Atomistic Molecular Dynamics Simulations

Dr Agnes Noy, University of York 
DNA is the molecule that nature uses as genetic material and it rarely exists in a relaxed state inside living beings. Rather, it is subjected to torsional stress generated in cellular processes such as gene expression and replication. In turn, this torsional stress is relieved by the coiling of the DNA helix around itself, which creates supercoiled loops or plectonemes, and by the disruption of the double helix. Changes in both the global and the local structure of the helix cause an alteration of its recognition properties towards other molecules and, as a consequence, alters its functionality. Here, I plan to use modelling techniques to describe DNA supercoiling at an atomic level.

Analysis of NGS Data

Dr Kanchon Dasmahapatra, University of York
Research in my group involves whole genome sequencing of study organisms using the Illumina sequencing platform to better understand the process of speciation (how new species are formed). Modern sequencing methods mean that sequencing genomes are now cheap and rapid. However, analysing the large datasets generated takes considerable computational effort. Access to additional computing facilities is required to enable these analyses to be performed in a reasonable time scale.

A Holistic Statistical Modelling Approach to Quantitative Discovery Proteomics and Metabolomics for Underpinning Integrative Systems Medicine

Dr Andrew Dowsey, University of Manchester
Through a series of funded grants, we have developed a next-generation raw-data centric statistical modelling workflow for differential expression analysis in mass spectrometry (MS) proteomics. In this project, we will develop and apply this statistical workflow to advance clinical utility, by delivering a production-quality software biomarker discovery and validation platform for routine use by MS engaged in biomarker discovery and validation. Including the new MRC-funded Stoller Biomarker Discovery Centre (SBDC) at The University of Manchester.

Chromatin organisation in cell nucleus

Dr Buddhapriya Chakrabarti, University of Sheffield 
Imagine packing a thread where separate regions are coloured differently inside a sphere. When tightly packed the segments of the thread that have the same colour need not be adjacent to one another. This problem is similar to the hierarchical organisation of chromatin inside the cell nucleus. Except, that regions of chromatin expressing the same gene are adjacent to each other in their packed configuration. The chromatin achieves this through a series of regulatory proteins. The main aim of this work would be to discern the physical principles behind such an organisation process and quantitatively predict contact maps based on simple models borrowed from polymer physics.

Phylogenetics of Streptococcus pneumoniae

Professor Ian Roberts, University of Manchester
Streptococcus pneumoniae is a species of bacteria that causes sore throats and ear infections, as well as more serious diseases, like pneumoniae and meningitis. Additionally, it lives in the back of the nose and throat without causing disease. We are investigating how thousands of Streptococcus isolates are related to each other in order to investigate genes that might determine which isolates survive better in humans. This research will use entire genomes — more than 2 million base pairs per isolate — and thousands of isolates to discover how Streptococcus has evolved through millions of years.

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