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Bayesian estimation of the number of protonation sites for urinary metabolites from NMR spectroscopic data

Surgery and Cancer, Computational and Systems Medicine, Imperial College London , London , UK 1 Maria De Iorio 2 Timothy M. D. Ebbels Introduction To aid the development of better algorithms for 1H NMR ... standards Conflict of interest Lifeng Ye, Maria De Iorio and Timothy M. D. Ebbels declare that they have no conflict of interest. Ethical approval This study analysed previously collected data which

Lower urinary tract symptoms that predict microscopic pyuria

Introduction and hypothesis Urinary dipsticks and culture analyses of a mid-stream urine specimen (MSU) at 105 cfu ml−1 of a known urinary pathogen are considered the gold standard investigations for diagnosing urinary tract infection (UTI). However, the reliability of these tests has been much criticised and they may mislead. It is now widely accepted that pyuria (≥1 WBC μl−1...

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine

). Compliance with Ethical Standards Conflict of Interest Gregory D. Tredwell, Jacob G. Bundy, Maria De Iorio and Timothy M. D. Ebbels declare that they have no conflict of interest. Ethical approval All

Significance testing in ridge regression for genetic data

Background Technological developments have increased the feasibility of large scale genetic association studies. Densely typed genetic markers are obtained using SNP arrays, next-generation sequencing technologies and imputation. However, SNPs typed using these methods can be highly correlated due to linkage disequilibrium among them, and standard multiple regression techniques...

Urinary ATP as an indicator of infection and inflammation of the urinary tract in patients with lower urinary tract symptoms

Background Adenosine-5′-triphosphate (ATP) is a neurotransmitter and inflammatory cytokine implicated in the pathophysiology of lower urinary tract disease. ATP additionally reflects microbial biomass thus has potential as a surrogate marker of urinary tract infection (UTI). The optimum clinical sampling method for ATP urinalysis has not been established. We tested the potential...

The time machine: a simulation approach for stochastic trees

In this paper, we consider a simulation technique for stochastic trees. One of the most important areas in computational genetics is the calculation and subsequent maximization of the likelihood function associated with such models. This typically consists of using importance sampling and sequential Monte Carlo techniques. The approach proceeds by simulating the tree, backward in...

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity

Beatriz Valcrcel Timothy M. D. Ebbels Antti J. Kangas Pasi Soininen Paul Elliot Mika Ala-Korpela Marjo-Riitta Jrvelin Maria de Iorio connections between genetic variants and complex traits: an ... . http://dx.doi.org/10.1098/rsif.2013.0908 Received: 6 October 2013 Accepted: 5 February 2014 Subject Areas: systems biology Author for correspondence: Maria de Iorio e-mail: Electronic supplementary

BATMAN—an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model

Motivation: Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject...

MetAssimulo:Simulation of Realistic NMR Metabolic Profiles

Background Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical...

Genetic Association Mapping via Evolution-Based Clustering of Haplotypes

Multilocus analysis of single nucleotide polymorphism haplotypes is a promising approach to dissecting the genetic basis of complex diseases. We propose a coalescent-based model for association mapping that potentially increases the power to detect disease-susceptibility variants in genetic association studies. The approach uses Bayesian partition modelling to cluster haplotypes...

Bayesian logistic regression using a perfect phylogeny

Oxford , Oxford , UK and Department of Epidemiology and Public Health, Imperial College , London, UK MARIA DE IORIO c The Author 2006. Published by Oxford University Press. All rights reserved. For

A Differential Network Approach to Exploring Differences between Biological States: An Application to Prediabetes

Background Variations in the pattern of molecular associations are observed during disease development. The comprehensive analysis of molecular association patterns and their changes in relation to different physiological conditions can yield insight into the biological basis of disease-specific phenotype variation. Methodology Here, we introduce a formal statistical method for...

Bayesian survival analysis in genetic association studies

Motivation: Large-scale genetic association studies are carried out with the hope of discovering single nucleotide polymorphisms involved in the etiology of complex diseases. There are several existing methods in the literature for performing this kind of analysis for case-control studies, but less work has been done for prospective cohort studies. We present a Bayesian method...

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies

Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in...

A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy

Petrovski 13 21 Ioanna Tachmazidou 20 Alison Coffey 20 Andrea Jorgensen 19 Hariklia Eleftherohorinou 15 Maria De Iorio 18 Marian Todaro 13 Tisham De 18 David Smith 23 Philip E. Smith 22 Margaret Jackson 17

Fregene: Simulation of realistic sequence-level data in populations and ascertained samples

Background FREGENE simulates sequence-level data over large genomic regions in large populations. Because, unlike coalescent simulators, it works forwards through time, it allows complex scenarios of selection, demography, and recombination to be modelled simultaneously. Detailed tracking of sites under selection is implemented in FREGENE and provides the opportunity to test...

Conserved Mosquito/Parasite Interactions Affect Development of Plasmodium falciparum in Africa

In much of sub-Saharan Africa, the mosquito Anopheles gambiae is the main vector of the major human malaria parasite, Plasmodium falciparum. Convenient laboratory studies have identified mosquito genes that affect positively or negatively the developmental cycle of the model rodent parasite, P. berghei. Here, we use transcription profiling and reverse genetics to explore whether...