provide a comparative evaluation 4 exosome protocols usability, yield purity, impact downstream omics approaches biomarker discovery. OptiPrep density gradient centrifugation outperforms ultracentrifugation ExoQuick Total Exosome Isolation precipitation terms...
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique features, clinically significant subtypes, potential therapeutic targets. found 61 somatic copy-number alterations (SCNAs) 46 significantly mutated genes (SMGs). Eleven SCNAs 11 SMGs had not been identified in previous TCGA studies the individual tumor types. functionally estrogen receptor-regulated long non-coding RNAs (lncRNAs)...
While long non-coding RNA (lncRNA) research in the past has primarily focused on discovery of novel genes, today it shifted towards functional annotation this large class genes. With thousands lncRNA studies published every year, current challenge lies keeping track which lncRNAs are functionally described. This is further complicated by fact that nomenclature not straightforward and scattered across different resources with their own quality metrics definition a lncRNA. To overcome issue,...
Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute large diverse class of Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods identify new (including sequencing annotation chromatin-state maps) applied in various studies resulting multiple unrelated lncRNA data sets. offers 21 488 annotated obtained from...
The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. majority these transcripts are long RNAs (lncRNAs) and novel lncRNA genes being identified at rapid pace. To streamline efforts, we created LNCipedia, an online repository annotation. Here, present LNCipedia 3.0 (http://www.lncipedia.org), the latest version publicly available database. Compared to previous database grew over five times in size, gaining 90 000 new Assessment protein-coding...
Many computational methods have been developed to infer cell type proportions from bulk transcriptomics data. However, an evaluation of the impact data transformation, pre-processing, marker selection, composition and choice methodology on deconvolution results is still lacking. Using five single-cell RNA-sequencing (scRNA-seq) datasets, we generate pseudo-bulk mixtures evaluate combined these factors. Both methodologies those that use scRNA-seq as reference perform best when applied in...
RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive counts from sequencing reads. While a number of benchmarking studies conducted, question remains how individual methods perform at accurately quantifying levels We performed an independent study using data well established MAQCA and MAQCB reference samples. reads were processed five workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq,...
MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs implicated in a wide variety cellular processes. Research this field is accelerating, and the growing number miRNAs emphasizes need for high-throughput sensitive detection methods. Here we present successful evaluation Megaplex reverse transcription format stem-loop primer-based real-time quantitative polymerase chain reaction (RT-qPCR) approach to quantify miRNA expression. The provides simultaneous 450 mature miRNAs,...
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface...
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides single entry point for accessing all types organisms. Since its launch in 2014, has integrated twelve new resources, taking the total number collaborating to 22, began importing data, such as modified nucleotides MODOMICS PDB. We created species-specific identifiers refer unique within context species. The website been subject continuous improvements focusing on...
Skeletal muscle is a heterogenous tissue comprised primarily of myofibers, commonly classified into three fiber types in humans: one "slow" (type 1) and two "fast" 2A type 2X). However, heterogeneity between within traditional remains underexplored. We applied transcriptomic proteomic workflows to 1050 1038 single myofibers from human vastus lateralis, respectively. Proteomics was conducted males, while transcriptomics included ten males females. identify metabolic, ribosomal, cell junction...
Rationale: Chronic obstructive pulmonary disease (COPD) is characterized by progressive inflammation in the airways and lungs combined with disturbed homeostatic functions of cells. MicroRNAs (miRNAs) have ability to regulate these processes interfering gene transcription translation.Objectives: We aimed identify miRNA expression induced sputum examined whether miRNAs differed between patients COPD subjects without airflow limitation.Methods: Expression 627 was evaluated supernatant 32...
Abstract Background Advances in high-throughput technologies and bioinformatics have transformed gene expression profiling methodologies. The results of microarray experiments are often validated using reverse transcription quantitative PCR (RT-qPCR), which is the most sensitive reproducible method to quantify expression. Appropriate normalisation RT-qPCR data stably expressed reference genes critical ensure accurate reliable results. Mi(cro)RNA profiles been shown be more disease...
Small non-coding RNAs, in particular microRNAs(miRNAs), regulate fine-tuning of gene expression and can act as oncogenes or tumor suppressor genes. Differential miRNA has been reported to be functional relevance for biology. Using next-generation sequencing, the unbiased absolute quantification small RNA transcriptome is now feasible. Neuroblastoma(NB) an embryonal with highly variable clinical course. We analyzed transcriptomes five favorable unfavorable NBs using SOLiD generating a total...