Centre for Functional Genomics (CfG)

Source: https://www.brookes.ac.uk/research/units/hls/centres/centre-for-functional-genomics Parent: https://www.brookes.ac.uk/research/research-centres

Director: Dr Casper Breuker

Contact:

cfg@brookes.ac.uk

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About us

Research impact

Leadership

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About us Research impact Leadership

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About us

Just like the genome is in the centre of a cell, genomic research is at the core of biological sciences.

The genome determines how species adapt to new habitats, how organisms react to internal and environmental pressures, or how cells change their morphology and behaviour during development and disease. Therefore, researchers of all disciplines in the life sciences are trying to understand the details of how the genome works.

The Centre for Functional Genomics at Oxford Brookes University aims to support scientists from evolutionary biology to biomedicine in their genomic research.

Part of

• School of Biological and Medical Sciences

Related courses

• Conservation Ecology (MSc / PGDip / PGCert)
• Biological Sciences (Genetics and Genomics) (BSc (Hons) / MBiol)
• Medical Genetics and Genomics (MSc / PGDip / PGCert)
• Primate Conservation

Research impact

The Centre for Functional Genomics 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 3 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.

Leadership

Dr Saad Arif

• sarif@brookes.ac.uk

Senior Lecturer

View profile for Saad Arif

Dr Casper Breuker

• +44 (0)1865 483244
• cbreuker@brookes.ac.uk

Subject Coordinator for Biology and MBiol Biology

View profile for Casper Breuker

Professor Vincent Nijman

• +44 (0)1865 483760
• vnijman@brookes.ac.uk

Professor in Anthropology

View profile for Vincent Nijman

Associated groups

[### Ecological and Evolutionary Genetics and Genomics

Dr Saad Arif](https://www.brookes.ac.uk/Research/Units/HLS/Groups/EEGG/ "Ecological and Evolutionary Genetics and Genomics")

[### Extracellular Vesicles and Cancer Biology

Dr Priya Samuel](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Extracellular-Vesicles-and-Cancer-Biology/ "Extracellular Vesicles and Cancer Biology")

[### Functional Genomics in Neuroscience

Dr Korneel Hens](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Functional-Genomics-in-Neuroscience/ "Functional Genomics in Neuroscience")

[### Genome Evolution

Dr Ravinder Kanda](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Genome-Evolution/ "Genome Evolution")

[### Molecular Genetics of Speech and Language

Dr Dianne Newbury](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Molecular-Genetics-of-Speech-and-Language/ "Molecular Genetics of Speech and Language")

[### Phenotypic Evolution and Adaptation

Dr Daniela Nunes](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Phenotypic-Evolution-and-Adaptation/ "Phenotypic Evolution and Adaptation")

[### Regulation of Gene Expression

Dr Sebastian Kittelmann](https://www.brookes.ac.uk/Research/Units/HLS/Groups/Regulation-of-Gene-Expression/ "Regulation of Gene Expression")

[### Nocturnal Primate Research Group

Professor Giuseppe Donati](https://www.brookes.ac.uk/Research/Units/HSS/Groups/Nocturnal-Primate-Research-Group/ "Nocturnal Primate Research Group")

[### Oxford Wildlife Trade Research Group

Professor Vincent Nijman](https://www.brookes.ac.uk/Research/Units/HSS/Groups/Oxford-Wildlife-Trade-Research-Group/ "Oxford Wildlife Trade Research Group")

Example Publications

2025 - 2022

• Baudouin Gonzalez, L., Schönauer, A., Harper, A., Arif, S., Leite, D.J., Steinhoff, P.O., Pechmann, M., Telizhenko, V., Pande, A., Schultz, Z.X. and Kosiol, C. (2025). Development and patterning of a highly versatile visual system in spiders. Proceedings B, 292(2042), p.20242069. DOI: 10.1098/rspb.2024.2069
• Ebdon, S., Mackintosh, A., Lohse, K., Hayward, A., Arif, S., Whitla, R., of Life, W.S.I.T. and Darwin Tree of Life Consortium (2025). The genome sequence of the Black-veined White butterfly, Aporia crataegi (Linnaeus, 1758). Wellcome Open Research, 7, p.81. DOI: 10.12688/wellcomeopenres.17709.2
• Nijman, V., Chavez, J., Simons, D., Siriwat, P., Widiaswari, R.A. and Svensson, M.S., 2025. Quantifying illegal rosewood trade, seizures and forestry law enforcement in Indonesia. Applied Geography, 176, p.103509. https://doi.org/10.1016/j.apgeog.2025.103509
• Torres-Oliva, M., Buchberger, E., Buffry, A.D. et al. (2025). Heterochrony in orthodenticle expression is associated with ommatidial size variation between Drosophila species. BMC Biol 23, 34.https://doi.org/10.1186/s12915-025-02136-8
• Wenborn MJ, Katjimbari R, Tjiseua J, Muheue K, Tjimuine U, Muundjua ST, Svensson MS, Nijman V (2025). Assessment of Mitigation of Human–Elephant Conflict in the Highlands of Northwest Namibia. Journal of Environment and Development, 0(0). https://doi.org/10.1177/10704965241311353
• Abdullah A, Ardiansyah A, Balestri M, Campera M, Chavez J, Dewi T, Fourage A, Hankinson EL, Hedger K, Leupen B, Manson S, Morcatty TQ, Nekaris KAI, Nijman V, Pereyra PER, Sintya E, Svensson MS, Xie M (2024). Parrot Trade and the Potential Risk of Psittacosis as a Zoonotic Disease in Indonesian Bird Markets. Birds 5(1), pp.137-154.
• Brooks SA (2024). Lectins as versatile tools to explore cellular glycosylation. European Journal of Histochemistry 68(1).
• Buffry, A.D., Currea, J.P., Franke-Gerth, F.A. et al. (2024). Evolution of compound eye morphology underlies differences in vision between closely related Drosophila species. BMC Biol 22, 67. https://doi.org/10.1186/s12915-024-01864-7
• Campera M, Chavez J, Humber C, Jain V, Cioci H, Aulia F, Alua KA, Prawerti DAD, Ali SRR, Swastika IW, Dusak PGBJ, Priatama IPA, Jones AK, Bulbert MW, Putra NGM, Kuntayuni, Sukmadewi DKT, Nijman V, Setiawan IM, Manson S (2024). Impact of Cropland Management on Invertebrate Richness and Abundance in Agroforestry Systems in Bali, Indonesia. Land 13(4).
• Chavez J, Nijman V, Sukmadewi DKT, Sadnyana MD, Manson S, Campera M (2024). Impact of Farm Management on Soil Fertility in Agroforestry Systems in Bali, Indonesia. Sustainability 16(18).
• Garber PA, Estrada A, Shanee S, Svensson MS, Arregoitia LV, Nijman V, Shanee N, Gouveia SF, Nekaris A, Chaudhary A, Bicca-Marques JC, Fris Hansen M (2024). Global wildlife trade and trafficking contribute to the world’s nonhuman primate conservation crisis. Frontiers in Conservation Science 5.
• Martínez J, Márquez R, Reinaga A, Campera M, Nijman V, Wallace RB (2024). Using occupancy modeling to provide insights into suitable habitat characteristics for the already restricted and critically endangered Olalla's titi monkey (Plecturocebus olallae). Primates [online first].
• McGinness AJ, Brooks SA, Strasser R Schoberer J, Kriechbaumer V (2024). Suborganellar resolution imaging for the localisation of human glycosylation enzymes in tobacco Golgi bodies. Journal of Microscopy [online first].
• Miller Chloe L., Herrmann Mareike, Carter David R.F., Turner Nicholas, Samuel Priya, Patel Bhavik Anil (2024). Monitoring the electroactive cargo of extracellular vesicles can differentiate various cancer cell lines. Biosensors and Bioelectronics 254.
• Nekaris KAI, Balestri M, Hedger K, Campera M, Adinda E, Ahmad N, Imron MA, Manson S, Saepurohman F, Nijman V (2024). Interactions between Javan slow lorises (Nycticebus javanicus) and domestic and wild carnivores in an anthropogenic landscape in Java, Indonesia. Folia Primatologica [online first].
• Nijman V, Abdullah A, Ardiansyah A, Campera M, Chavez J, Dewi T, Hankinson E, Hedger K, Imron MA, Manson S, Morcatty TQ, Payuse INAD, Rapone BC, Shepherd CR, Siriwat P, Svensson MS, Nekaris KAI (2024). Trade in Prevost’s squirrels: legality, risk for introduction and disease transmission. European Journal of Wildlife Research 70.
• Nijman V, Adbullah A, Adinda E, Ardiansyah A, Campera M, Chavez J, Dewi T, Hedger K, Imron MA, Shepherd CR, Sukmadewi DKT, Wirdateti W, Nekaris KAI (2024). Indonesia's sustainable development goals in relation to curbing and monitoring the illegal wildlife trade. Sustainable Development [online first].
• Nunes MDS, McGregor AP (2024). Developmental evolution in fast-forward: insect male genital diversification. Trends in Genetics [online first].
• Ridgway Amber M., Hood Emily J., Jimenez Javier Figueras, Nunes Maria D.S., McGregor Alistair P. (2024). Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species. Current Biology 34(5), pp.1114-1121.
• Simbi B, Pink RC, Whatford L, Lawson C (2024). Particles in Raw Sheep Milk Can Modulate the Inflammatory Response in THP-1, a Human Monocyte Cell Line, In Vitro. Dairy 5(1), pp.161-172.
• Vizcaíno-Castillo A, Kotila T, Kogan K, Yanase R, Como J, Antenucci L, Michelot A, Sunter JD, Lappalainen P (2024). Leishmania profilin interacts with actin through an unusual structural mechanism to control cytoskeletal dynamics in parasites. Journal of Biological Chemistry 300(3).
• Welsh Joshua A., Goberdhan Deborah C. I., O'Driscoll Lorraine, Buzas Edit I., Blenkiron Cherie, Bussolati Benedetta, Cai Houjian, Di Vizio Dolores, Driedonks Tom A. P., Erdbrügger1 Uta, Falcon‐Perez Juan M., Fu Qing‐Ling, Hill Andrew F., Lenassi Metka, Lim Sai Kiang, Mahoney Mỹ G., Mohanty Sujata, Möller Andreas, Nieuwland Rienk, Ochiya Takahiro, Sahoo Susmita, Torrecilhas Ana C., Zheng Lei, Zijlstra Andries, Abuelreich Sarah, Bagabas Reem, Bergese Paolo, Bridges Esther M., Brucale Marco, Burger Dylan, Carney Randy P., Cocucci Emanuele, Colombo Federico, Crescitelli Rossella, Hanser Edveena, Harris Adrian L., Haughey Norman J., Hendrix An, Ivanov Alexander R., Jovanovic‐Talisman Tijana, Kruh‐Garcia Nicole A., Ku'ulei‐Lyn Faustino Vroniqa, Kyburz Diego, Lässer Cecilia, Lennon Kathleen M., Lötvall Jan, Maddox Adam L., Martens‐Uzunova Elena S., Mizenko Rachel R., Newman Lauren A., Ridolfi Andrea, Rohde Eva, Rojalin Tatu, Rowland Andrew, Saftics Andras, Sandau Ursula S., Saugstad Julie A., Shekari Faezeh, Swift Simon, Ter‐Ovanesyan Dmitry, Tosar Juan P., Useckaite Zivile, Valle Francesco, Varga Zoltan, van der Pol Edwin, van Herwijnen Martijn J. C., Wauben Marca H. M., Wehman Ann M., Williams Sarah, Zendrini Andrea, Zimmerman Alan J., MISEV Consortium, Théry Clotilde, Witwer Kenneth W. (2024). Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. Journal of Extracellular Vesicles, 13(2).
• Buffry AD, Kittelmann S, McGregor AP (2023). Characterisation of the role and regulation of Ultrabithorax in sculpting fine-scale leg morphology. Front Cell Dev Biol. 11:1119221.
• Blair ME, Cao GT, López-Nandam EH, Veronese-Paniagua DA, Birchette MG, Kenyon M, Md-Zain BM, Munds RA, Nekaris KAI, Nijman V, Roos C 2023. Molecular phylogenetic relationships and unveiling novel genetic diversity among slow and pygmy lorises, including resurrection of Xanthonycticebus intermedius. Genes 14(3), 643.
• Winant M, Buhler K, Clements J, De Groef S, Hens K, Vulsteke V, Callaerts P (2022). Genome-wide analysis identifies Homothorax and Extradenticle as regulators of insulin in Drosophila Insulin-Producing cells. PLoS Genet. 18(9):e1010380.
• Nekaris KAI, Nijman V 2022. A new genus name for pygmy lorises, Xanthonycticebus gen. nov. (Mammalia, primates). Zoosystematics and Evolution 98(1), 87-92.
• Nijman V, Stein FM 2022. Meta-analyses of molecular seafood studies identify the global distribution of legal and illegal trade in CITES-regulated European eels. Current Research in Food Science 5, 191-195.

\

2021 - 2019

• Arif S, Gerth M, Hone-Millard WG, Nunes MDS, Dapporto L, Shreeve TG (2021). Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles. Mol Ecol. 30(20):5196-5213.
• Baudouin-Gonzalez L, Schoenauer A, Harper A, Blakeley G, Seiter M, Arif S, Sumner-Rooney L, Russell S, Sharma PP, McGregor AP (2021). The Evolution of Sox Gene Repertoires and Regulation of Segmentation in Arachnids. Mol Biol Evol. 38(8):3153-3169.
• García-Castro H, Kenny NJ, Iglesias M, Álvarez-Campos P, Mason V, Elek A, Schönauer A, Sleight VA, Neiro J, Aboobaker A, Permanyer J, Irimia M, Sebé-Pedrós A, Solana J (2021). ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biol. 22(1):89.
• Hagen JFD, Mendes CC, Booth SR, Figueras Jimenez J, Tanaka KM, Franke FA, Baudouin-Gonzalez L, Ridgway AM, Arif S, Nunes MDS, McGregor, AP (2021). Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species. Mol Biol Evol. 38(2):437-448.
• Kittelmann S, Preger-Ben Noon E, McGregor AP, Frankel, N (2021). A complex gene regulatory architecture underlies the development and evolution of cuticle morphology in Drosophila. Curr Opin Genet Dev. 69:21-27.
• Stein, F.M., Frankowski, J., Nijman, V., Absil, C., Kranendonk, I. and Dekker, W., 2021. Chinese eel products in EU markets imply the effectiveness of trade regulations but expose fraudulent labelling. Marine Policy, 132, p.104651.
• Arif, S., Gerth, M., Hone-Millard, W. G., Nunes, M. D. S., Dapporto, L. and Shreeve, T. G. (2020). Multiple colonisations and Wolbachia infections influence the fine-scale population structure of the widespread Common Blue butterfly (Polyomattus icarus) in the British Isles. bioRXiv, doi: https://doi.org/10.1101/2020.09.03.267203.
• Hagen, J. F. D., Mendes, C. C., R. Booth, S., Figueras Jimenez, J., Tanaka, K. M., Franke, F. A., Baudouin-Gonzalez, L., Ridgway, A. M., Arif, S., Nunes, M. D. S. and McGregor, A. P. (2020). Unravelling the genetic basis for the rapid diversification of male genitalia between Drosophila species. Molecular Biology and Evolution, msaa232, https://doi.org/10.1093/molbev/msaa232.
• García-Castro, H., Kenny, N. J., Álvarez-Campos, P., Mason, V., Schönauer, A., Sleight, V. A., Neiro, J., Aboobaker, A., Permanyer, J., Iglesias, M., Irimia, M., Sebé-Pedrós, A. and Solana, J. (2020). ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. bioRiv, doi: https://doi.org/10.1101/2020.05.26.117234.
• Harper, A., Baudouin-Gonzalez, L., Schönauer, A., Seiter, M., Holzem, M., Arif, S., McGregor, A. P., Sumner-Rooney, L. (2020). Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates. bioRxiv, doi: https://doi.org/10.1101/2020.07.10.177725.
• Buffry, A. D., Kittelmann, S. and McGregor, A. P. (2020). Characterisation of the role and regulation of Ultrabithorax in sculpting fine-scale leg morphology. bioRxiv, doi: https://doi.org/10.1101/2020.06.17.152918.
• Baudouin-Gonzalez, L*., Schoenauer, A*., Harper, A., Blakeley, G., Seiter, M., Arif, S., Sumner-Rooney, L., Russell, S., Sharma, P. P. and McGregor, A. P. (2020). The evolution of Sox gene repertoires and regulation of segmentation in arachnids bioRxiv, doi: https://doi.org/10.1101/2020.06.04.133389. *Contributed equally.
• Gaspar, P., Arif, S., Sumner-Rooney, L., Kittelmann, M., Bodey, A. J., Stern, D. L., Nunes, M. D. S. and McGregor, A. P. (2020) Characterization of the genetic architecture underlying eye size variation within Drosophila melanogaster and Drosophila simulans. G3,10:1005-1018. doi: https://doi.org/10.1534/g3.119.400877.
• Thomas, G. W. C. et al., (2020). Gene content evolution in the arthropods. Genome Biology 21:15. doi: https://doi.org/10.1186/s13059-019-1925-7.
• Herndon, N. et al., (2020). Enhanced genome assembly and a new official gene set for Tribolium castaneum. BMC Genomics 21:47. doi: https://doi.org/10.1186/s12864-019-6394-6.
• Ang, A., Roesma, D.I., Nijman, V., Meier, R. and Srivathsan, A. (2020). Faecal DNA to the rescue: Shotgun sequencing of non-invasive samples reveals two subspecies of Southeast Asian primates to be Critically Endangered species. Scientific Reports, 9396.
• Jackson A, Nijman V. 2020. DNA barcoding of primates and the selection of molecular markers using African Great Apes as a model. Journal of Anthropological Sciences (in press).
• Königer A., Arif, S. amd Grath, S. (2019). Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae. G3, 9(11):3715-3725. https://doi.org/10.1534/g3.119.400453.
• Fox, G., Preziosi, R.F., Antwis, R.E., Benavides-Serrato, M., Combe, F.J., Harris, W.E., Hartley, I.R., Kitchener, A.C., de Kort, S.R., Nekaris, K.A.I. and Rowntree, J.K. (2019). Multi-individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi). Molecular Ecology Resources 19: 1672-1680.
• Hagen, J. F. D., Mendes, C. C., Tanaka, K. M., Gaspar, P., Kittelmann, M., McGregor, A. P. and Nunes, M. D. S. (2019). tartan underlies the evolution of male Drosophila genital morphology. PNAS USA 116, 19025-19030.
• Nijman, V. (2019). Presbytis neglectus or P. femoralis, colobine molecular phylogenies, and GenBank submission of newly generated DNA sequences. Folia Primatologica, 1-12.
• Nijman, V., Smith, J.H. and Kanda, R.K. (2019). Phylogeography, population genetics, and conservation of Javan gibbons (Hylobates moloch). International Journal of Primatology 40, 156-161.

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