Latest

• Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies
• Congratulations to Dr. Morlion
• Unveiling cancer signals in liquid biopsy cell-free RNA profiles
• A doctorate as a flight
• Congratulations to Dr. Verwilt
• Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies
• Congratulations to Dr. Deleu
• Extracellular RNA in liquid biopsies: entering a new era for cancer treatment monitoring?
• Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
• Congratulations to Dr. Schoofs
• Nucleic acid biomarkers in blood from patients with esophageal adenocarcinoma: finding the needle in the haystack
• Congratulations to Dr. Vromman
• Chasing circles: developing a toolbox for circRNA detection and validation
• Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls
• OncoRNALab @ ANR meeting 2023
• Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics
• Artifacts and biases of the reverse transcription reaction in RNA sequencing
• Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation
• OncoRNALab lab weekend
• Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation
• Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA
• Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study
• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA
• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel, and secondary fusion transcripts in FFPE tissue: a sarcoma showcase
• Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes
• CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification
• CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
• Congratulations to Dr. Dewaele!
• RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer
• The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19
• Congratulations to Dr. Hulstaert!
• Exploring RNA signatures in human biofluids as novel liquid biopsy tool
• Custom long non-coding RNA capture enhances detection sensitivity in different human sample types
• Validation of Circular RNAs Using RT‐qPCR After Effective Removal of Linear RNAs by Ribonuclease R
• Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls
• The RNA Atlas expands the catalog of human non-coding RNAs
• Congratulations to Dr. Lorenzi!
• Charting regulatory RNAs in the human transcriptome using RNA-sequencing
• Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas
• Candidate RNA biomarkers in biofluids for early diagnosis of ovarian cancer: A systematic review
• Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2
• When DNA gets in the way: A cautionary note for DNA contamination in extracellular RNA-seq studies
• To pool or not to pool?
• Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for diagnostic screening purposes
• Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study
• The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020
• Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome
• Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development
• On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
• OncoRNALab against corona
• Statistical methods for testing differential gene expression in bulk and single-cell RNA sequencing data
• Congratulations to Dr. Everaert!
• Development of extracellular RNA sequencing technologies and applications for cancer diagnosis and monitoring
• SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data
• circRNA
• Closing the circle: current state and perspectives of circular RNA databases
• Vapor nanobubble is the more reliable photothermal mechanism for inducing endosomal escape of siRNA without disturbing cell homeostasis
• Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
• Charting extracellular transcriptomes in The Human Biofluid RNA Atlas
• The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35
• The RNA Atlas, a single nucleotide resolution map of the human transcriptome
• Data analysis methods for digital PCR quantification
• Deciphering complete cancer transcriptomes from bulk to single cell level
• Probabilistic index models for testing differential expression in single cell RNA sequencing data
• The generation and use of recombinant extracellular vesicles as biological reference material
• A comprehensive dataset of TLX1 positive ALL-SIL lymphoblasts and primary T-cell acute lymphoblastic leukemias
• SMARTer single cell total RNA sequencing
• Congratulations to Prof. Vandesompele, Prof. De Preter, and Prof. Mestdagh for the prestigious Antoine Faes prize
• Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes
• Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes
• Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer’s disease
• Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR
• Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer: not ready for prime time
• A mechanistic classification of clinical phenotypes in neuroblastoma
• Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients
• Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction
• In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
• Long noncoding RNA expression profiling in cancer: Challenges and opportunities
• LNCipedia 5: towards a reference set of human long non-coding RNAs
• Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines
• Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
• On determining the power of digital PCR experiments
• A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing
• Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope?
• The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation
• Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice
• Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background
• A high-throughput 3’ UTR reporter screening identifies microRNA interactomes of cancer genes
• Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
• Localization and Expression of Nuclear Factor of Activated T-Cells 5 in Myoblasts Exposed to Pro-inflammatory Cytokines or Hyperosmolar Stress and in Biopsies from Myositis Patients
• Computational deconvolution of transcriptomics data from mixed cell populations
• Prognostic and Therapeutic Implications of Circulating Androgen Receptor Gene Copy Number in Prostate Cancer Patients Using Droplet Digital Polymerase Chain Reaction
• The mutational landscape of <i>MYCN, Lin28b</i> and <i>ALK^F1174L</i> driven murine neuroblastoma mimics human disease
• The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease
• Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR
• MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation
• High-throughput PCR assay design for targeted resequencing using primerXL
• Expression Profiling Identifies the Noncoding Processed Transcript of HNRNPU with Proliferative Properties in Pancreatic Ductal Adenocarcinoma
• A unified censored normal regression model for qPCR differential gene expression analysis
• Quality control of digital PCR assays and platforms
• Dual targeting of MDM2 and BCL2 as a therapeutic strategy in neuroblastoma
• Thermodynamic framework to assess low abundance DNA mutation detection by hybridization
• Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products
• decodeRNA— predicting non-coding RNA functions using guilt-by-association
• Zipper plot: visualizing transcriptional activity of genomic regions
• Long non-coding RNAs in cutaneous melanoma: clinical perspectives
• MicroRNA-184 is a downstream effector of albuminuria driving renal fibrosis in rats with diabetic nephropathy
• Model-Based Classification for Digital PCR: Your Umbrella for Rain
• Influence of microRNAs and Long Non-Coding RNAs in Cancer Chemoresistance
• Reply: Direct Detection of Circulating MicroRNAs Unveiled the Absence of MicroRNA-218-5p in Smoker Subjects
• EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research
• Erratum: Corrigendum: Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay
• miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure
• Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
• The transcriptome of lung tumor-infiltrating dendritic cells reveals a tumor-supporting phenotype and a microRNA signature with negative impact on clinical outcome
• Exploring the neuroblastoma DNA methylome: from biology to biomarker
• Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay
• Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait
• MicroRNA Profiling Reveals a Role for MicroRNA-218-5p in the Pathogenesis of Chronic Obstructive Pulmonary Disease
• Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR
• Flexible analysis of digital PCR experiments using generalized linear mixed models
• Asthma inflammatory phenotypes show differential microRNA expression in sputum
• CiLiQuant
• CIRCprimerXL
• digital PCR
• EV-TRACK
• LNCipedia
• miRBase Tracker
• miSTAR
• primerXL
• RDML database
• ZipperPlot
• Melanoma addiction to the long non-coding RNA SAMMSON
• Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples
• DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
• Renal microRNA- and RNA-profiles in progressive chronic kidney disease
• Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma
• Targeted resequencing and variant validation using pxlence PCR assays
• Exploring lncRNAs in cancer: tools for discovery and characterization of cancer associated lncRNAs
• Inhibition of CDK4/6 as a novel therapeutic option for neuroblastoma
• RNA expression signatures and posttranscriptional regulation in diabetic nephropathy
• MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma
• miRNome-wide high-throughput microRNA target identification
• Alternative Routes to Induce Naïve Pluripotency in Human Embryonic Stem Cells
• Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
• RDML-Ninja and RDMLdb for standardized exchange of qPCR data
• Massively parallel sequencing technologies in neuroblastoma research
• Non-coding RNAs in the pathogenesis of COPD
• Identification of miRNAs contributing to neuroblastoma chemoresistance
• RT-qPCR-Based Quantification of Small Non-Coding RNAs
• Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma
• Individual patient risk stratification of high-risk neuroblastomas using a two-gene score suited for clinical use
• Flexible, Scalable, and Efficient Targeted Resequencing on a Benchtop Sequencer for Variant Detection in Clinical Practice
• CASP8 SNP D302H (rs1045485) Is Associated with Worse Survival in MYCN-Amplified Neuroblastoma Patients
• An update on LNCipedia: a database for annotated human lncRNA sequences
• MiR-34a deficiency accelerates medulloblastoma formationin vivo
• Expressed Repeat Elements Improve RT-qPCR Normalization across a Wide Range of Zebrafish Gene Expression Studies
• The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling
• miRBase Tracker: keeping track of microRNA annotation changes
• Illumina sequencing of 15 deafness genes using fragmented amplicons
• miR-542-3p exerts tumor suppressive functions in neuroblastoma by downregulating Survivin
• Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study
• Characterization of the p53 network and new therapeutic opportunities in neuroblastoma
• Early Targets of miR-34a in Neuroblastoma
• Lung tumours reprogram pulmonary dendritic cell immunogenicity at the microRNA level
• Selection of Reliable Reference Genes for RT-qPCR Analysis
• Target enrichment using parallel nanoliter quantitative PCR amplification
• Lack of association betweenMDM2promoter SNP309 and clinical outcome in patients with neuroblastoma
• Pharmacologic activation of wild-type p53 by nutlin therapy in childhood cancer
• The need for transparency and good practices in the qPCR literature
• Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells
• Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays
• Effective Alu Repeat Based RT-Qpcr Normalization in Cancer Cell Perturbation Experiments
• The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments
• CLL Cells Respond to B-Cell Receptor Stimulation with a MicroRNA/mRNA Signature Associated with MYC Activation and Cell Cycle Progression
• Regulatory microRNA Network Identification in Bovine Blastocyst Development
• MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A
• Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes
• LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression
• LNCipedia: a database for annotated human lncRNA transcript sequences and structures
• Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
• Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications
• Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer
• Identification of miR-145 as a Key Regulator of the Pigmentary Process
• Synthetic lethality between Rb, p53 and Dicer or miR-17–92 in retinal progenitors suppresses retinoblastoma formation
• Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform
• Development of bioinformatics tools for high-throughput PCR applications
• Cancer Gene Prioritization for Targeted Resequencing Using FitSNP Scores
• N-Cadherin in Neuroblastoma Disease: Expression and Clinical Significance
• Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis
• Accurate RT-qPCR gene expression analysis on cell culture lysates
• miRNA Expression Profiling: From Reference Genes to Global Mean Normalization
• Whole-Genome RT-qPCR MicroRNA Expression Profiling
• Neuroblastoma epigenetics: From candidate gene approaches to genome-wide screenings
• Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics
• The microRNA body map: dissecting microRNA function through integrative genomics
• Neuroblastoma genetics and phenotype: A tale of heterogeneity
• Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma
• Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas
• Molecular portraits of non-coding RNAs in neuroblastoma
• Primer Sequence Disclosure: A Clarification of the MIQE Guidelines
• Measurable impact of RNA quality on gene expression results from quantitative PCR
• New options for molecular therapy of neuroblastoma: from p53 to gene therapy
• Differential mucosal expression of Th17-related genes between the inflamed colon and ileum of patients with inflammatory bowel disease
• The miR-17-92 MicroRNA Cluster Regulates Multiple Components of the TGF-β Pathway in Neuroblastoma
• MicroRNA Expression in Induced Sputum of Smokers and Patients with Chronic Obstructive Pulmonary Disease
• Prognostic Impact of Gene Expression–Based Classification for Neuroblastoma
• Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline
• Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
• Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma.
• Accurate prediction of neuroblastoma outcome based on miRNA expression profiles
• MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer
• Improved Molecular Diagnostics of Idiopathic Short Stature and Allied Disorders: Quantitative Polymerase Chain Reaction-Based Copy Number Profiling ofSHOXand Pseudoautosomal Region 1
• miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis
• Accurate and objective copy number profiling using real-time quantitative PCR
• Improved outcome prediction of children with neuroblastoma using a multigene expression signature
• Selection of reference genes for quantitative real-time PCR in equine in vivo and fresh and frozen-thawed in vitro blastocysts
• How to do successful gene expression analysis using real-time PCR
• RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts
• Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
• Antitumor Activity of the Selective MDM2 Antagonist Nutlin-3 Against Chemoresistant Neuroblastoma With Wild-Type p53
• 59-gene prognostic signature sub-stratifies high-risk neuroblastoma patients
• Comparison of miRNA profiles of microdissected Hodgkin/Reed-Sternberg cells and Hodgkin cell linesversusCD77+B-cells reveals a distinct subset of differentially expressed miRNAs
• Amphiregulin and Epiregulin mRNA Expression in Primary Tumors Predicts Outcome in Metastatic Colorectal Cancer Treated With Cetuximab
• External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data
• External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data
• The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy
• Chromosome 3p Microsatellite Allelotyping in Neuroblastoma: A Report on the Technical Hurdles
• A novel and universal method for microRNA RT-qPCR data normalization
• Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study
• Unreliable Real-Time PCR Analysis of Human Endogenous Retrovirus-W (HERV-W) RNA Expression and DNA Copy Number in Multiple Sclerosis
• The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
• Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral and cerebellar cortex of sheep
• High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA
• Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas
• Aberrant methylation of candidate tumor suppressor genes in neuroblastoma
• Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
• CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23
• Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma
• A Constitutional Translocation t(1;17)(p36.2;q11.2) in a Neuroblastoma Patient Disrupts the Human NBPF1 and ACCN1 Genes
• Standardization of real-time PCR gene expression data from independent biological replicates
• High resolution genome analysis for improved prognostic stratification and candidate gene selection in neuroblastoma
• Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans
• Identification of MYCN transcriptional target genes in neuroblastoma
• High throughput analyses for assessment of DNA copy number and methylation status for chromosome 3p genes in high-risk neuroblastoma
• Delineation of the heterogeneous pattern of genomic changes and identifacation of differentially expressed genes in neuroblastoma