Centre for Functional Genomics

The Centre for Functional Genomics at Oxford Brookes University uses state-of-the-art methods to decipher how genes control life and how genetic changes cause differences between organisms. Recent years have brought great progress in sequencing techniques and research methods in the area of genomics. Hence, the three Research Groups associated with the Centre explore different next generation sequencing approaches to understand the genomic and genetic principles that govern biological form and function.

In addition to the focus on their own research themes, members of the Centre also provide services in the areas of sequencing data analysis and project design for external and internal collaborators. They are also involved in student teaching and offer short courses and training opportunities in cutting-edge methods for sequencing data analysis.

Personnel

Saad Arif

Saad Arif's research interests are Ecological and Evolutionary Genomics.

Korneel Hens

Korneel Hens maps gene regulatory networks that regulate cell fate maintenance and nutritional homeostasis in adult organisms.

Sebastian Kittelmann

Sebastian Kittelmann studies the role of enhancers in evolution and development and how enhancer sequence variation translates into functional differences.

Publications

• Ang, Roesma, Nijman, Meier & Srivathsan, 2019. Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species. bioRxiv: 867986. https://doi.org/10.1101/867986
• Königer, Arif & Grath, 2019. Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae. G3 (Bethesda) 9(11):3715-3725. https://doi.org/10.1534/g3.119.400453
• Gaspar, Arif, Sumner-Rooney, Kittelmann, Bodey, Stern, Santos Nunes & McGregor, 2020. Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans. G3 (Bethesda) [Online ahead of print]. https://doi.org/10.1534/g3.119.400877
• Herndon, Shelton, Gerischer, Ioannidis, Ninova, Dönitz, Waterhouse, Liang, Damm, Siemanowski, Kitzmann, Ulrich, Dippel, Oberhofer, Hu, Schwirz, Schacht, Lehmann, Montino, Posnien, Gurska, Horn, Seibert, Vargas Jentzsch, Panfilio, Li, Wimmer, Stappert, Roth, Schröder, Park, Schoppmeier, Chung, Klingler, Kittelmann, Friedrich, Chen, Altincicek, Vilcinskas, Zdobnov, Griffiths-Jones, Ronshaugen, Stanke, Brown & Bucher, 2019. Enhanced genome assembly and a new official gene set for Tribolium castaneum . BMC Genomics, 21 (1), 47. https://doi.org/10.1186/s12864-019-6394-6
• Nijman, 2019. Presbytis neglectus or P. femoralis, colobine molecular phylogenies, and GenBank submission of newly generated DNA sequences. Folia Primatol (Basel), 1-12. https://doi.org/10.1159/000502093
• Nijman, Smith & Kanda, 2019. Phylogeography, population genetics, and conservation of Javan gibbons (Hylobates moloch). Int J Primatol 40, 156-161. https://doi.org/10.1007/s10764-019-00080-3

Courses

The Centre for Functional Genomics offers courses to external and internal researchers who want to learn about sequencing data analysis techniques. The following courses are planned:

Services and Consultancy

I have generated sequencing data. What next?

Sequencing techniques are being used by researchers working in all kinds of different fields to answer very different questions. However, it is not always clear to every scientist what their data can be used for. The Centre for Functional Genomics provides three different kinds of services to help.

Project Planning

Often scientists are unsure how they can use sequencing technologies to help them answer their specific question. We can help with project design and planning, especially for next generation sequencing projects (e.g. RNAseq or ChIP-seq). This should be done as early in the project planning as possible, since a successful grant application depends on a convincing research strategy.

Data Analysis

In cases where scientists have already generated sequencing data but have no trained personnel to analyse them, we can provide this service. Also the re-analysis of published datasets for a different purpose or the comparison of different datasets can be done. We offer to either analyse datsets ourselves or to train other researchers in data analysis in a one-to-one fashion.

Computational Support

The analysis of large datasets requires high computational power in order to be fast and efficient.We have high spec computers in the Centre that can be used also remotely by other researchers at Oxford Brookes University to conduct genomics data analysis.