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Computational Genomics


The Computational Genomics team, led by Sarah Ayling, is responsible for implementing and executing high-throughput analysis pipelines to analyse plant, animal and viral genomes.

The Ayling group  focuses on supporting crop improvement through the application of genomics approaches. The group develops and implements assembly approaches for complex plant genomes; identifying and characterising genetic diversity and its effects for traits of agronomic interest; and developing genomic tools and resources for plant breeders, researchers and genebanks.


The Computational Genomics team is also part of the BBSRC funded LoLa project “Wheat Genomics for Sustainable Agriculture” . The project aims to generate wheat gene models assigned to specific chromosome arms, and improved assemblies for wheat chromosomes 2B, 4B and 4D.

As part of the UK's barley sequencing consortium, they have been analysing barley RNA-Seq data in collaboration with the James Hutton Institute. In addition, they will be calling variants from exome capture data from diverse barley lines.

The team is part of the EU TransPLANT project “Trans-national infrastructure for plant genomic science”, where they lead the work package on implementation of resource-intensive algorithms for plant genomics data. The team's focus is on the evaluation and development of strategies for genome sequencing and assembly.

In addition they are working on several virus projects with collaborators from the Centre for Virus Research, Institute for Animal Health and the Animal Health Trust.

As part of the International Wheat Genome Sequencing Consortium , the Crop Genomics team is working to assemble flow-sorted chromosome arms for the Chromosome Survey Sequence of hexaploid bread wheat. Assembled chromosomes are available from URGI .

Future Developments

Continue to work with the Genetic Resources community to help develop guidelines and resources through participating in initiatives such as DivSeek

Integrate phenomics and genomics data to develop resources for crop researchers

Develop informatics tools and resources for breeders through increasing interactions to ensure that their needs are correctly identified and met

Selected Publications
  • I.W.G.S.C. (2014-7) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 18 July 2014: Vol. 345 no. 6194 DOI: 10.1126/science.1251788
  • Cocker et al., (2015-4) Oakleaf: an S locus-linked mutation of Primula vulgaris that affects leaf and flower development. New Phytol. 2015 Apr 9. doi: 10.1111/nph.13370. 
    Li et al., (2015-4) Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization. New Phytol. 2015 Apr 9. doi: 10.1111/nph.13373.
  • Ramamurthy et al., (2015) Skeletonization of 3D Plant Point Cloud Using a Voxel Based Thinning Algorithm. Accepted by IEEE EUSIP 2015. EURASIP Journal in Signal Processing (
  • Groenen M.A.M, et al. Pig genomes provide insight into porcine demography and evolution (accepted)
  • The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature doi:10.1038/nature11543
  • Clavijo B., Ayling S., Caccamo M. “Quality metrics for assessing de novo assemblies” ECCB 2012, September 2012, Basel, Switzerland
  • Leggett R., Ramirez-Gonzalez R., Caccamo M., “MetaCortex: Classification of short read sequences from environmental samples” Genome Informatics, September 2012, Cambridge, UK
  • Enriquez-Gasca M.R., Ayling S., Murcia P., Caccamo M. "Intra-and inter-host evolutionary dynamics of mammalian influenza viruses”  17th international bioinformatics workshop on Virus Evolution and Molecular Epidemiology, September 2012, Serbia
  • Sampath D., Ayling S., Swarbreck D., Febrer M., Hedley P.E., Pfeifer M., Steuernagel B., Mayer K., Waugh R., Caccamo M., Rogers J. “A comparison of approaches for RNA-Seq differential expression analysis in barley” –  UK-NGS Meeting  August 2012, Nottingham, UK
  • Clark M., Leggett R., Heavens D., Vasoya D., Drou N., CaccamoM. “The long and the short of it: de novo assembly of extreme GC content microbial genomes”, The Biology of Genomes, Cold Spring Harbor, May 2012.
  • Ramirez-Gonzalez R., Leggett R., Caccamo M. “Efficient short-read assemblies with paired-end k-mers”, Genome Informatics, Cold Spring Harbor, November 2011.
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