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Search: authors:"Marc Chadeau-Hyam"

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Causal diagrams in systems epidemiology

Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed. The...

Dynamics of smoking-induced genome-wide methylation changes with time since smoking cessation

Several studies have recently identified strong epigenetic signals related to tobacco smoking. However, an aspect that did not receive much attention is the evolution of epigenetic changes with time since smoking cessation. We conducted a series of epigenome-wide association studies to capture the dynamics of smoking-induced epigenetic changes after smoking cessation, using...

Epigenome-wide association study reveals decreased average methylation levels years before breast cancer diagnosis

Flower 1 Ed Curry 1 Nicholas Orr Katarzyna Tomczyk Michael E. Jones Alan Ashworth Anthony Swerdlow Marc Chadeau-Hyam 4 Eiliv Lund Montserrat Garcia-Closas Torkjel M. Sandanger James M. Flanagan 0 1 Paolo

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...

Blood Erythrocyte Concentrations of Cadmium and Lead and the Risk of B-Cell Non-Hodgkin’s Lymphoma and Multiple Myeloma: A Nested Case-Control Study

BackgroundCadmium (Cd) and lead (Pb) are hypothesised to be risk factors for non-Hodgkin’s lymphoma (NHL), a group of haematological malignancies with a suspected environmental aetiology. Within the EnviroGenoMarkers study we utilised pre-diagnostic erythrocyte concentrations of Cd and Pb to determine whether exposure was associated with risk of B-cell NHL and multiple myeloma...

ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration

Summary: ESS++ is a C++ implementation of a fully Bayesian variable selection approach for single and multiple response linear regression. ESS++ works well both when the number of observations is larger than the number of predictors and in the ‘large p, small n’ case. In the current version, ESS++ can handle several hundred observations, thousands of predictors and a few...

GUESS-ing Polygenic Associations with Multiple Phenotypes Using a GPU-Based Evolutionary Stochastic Search Algorithm

received funding from the Wellcome Trust Value-in-People award. Leonardo Bottolo and Sylvia Richardson acknowledge support from the Medical Research Council (grant G1002319). Marc Chadeau-Hyam acknowledges

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...