R
R is a free, open source, platform independent programming language for statistics and publication quality graphics. It is supported by a highly active user community that develops open source code, much of which is available at the Comprehensive R Archive Network. R is widely used in bioinformatics, with numerous libraries available as part of the BioConductor project.
See the R Project homepage for more information.
For queries about this topic, contact Richard Edwards.
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Projects
Automated selection of suitable atmospheric calibration sites for satellite imagery
Robin Wilson (Investigator)
Ground calibration targets (GCTs) play a vital role in atmospheric correction of satellite sensor data in the optical region, but selecting suitable targets is a subjective and time- consuming task. This project is developing methods to automatically select suitable GCTs, using a combination of remotely sensed multispectral and topographic data.
Integrated in silico prediction of protein-protein interaction motifs
Richard Edwards (Investigator), Kieren Lythgow
Many vital protein-protein interactions are mediated by Short Linear Motifs (SLiMs) which are short proteins typically 5-15 amino acids long containing only a few positions crucial to function. This project integrates a number of leading computational techniques to predict novel SLiMs and add crucial detail to protein-protein interaction networks.
Interactome-wide prediction of short linear protein interaction motifs in humans
Richard Edwards (Investigator)
Short Linear Motifs (SLiMs) are important in many protein-protein interactions. In previous work, we have developed a computational tool, SLiMFinder, which places the interpretation of evidence for motifs within a statistical framework with high specificity, and subsequently enhanced sensitivity through application of conservation-based sequence masking. We are now applying these tools to a comprehensive set of human protein-protein interactions in order to predict novel human SLiMs in silico.
Modelling Macro-Nutrient Release & Fate Resulting from Sediment Resuspension in Shelf Seas
Chris Wood
This study involves adapting a previously-published model to take into account the effect resuspension events (both natural and anthropogenic) may have on nutrient dynamics at the sediment-water interface, and hence produce better estimates for the total nutrient budgets for shelf seas.
Network Analysis of Roman Transport Routes in the Imperial Roman Mediterranean
David Potts
This research is designed to explore the nature of the relationships between Portus, Rome, and other selected ports in the Mediterranean and to establish patterns and the changing nature of trading networks derived from the distribution of known Roman artefacts.
Scalability of Energy Efficient Routing Algorithms in WSN
Davide Zilli
This project compares two broad classes of routing algorithms for Wireless Sensor Networks, message flooding and single path, by means of a simulation model. In particular, we want to understand how the two scale in terms of energy efficiency on large networks of sensors.
Structured low-rank approximation
Ivan Markovsky
Today's state-of-the-art methods for data processing are model based. We propose a fundamentally new approach that does not depend on an explicit model representation and can be used for model-free data processing. From a theoretical point of view, the prime advantage of the newly proposed paradigm is conceptual unification of existing methods. From a practical point of view, the proposed paradigm opens new possibilities for development of computational methods for data processing.
Tag based transcriptome analysis of gene expression in a promising green algae
Richard Edwards, Andreas Johansson
We use SuperSAGE in combination with next-generation sequencing to compare differences in gene expression between selected mutants and the wild type of a green algae. The data in the form of millions of 26 bp tags representing short stretches of expressed genes, will be analysed to find patterns of variation in gene expression under different conditions.
People
Andrew CollinsProfessor, Medicine (FM)
Ivan MarkovskyLecturer, Electronics and Computer Science (FPAS)
Reno ChoiSenior Research Fellow, Geography (FSHS)
Richard EdwardsSenior Research Fellow, Biological Sciences (FNES)
Guy AbelResearch Fellow, Social Sciences (FSHS)
Jane GibsonResearch Fellow, Medicine (FM)
Gunnar MallonResearch Fellow, Geography (FSHS)
Jordi ArranzPostgraduate Research Student, Electronics and Computer Science (FPAS)
Ashley BoothPostgraduate Research Student, Electronics and Computer Science (FPAS)
Aleksander DubasPostgraduate Research Student, Engineering Sciences (FEE)
Pepe FalahatPostgraduate Research Student, Electronics and Computer Science (FPAS)
Tom HebbronPostgraduate Research Student, Electronics and Computer Science (FPAS)
James HeppellPostgraduate Research Student, Electronics and Computer Science (FPAS)
Joshua Jeeson DanielPostgraduate Research Student, Engineering Sciences (FEE)
Leo JofehPostgraduate Research Student, Electronics and Computer Science (FPAS)
Andreas JohanssonPostgraduate Research Student, National Oceanography Centre (FNES)
David PottsPostgraduate Research Student, Humanities (FH)
Sonya RiddenPostgraduate Research Student, Mathematics (FSHS)
Barbara SanderPostgraduate Research Student, Chemistry (FNES)
Nick SynesPostgraduate Research Student, Electronics and Computer Science (FPAS)
Angela WatkinsPostgraduate Research Student, Biological Sciences (FNES)
Iain WeaverPostgraduate Research Student, Electronics and Computer Science (FPAS)
Robin WilsonPostgraduate Research Student, Geography (FSHS)
Chris WoodPostgraduate Research Student, Ocean & Earth Science (FNES)
Davide ZilliPostgraduate Research Student, Electronics and Computer Science (FPAS)
Matthew HigginsUndergraduate Research Student, Biological Sciences (FNES)
Elena VatagaTechnical Staff, iSolutions
Petrina ButlerAdministrative Staff, Research and Innovation Services
Kieren LythgowAlumnus, Health Protection Agency
Mohsen MesgarpourAlumnus, University of Southampton