Some of the projects listed below are for 2013 or 2012, but there is unlikely to be substantial change for 2016 entry :
Julie Ahringer - Chromatin regulation in Gene expression / The establishment and Transduction of Cell Polarity in C. elegans
We use the power of functional genetics and genomics in C. elegans to address fundamental questions in chromatin regulation and transcriptional control. Chromatin is the organization of genomic DNA with histones that can have a wide range of post-translational modifications, along with hundreds of associated proteins and RNAs. The composition and structure of chromatin determines activity state and is central to the control of transcription, the expression of cell identity, the maintenance of pluripotency, and the transformation to cancer. However, our understanding of chromatin regulation in gene expression is still at a basic level. C. elegans has a complement of core chromatin factors very similar to that of humans (many with existing mutants), a small well-annotated genome (30x smaller than human), RNAi for loss of function studies, and well-characterised cell fates.
We combine wet-lab and computational approaches to a range of problems in chromatin biology and transcriptional control, such as genome organization, promoter and enhancer function, roles of histone modifications, heterochromatin formation and function, and the regulation of chromatin in developmental transitions.
Specific projects would depend on student interest 
Christine Farr - Vertebrate Chromosome Biology
- The functional organisation of centromere domains
- The role of toposiomerase II at the centromere and the influence of SUMOylation
- The role of TOPBP1 and PICH in mitotic chromosome segregation
Anne Ferguson-Smith - Pre- and Post-natal Mammalian Development
[Not accepting PhD students 2016]
Ian Furner - Epigenetics in Arabidopsis thaliana
Projects on the molecular genetics and genomics of gene silencing, DNA methylation, siRNA and RNAi
David Glover - The Regulation of Mitosis and Meiosis
- Drosophila molecular genetics provides an inroad to understand the regulation of the progression through mitosis and meiosis, and the important roles played by such structures as the centrosome, kinetochore and the spindle itself. We can progress from this fundamental knowledge to study the abnormal behaviour of the mitotic apparatus in human tumours
Chris Illingworth - Microbial Evolution
- Next-generation sequencing data grants an unprecedented level of insight into the composition of microbial populations. We are interested in developing novel computational approaches for the analysis of genome sequence data, in order to gain insights into rapid evolutionary processes.
- Our work is currently focused on two main topics : Understanding the global and within-host evolution of viral pathogens, and, via collaboration with experimental groups, the interpretation of genetic data from evolutionary experiments. We welcome applications not only from geneticists, but also from students in other quantitative disciplines (mathematics, physics, computer science etc.)
Frank Jiggins - Host-Parasite Evolution and Genetics
- The first project is to investigate the causes of variation in susceptibility to infection by identifying the genes that cause variation in the resistance of Drosophila to viruses. Using whole-genome approaches we will identify polymorphisms controlling resistance. We can then go on to study how natural selection is acting on this variation in natural populations, which will provide insights into how parasites drive the evolution of their hosts
- The second project aims to understand why the mosquito Aedes aegypti varies in its ability to transmit disease. Populations of this important disease vector vary in many key traits relating to disease transmission, including susceptibility to important human pathogens. This project would combine work in the insectary and large-scale genome sequencing to understand the molecular and evolutionary causes of this variation
- The cell cycle coordinates with development and differentiation in order to form and maintain the body and distinct organs in multicellular organisms. We are eager to understand how cell cycle progression is controlled in the body of the developing organism and how the cell cycle is coupled to differentiation. Our current focus is the regulation and functions of the APC/C ubiquitin ligase and the centrosome in Drosophila neural stem cells. We utilise Drosophila as an in vivo model system, combining biochemistry and molecular biology
Buon-Kyoung Koo - Homeostatic Regulation of Adult Stem Cells
[Not accepting PhD students until at least 2016]
Alfonso Martinez Arias - Integration of Cell Signalling in Development
- We studyhow different signalling pathways interact with each other during development and with transcription factor networks during development to fuel state transitions between cell states. We have a special interest in Notch and Wingless signalling and are using mouse embryonic stem cells and the stem cells of the gut in Drosophila, as systems to explore these questions. The lab has an emphasis on interdisciplinarity and quantitative approaches to developmental problems. Projects include:
- Lineage analysis in vivo and in culture
- Monitoring gene expression live through fluorescent reporters and analyzing the effects that signalling pathways have on this dynamics
- Analysis of cell fate decisions in mouse embryonic stem cells
- Development of quantitative methods for the analysis of live gene expression
Liria Masuda-Nakagawa - Circuit mechanisms for regulation of sensory discrimination in Drosophila larval brain
Discrimination of sensory stimuli is essential for animals to form and retrieve specific memories. I am interested in the neuronal circuitry of this process, using the Drosophila larva as a model, with powerful tools for targeted manipulation of neurons, optogenetics, calcium imaging, and connectomics. I use the sensory input region of the larval mushroom bodies, with low cellular redundancy but similar processing principles as in mammals. Of particular interest is how neuromodulatory inputs regulate the sensitivity and specificity of processing, and integrate it with other physiological states. 
Erik Miska - Small Regulatory RNA
[Information to be supplied]
Cahir O'Kane - Molecular Analysis of Synaptic Function and Membrane Traffic in Drosophila
- Structure and function of axonal endoplasmic reticulum, and the interplay between axonal membrane traffic and axon degeneration
- Roles of Hereditary Spastic Paraplegia disease gene products in neuronal membrane traffic and organisation and signalling in Drosophila
Steven Russell - Genomics and Systems Biology of Drosophila
We are particularly interested in the function of Sox-domain transcription factors in CNS and testis development, and the role of Hox proteins in morphogenesis
- Investigating demography and speciation within the great apes and other primates using whole-genome sequence data
- Development of computational approaches in evolutionary genomics
Chromosomal segregation along an axis of cell polarity is a hallmark of asymmetric cell divisions throughout evolution. The budding yeast S. cerevisiae is a unique model to explore spindle orientation linked to cell polarity. In budding yeast, pole-derived astral microtubules target the spindle poles asymmetrically (bud versus mother cell) orienting the spindle to intersect the bud neck. Spindle pole components are evolutionary conserved and studies in yeast have effectively predicted similar centrosome asymmetry in stem cell self-renewing divisions. We seek to bridge the mechanisms of cell polarity, spindle orientation and cell fate under cell cycle control as is only attainable at this time using budding yeast to uncover fundamental principles for establishment of centrosome asymmetry.
Daniel St Johnston - Molecular analysis of Cell Polarity and mRNA Localization in Drosophila
- The two main body axes of Drosophila are determined by the localization of three maternal mRNAs to different positions within the oocyte. Our goal is to elucidate the mechanisms that underlie the polarization of the oocyte and the localization of these mRNAs, and to examine whether they are conserved in other polarized cells, such as epithelia and neurons
David Summers - Microbial Genetics and Cell Signalling
Current research in the Summers laboratory is focused on the role of indole in bacterial cell signaling. We have recently demonstrated the involvement of a novel mode of indole action (pulse signaling) during E. coli stationary phase entry. We also study the role of indole in the response of bacteria to a range of environmental insults including temperature, antibiotics and oxidizing agents.
Projects available focus on the role of indole as an intra-cellular messenger regulating key aspects of the bacterial cell cycle. In particular we are interested in the role of indole-induced changes in trans-membrane potential as part of the signaling mechanism. In the biophysical aspects of our work we collaborate closely with Ulrich Keyser’s group at the Cavendish Physics laboratory.
The laboratory also has translational interests in the exploitation of E. coli as a cell factory and the development of novel antibacterial agents.
John Welch - Molecular Evolution
- Adaptive genome evolution of bacterial pathogens (particularly S. aureus, and the genus Rickettsia)
- Interpreting genomic regions of enhanced differentiation (particularly in Mytilus mussels)
- The evolution of reproductive isolation
A full listing of Groups in the Department appears here, and a description of research by themes here, but please note that only the labs listed on this page are currently accepting Graduate students.
Doctoral Training ProgrammesSome Group Leaders also participate in the MRC-DTP and BBSRC-DTP programmes: follow the links for project listings