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Statistical and Population Genomics

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

My research field is in Quantitative and Population Genetics, with major research interests in understanding the genetic architectures and mechanisms that underlie quantitative genetic variations, using both theoretical and experimental approaches. Our recent projects include:

Development of Theoretical and Experimental Strategies for Dissecting Complex Traits.
Dissection of polygenic variation at molecular level has been a long standing target in classical genetics but still a challenging task in modern genomics. Although the last two decades have witnessed the dominance of research on mapping quantitative trait loci (QTL) in man, animal and plant species, the mapping precision and resolution that leads itself to molecular cloning of the target genes has remained a rare event. This project develops theoretical approaches for mapping and identifying the major effect genes that contribute to phenotypic variation of polygenic traits through altered coding sequence or expression of the genes. We have established an experimental model with budding yeast (S. cerevisiae) to dissect genic and transcriptional regulation network that affects natural variation in ethanol tolerance through integrating genomic, transcripteomic and proteomic information.

Theory and Methods for Reconstructing Genetic Linkage Maps in Autotetraploid Species.
Construction of genetic linkage maps is usually the first milestone in launching a genome project for an organism. In the era of genomics, genetic linkage maps are now available or quickly becoming available in humans and in almost all important animal and plant species. In sharp contrast, the corresponding study in polyploid species is theoretically challenging and still in its infancy. Our research on this topic focuses on developing theory and statistical approaches for genetic map construction and for modeling population genetic data in autotetraploid species, an example of which is cultivated potato, the world fourth most important food crop and the world food of future.

Evolutionary Comparative Genomics.
Taking advantage of rapidly accumulating public databases of omics studies and the datasets collected from our own experiments, we investigate the process and molecular mechanisms driving the divergent evolution of duplicate genes in the yeast protein-protein interaction network, the evolution of enzymatic genes in the yeast metabolic network, and the expression divergence between duplicate genes in the yeast genome.
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To find out more about studying for a PhD at the University of Birmingham, including full details of the research undertaken in each school, the funding opportunities for each subject, and guidance on making your application, you can now order your copy of the new Doctoral Research Prospectus, at: http://www.birmingham.ac.uk/students/drp.aspx
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Please find additional funding text below. For further funding details, please see the ‘Funding’ section.
The School of Biosciences offers a number of UK Research Council (e.g. BBSRC, NERC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for research council studentships is 31 January each year.

Each year we also have a number of fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this scheme is also 31 January each year.

Funding Notes

All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students and encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).

The postgraduate funding database provides further information on funding opportunities available View Website and further information is also available on the School of Biosciences website View Website

References

Lindsey J. Leach, Lin Wang, Michael J. Kearsey and Zewei Luo (2010). A multilocus tetrasomic linkage analysis using hidden Markov chain model. Proceedings of National Academy of Sciences USA [Pub ahead print].

Wang MH, XH Hu, G Li, Lindsey J Leach, E Potokina, A Druka, R. Waugh, M J Kearsey and ZW Luo (2009) Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data. PLoS Computational Biology 5(3) e1000317.

Chenqi Lu, Xiaohua Hu, Guiying Wang, L. J. Leach, Shengjie Yang, M. J. Kearsey and Z.W. Luo (2010) Why do essential proteins tend to be clustered in the yeast interactome network? Molecular BioSystems DOI: 10.1039

Wang GY, Lu CQ, Zhang RM, Hu XH and Luo ZW (2008) The E-cadherin gene polymorphism -160 CA and Cancer Risk: A Meta-Analysis of Twenty-Six Case-Control Studies. Am J Epidemiol. 167: 7-14.
Potokina E, Druka A, Luo ZW, Wise R, Waugh R and Kearsey M. (2008) Gene expression quantitative trait locus analysis of 16,000 barley genes reveals a complex pattern of genome wide transcriptional regulation. Plant Journal 53: 90-101.

Hu XH, MH Wang, T Tan, JR Li, H Yang, L Leach, RM Zhang and ZW Luo (2007). Genetic dissection of ethanol tolerance in budding yeast S. cerevisiae. Genetics 175: 1479-88.

Leach LJ, Z Zhang, CQ Lu, MJ Kearsey and ZW Luo (2007). The Role of Cis-Regulatory Motifs and Genetical Control of Expression in the Divergence of Yeast Duplicate Genes. Molecular Biology and Evolution 24: 2556-65.

Lu CQ, Z Zhang, LJ Leach, MJ Kearsey and ZW Luo (2007). Impacts of Yeast Metabolic Network Structure on Enzyme Evolution. Genome Biology 8: 407.

Luo ZW, E Potokina, A Druka, R Wise, R Waugh and MJ Kearsey (2007) SFP Genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators. Genetics 176: 789–800.

Luo ZW, Zhang Z, Leach L, Zhang RM, Bradshaw JE, Kearsey MJ. (2006). Constructing genetic linkage maps under a tetrasomic model. Genetics 172: 2635-2645.

Zhang HT, XF Chen, MH Wang, JC Wang, QY Qi, RM Zhang, WQ Xu, QY Fei, QQ Cheng, F Chen, CS Zhu, SH Tao and ZW Luo (2004). Defective expression of TGF?RII is associated with CpG methylated promoter in primary non-small cell lung cancer. Clinical Cancer Research 10: 2359-67.

Luo ZW, RM Zhang and MJ Kearsey (2004). Theoretical basis for genetic linkage analysis in autotetraploid species. Proc. Natl. Acad. Sci. USA 101: 7040-45.

How good is research at University of Birmingham in Biological Sciences?

FTE Category A staff submitted: 42.80

Research output data provided by the Research Excellence Framework (REF)

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