Sue Jones
Bioinformatics Group Leader at the James Hutton Institute, Dundee. I am a computational biologist with research interests in the development and application of computational methods for virus diagnostics, microbiome analysis, functional genomics, transcription regulation and protein-nucleic-acid interactions.
Current research interests
My current research interests are in plant pathogen detection and data analysis using next generation sequencing (NGS) technologies. I am currently collaborating on a number of projects including; plant virus diagnostics using NGS data, modelling virus-protein interactions in plants, developing virus detection protocols for water samples, predicting antimicrobial peptides using NGS data from soils, and analysis of plant microbiomes. I am also currently a collaborator, providing bioinformatics expertise, on the BBSRC funded UK Crop Microbiome Cryobank project.
Past research
Past research projects and interests have included
- Prediction of DNA-binding effectors from plant pathogens
- Identification of cis-regulatory modules in heat stress genes in crops
- Identification of epitopes in parasite proteins and their potential display sites in virus like particles
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Analysis and prediction of proteins that bind to RNA using sequence information
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Modelling protein-protein interaction sites using 3D structure information
- Identification of candidate genes involved in the interferon gamma response to Tuberculosis
- Identification of responsive elements in the Epstein Barr Virus genome as targets of epigenetic reprogramming.
Bibliography
- Materatski , P.; Jones, S.; Patanita, M.; Doroteia Campos, M.; Bento Dias, A.; do Rosário Félix, M.; Varanda, C.M.R. (2021) A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae, Viruses, 13(10), Art. 2035
- Jones, S.; Cowan, G.; MacFarlane, S.; Mukoye, B.; Mangeri, B.C.; Were, H.; Torrance, L. (2020) RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV), Virus Research, 277, art.197837
- Hurst, C.H.; Wright, K.M.; Turnbull, D.; Leslie, K.; Jones, S.; Hemsley, P.A. (2019) Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function, Scientific Reports, 9, art.12818
- Jones, S.; McGavin, W.; MacFarlane, S (2019) The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection, Virus Research, 265, 162-165
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology, 100(3), 533-542
- Cowan, G.H.; Roberts, A.G.; Jones, S.; Kumar, P.; Kalyandurg, P.B.; Gil, J.F.; Savenkov, E.I.; Hemsley, P.A.; Torrance, L. (2018) Potato Mop-Top Virus Co-Opts the Stress Sensor HIPP26 for Long-Distance Movement, Plant Physiology, 176(3), 2052-2070
- Jones, S.; Baizan-Edge, A.; MacFarlane, S.; Torrance, L. (2017) Viral diagnostics in plants using next generation sequencing: computational analysis in practice., Frontiers in Plant Science, 8, Article No. 1770.
- Jones, S. (2016) Protein-RNA Interactions: structural biology and computational modeling techniques., Biophysical Reviews, 8, 359-367.
- Motion, G.B.; Howden, A.J.M.; Huitema, E.; Jones, S. (2015) DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool., Nucleic Acids Research, 43, Article No.e158.
- Thomas, D.; Finan, C.; Newport, M.J.; Jones, S. (2015) DNA-entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters., Computational Biology and Chemistry, 58, 19-24.
- Jones, C.I.; Grima, D.P.; Waldron, J.A.; Jones, S.; Parker, H.N.; Newbury, S.F. (2013) The 5 '-3 ' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs, RNA Biology, 10, 1345-1355.
- Awofala, A.A.; Davies, J.A.; Jones, S. (2012) Functional roles for redox genes in ethanol sensitivity in Drosophila., Functional and Integrative Genomics, 12, 305-315.
- Flower, K.; Thomas, D.; Heather, J.; Ramasubramanyan, S.; Jones, S.; Sinclair, A.J. (2011) Epigenetic control of viral life-cycle by a DNA-methylation dependent transcription factor., PLoS ONE, 6, Article No. e25922.
- Materatski , P.; Jones, S.; Patanita, M.; Doroteia Campos, M.; Bento Dias, A.; do Rosário Félix, M.; Varanda, C.M.R. (2021) A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae, Viruses, 13(10), Art. 2035
- Jones, S.; Cowan, G.; MacFarlane, S.; Mukoye, B.; Mangeri, B.C.; Were, H.; Torrance, L. (2020) RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV), Virus Research, 277, art.197837
- Hurst, C.H.; Wright, K.M.; Turnbull, D.; Leslie, K.; Jones, S.; Hemsley, P.A. (2019) Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function, Scientific Reports, 9, art.12818
- Jones, S.; McGavin, W.; MacFarlane, S (2019) The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection, Virus Research, 265, 162-165
- Baizan-Edge, A.; Cock, P.; MacFarlane, S.; McGavin, W.; Torrance, L.; Jones, S. (2019) Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data, Journal of General Virology, 100(3), 533-542
- Cowan, G.H.; Roberts, A.G.; Jones, S.; Kumar, P.; Kalyandurg, P.B.; Gil, J.F.; Savenkov, E.I.; Hemsley, P.A.; Torrance, L. (2018) Potato Mop-Top Virus Co-Opts the Stress Sensor HIPP26 for Long-Distance Movement, Plant Physiology, 176(3), 2052-2070
- Jones, S.; Baizan-Edge, A.; MacFarlane, S.; Torrance, L. (2017) Viral diagnostics in plants using next generation sequencing: computational analysis in practice., Frontiers in Plant Science, 8, Article No. 1770.
- Jones, S. (2016) Protein-RNA Interactions: structural biology and computational modeling techniques., Biophysical Reviews, 8, 359-367.
- Motion, G.B.; Howden, A.J.M.; Huitema, E.; Jones, S. (2015) DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool., Nucleic Acids Research, 43, Article No.e158.
- Thomas, D.; Finan, C.; Newport, M.J.; Jones, S. (2015) DNA-entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters., Computational Biology and Chemistry, 58, 19-24.
- Jones, C.I.; Grima, D.P.; Waldron, J.A.; Jones, S.; Parker, H.N.; Newbury, S.F. (2013) The 5 '-3 ' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs, RNA Biology, 10, 1345-1355.
- Awofala, A.A.; Davies, J.A.; Jones, S. (2012) Functional roles for redox genes in ethanol sensitivity in Drosophila., Functional and Integrative Genomics, 12, 305-315.
- Flower, K.; Thomas, D.; Heather, J.; Ramasubramanyan, S.; Jones, S.; Sinclair, A.J. (2011) Epigenetic control of viral life-cycle by a DNA-methylation dependent transcription factor., PLoS ONE, 6, Article No. e25922.
- Jones, S. (2016) Protein-RNA Interactions: structural biology and computational modeling techniques., Biophysical Reviews, 8, 359-367.
- Holmes, A.; Jones, S.; Watts, L.; Humphris, S.; Cheetham, A.; Toth, I. (2022) Can microbiome profiles be used as an indicator of soil health to investigate the impacts from compaction and potato cropping, 3rd Plant Microbiome Symposium 2022, 24-26 May 2022, Dundee
- Torrance, L.; Cowan, G.; Roberts, A.; Jones, S.; Kumar, P.; Hemsley, P.; Savenkov, E. (2018) Potato mop-top virus TGB1 co-opts HIPP26 to activate abiotic stress signalling for long distance virus movement., Phytopathology, 108, S1.302. Abstract.
- Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
