David Quigley

Learn More
Unionfs is a stackable file system that virtually merges a set of directories (called branches) into a single logical view. Each branch is assigned a priority and may be either read-only or read-write. When the highest priority branch is writable, Unionfs provides copy-on-write semantics for read-only branches. These copy-on-write semantics have lead to(More)
Inferring gene regulatory networks from high-throughput genomic data is one of the central problems in computational biology. In this paper, we describe a predictive modeling approach for studying regulatory networks, based on a machine learning algorithm called MEDUSA. MEDUSA integrates promoter sequence, mRNA expression, and transcription factor occupancy(More)
Analysis of gene expression patterns in normal tissues and their perturbations in tumours can help to identify the functional roles of oncogenes or tumour suppressors and identify potential new therapeutic targets. Here, gene expression correlation networks were derived from 92 normal human lung samples and patient-matched adenocarcinomas. The networks from(More)
Calcium carbonate is an abundant substance that can be created in several mineral forms by the reaction of dissolved carbon dioxide in water with calcium ions. Through biomineralization, organisms can harness and control this process to form various functional materials that can act as anything from shells through to lenses. The early stages of calcium(More)
INTRODUCTION Time-sensitive chemicals are those chemicals that when stored for prolonged periods can develop hazards that were not present in the original formulation. These additional hazards develop from inappropriate and improper storage conditions as well as simply storing the chemicals too long. In the field of chemical management , unfortunately we(More)
Psoriasis is a chronic inflammatory skin disease driven by aberrant signals from the immune system. In this issue, Li et al. present the first large RNA-seq analysis of gene expression in normal skin and psoriasis lesions, providing a more comprehensive view of mRNA expression than earlier microarray studies. This study's size enables gene co-expression(More)
The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to(More)