Karim Gharbi

Head of Genomics Pipelines


Contact details:

  • +44 (0) 1603 450 072



Karim leads the Genomics Pipelines Group, which underpins the National Capability in Genomics, providing EI researchers and the wider UK bioscience community with access to cutting-edge expertise and the latest technology platforms.

Karim is a biologist with over two decades of experience in genomics and a passion for scientific discovery and innovation. He has been at the forefront of next-generation sequencing since the early days of the technology, shaping the development of Edinburgh Genomics as a major NGS facility at the University of Edinburgh before joining EI in 2018. He has collaborated on over 50 publications across the breadth of NGS applications and shared his knowledge of the field with others through numerous workshops and courses.

Karim did his PhD at the French National Institute for Agricultural Research (INRA) in Jouy-en-Josas (France), investigating complex patterns of evolution in the genome of polyploid fish in the salmon family. After completing his PhD in 2001, he moved to the University of Guelph (Canada) for a postdoc on the genetic basis of production traits in aquaculture fish. He returned to Europe in 2006, holding a Kelvin-Smith Fellowship in aquatic epidemiology and immunogenomics at the University of Glasgow before joining the University of Edinburgh in 2009, where he held several management positions within Edinburgh Genomics while teaching bioinformatics as a Senior Lecturer.

Karim has a soft spot for fish and other aquatic creatures but enjoys working on any organism with intriguing biology. He keeps a close watch on technology developments in the field and is always happy to discuss new ideas.


Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

R. Leblois, M. Gautier, A. Rohfritsch, J. Foucaud, C. Burban, M. Galan, A. Loiseau, L. Sauné, M. Branco, and K. Gharbi, Molecular Ecology, vol. 27, no. 1, pp. 264–278, 2018.

Development of a medium density combined-species SNP Array for Pacific and European oysters (Crassostrea gigas and Ostrea edulis)

P. Gutierrez, F. Turner, K. Gharbi, R. Talbot, N. R. Lowe, C. Peñaloza, M. McCullough, P. A. Prodöhl, T. P. Bean, and R. D. Houston,  G3: Genes, Genomes, Genetics, vol. 7, no. 7, pp. 2209–2218, 2017.

The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

J. L. Younger, G. V. Clucas, D. Kao, A. D. Rogers, K. Gharbi, T. Hart, and K. J. Miller, Molecular Ecology, 2017.

Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems

C. Y. Jordan, K. Lohse, F. Turner, M. Thomson, K. Gharbi, and R. A. Ennos, Molecular Ecology, 2017.

11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to Western diet

J. S. Johnson, M. N. Opiyo, M. Thomson, K. Gharbi, J. R. Seckl, A. Heger, and K. E. Chapman, Journal of Endocrinology, vol. 232, no. 2, pp. 273–283, 2017.

Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes

A. Jacobs, R. Womack, M. Chen, K. Gharbi, and K. R. Elmer, Genetics, vol. 207, no. 2, pp. 741–754, 2017.

Maternal inheritance of deltamethrin resistance in the salmon louse Lepeophtheirus salmonis (Krøyer) is associated with unique mtDNA haplotypes

G. Carmona-Antoñanzas, M. Bekaert, J. L. Humble, S. Boyd, W. Roy, D. I. Bassett, R. D. Houston, K. Gharbi, J. E. Bron, and A. Sturm, PLoS One, vol. 12, no. 7, p. e0180625, 2017.

Differential gene expression according to race and host plant in the pea aphid

I. Eyres, J. Jaquiéry, A. Sugio, L. Duvaux, K. Gharbi, J. J. Zhou, F. Legeai, M. Nelson, J. C. Simon, and C. M. Smadja, Molecular Ecology, vol. 25, no. 17, pp. 4197–4215, 2016.

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

S. Qiu, R. Bergero, S. Guirao Rico, J. L. Campos, T. Cezard, K. Gharbi, and D. Charlesworth, “,” Molecular Ecology, vol. 25, no. 1, pp. 414–430, 2016.

Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

G. V. Clucas, J. L. Younger, D. Kao, A. D. Rogers, J. Handley, G. D. Miller, P. Jouventin, P. Nolan, K. Gharbi, and K. J. Miller, BMC evolutionary biology, vol. 16, no. 1, p. 211, 2016.

For a full list of publications please visit Google Scholar.

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