A5037818042- Gene expression and cancer classification
- Genomic variations and chromosomal abnormalities
- Cancer Genomics and Diagnostics
- Platelet Disorders and Treatments
- Spectroscopy and Chemometric Analyses
- Single-cell and spatial transcriptomics
- Statistical Methods and Inference
- Advanced Statistical Methods and Models
- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Genomics and Rare Diseases
- Cancer-related molecular mechanisms research
- Cell Adhesion Molecules Research
- Genetic Associations and Epidemiology
- Optimal Experimental Design Methods
- Genetic factors in colorectal cancer
- Statistical Methods in Clinical Trials
- Acute Myeloid Leukemia Research
- Cell Image Analysis Techniques
- Spectroscopy Techniques in Biomedical and Chemical Research
- Atherosclerosis and Cardiovascular Diseases
- Fibromyalgia and Chronic Fatigue Syndrome Research
- Power System Optimization and Stability
- Power System Reliability and Maintenance
- Myeloproliferative Neoplasms: Diagnosis and Treatment
University of Leeds
2015-2024
Cyprus University of Technology
2022
King Saud University
2014
Illumina (United Kingdom)
2014
Karolinska Institutet
2003-2013
Medical Research Council
2005-2010
MRC Biostatistics Unit
2005-2009
University College Cork
2007
Institute for Medical Informatics and Biostatistics
2007
GTx (United States)
2007
Abstract The question of what significance threshold is appropriate for genomewide association studies somewhat unresolved. Previous theoretical suggestions have yet to be validated in practice, whereas permutation testing does not resolve a discrepancy between the multiplicity experiment and subset markers actually tested. We used genotypes from Wellcome Trust Case‐Control Consortium estimate UK Caucasian population. subsampled at increasing densities, using nominal P ‐value 5% family‐wise...
Motivation: In microarray data studies most researchers are keenly aware of the potentially high rate false positives and need to control it. One key statistical shift is move away from well-known P-value discovery (FDR). Less discussion perhaps has been spent on sensitivity or associated negative (FNR). The purpose this paper explain in simple ways why FDR for assessment necessary, elucidate determining factors and, a two-sample comparative study, discuss its via sample size at design stage.
Abstract Hematopoiesis is a carefully controlled process that regulated by complex networks of transcription factors are, in part, signals resulting from ligand binding to cell-surface receptors. To further understand hematopoiesis, we have compared gene expression profiles human erythroblasts, megakaryocytes, B cells, cytotoxic and helper T natural killer granulocytes, monocytes using whole genome microarrays. A bioinformatics analysis these data was performed focusing on factors,...
Abstract Motivation: Comparison of read depths from next-generation sequencing between cancer and normal cells makes the estimation copy number alteration (CNA) possible, even at very low coverage. However, estimating CNA patients' tumour samples poses considerable challenges due to infiltration with aneuploid genomes. Here we provide a method that corrects contamination adjusts for genomes different sizes so actual each region can be estimated. Results: The procedure consists several steps....
The literature exploring the executive function correlates of bilingualism is vast, but to date, few studies have concentrated on children, for whom bilingual advantage appears even more inconsistent than adults. We investigate a highly heterogeneous group children (in terms experience and socioeconomic status) identify critical threshold from which an can be observed at level. modeling methods adopted allow use fine-grained, continuous factors age status, thereby effectively controlling...
Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all neoplasms. Patients receive surgery and chemoradiotherapy but almost always fatally recur.
Abstract This meta-analysis was conducted to clarify the role of klotho and fibroblast growth factor 23 (FGF-23) in human arterial remodeling across recent studies, terms calcification, thickness, stiffness. A systematic literature search on five databases for articles up December 2023. Arterial stiffness were determined using calcification score artery affected, carotid intima–media thickness (CIMT), pulse wave velocity (PWV), respectively. Sixty-two studies with a total 27,459 individuals...
Abstract Motivation: The false discovery rate (fdr) is a key tool for statistical assessment of differential expression (DE) in microarray studies. Overall control the fdr alone, however, not sufficient to address problem genes with small variance, which generally suffer from disproportionally high positives. It desirable have an fdr-controlling procedure that automatically accounts gene variability. Methods: We generalize local as function multiple statistics, combining common test...
The diagnosis of follicular thyroid carcinoma (FTC) in the absence metastasis can only be established postoperatively. Moreover, high-risk FTCs are often not identifiable at time diagnosis. In this study, we aimed to identify transcriptional markers malignancy and disease tumors. expression levels 26 potential were determined a panel 75 tumors by TaqMan quantitative RT-PCR approach. Logistic regression analysis (LRA) was used for gene selection generation diagnostic prognostic algorithms. An...
Glioblastoma (GBM), the most aggressive adult brain cancer, comprises a complex tumour microenvironment (TME) with diverse cellular interactions driving progression and pathobiology. How these spatial patterns evolve treatment remains unclear. Here, we apply imaging mass cytometry to analyse protein-level changes in paired pre- post-treatment GBM samples from five patients. We find significant increase normal cells alongside reduction vascular cells. Moreover, despite minimal overall change...
What is the optimal level of questionnaire detail required to measure bilingual language experience? This empirical evaluation compares alternative measures exposure varying cost (i.e., detail) in terms their performance as predictors oral outcomes. The were derived from Q-BEx data collected a diverse sample 121 heritage bilinguals (5- 9-years age) growing up France, Netherlands and UK. Outcome consisted morphosyntax vocabulary (in societal language) parental estimates proficiency language)....
The richness of bilingual children’s language experience is typically expressed as a composite score using parental questionnaire data. This study unpacks the concept input by examining one such (Q-BEx; De Cat et al., 2022b) to determine whether it reliably predicts abilities, no more complex than required, and user-friendly possible. Data were collected from 173 children aged 5 8 across three countries (France, Netherlands, UK) with various heritage languages in each. Parents completed...
Purpose: Clinical triage, but also inclusive population sampling in research, requires efficient detection of children likely to be at risk for language impairment (LI), a significant challenge the case bilingual children. Our goal was derive automatic factor indices from parental questionnaire and compare their usefulness initial identification LI.Method: Alternative were derived Q-BEx online backend calculator, differing weight detail given proficiency. Each index applied two datasets...
Array comparative genomic hybridization (aCGH) provides a genome-wide technique to screen for copy number alteration. The existing segmentation approaches analyzing aCGH data are based on modeling as series of discrete segments with unknown boundaries and heights. Although the biological process alteration is discrete, in reality variety experimental factors can cause signal deviate from stepwise function. To take this into account, we propose smooth (smoothseg) approach.To achieve robust...
Current high-throughput sequencing has greatly transformed genome sequence analysis. In the context of very low-coverage (<0.1×), performing 'binning' or 'windowing' on mapped short sequences ('reads') is critical to extract genomic information interest for further evaluation, such as copy-number alteration If window size too small, many windows will exhibit zero counts and almost no pattern can be observed. contrast, if wide, patterns features 'smoothed out'. Our objective identify an...
Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between cellular landscape tumor phenotypes or clinical correlates. We aimed to develop tool that deconvolutes immune neoplastic cells GBM microenvironment from bulk RNA sequencing data.
Abstract Completion of the fission yeast genome sequence has opened up possibilities for post‐genomic approaches. We have constructed a DNA microarray genome‐wide gene expression analysis in yeast. The contains fragments, PCR‐amplified from genomic template, that represent > 99% 5000 or so annotated genes, as well number control sequences. GenomePRIDE software used attempts to design similarly sized fragments corresponding regions within single exons, near 3′‐end genes lack homology other...
It is widely accepted that atherosclerosis and inflammation are intimately linked. Monocytes play a key role in both of these processes we hypothesized activation inflammatory pathways monocytes would lead to, among others, proatherogenic changes the monocyte transcriptome. Such differentially expressed genes circulating be strong candidates for further investigation disease association studies.Endotoxin, lipopolysaccharide (LPS), or saline control was infused healthy volunteers. Monocyte...