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Dr Steven Kelly

Browne Senior Research Fellow in Biological Sciences

Introduction          

I went to Sandford Park School in Dublin Ireland, and studied for my undergraduate degree at the University of Dublin, Trinity College. I moved to Oxford in 2003 to undertake a DPhil in the laboratory of Prof Keith Gull at the Sir William Dunn School of Pathology. Following my DPhil I spent a short post-doctoral period in the Oxford Centre for Integrative Systems Biology and the Centre for Mathematical Biology before taking up a Leverhulme Early Career Fellowship and Browne Junior Research Fellowship at the Department of Plant Sciences and the Queen’s College. I now hold a Royal Society University Fellowship at the Department of Plant Sciences and I am the Browne Senior Research Fellow at Queen’s.

Teaching

I teach across a range of subjects in the biological sciences from the genetics of early plant domestication to computational approaches to understanding gene regulatory networks.

Research

Plants use ~3000 genes to convert light energy from the sun into sugars. These genes encode enzymes that catalyse the reactions as well as structural building blocks that are needed to make subcellular compartments where the light energy is captured and stored. This cohort of ~3000 genes is dynamically regulated during plant development and in response to changing environmental conditions. Moreover, these genes have also been subject to a multitude of evolutionary modifications leading to a wide variety of plants with contrasting photosynthetic efficiencies. My research uses a combination of bioinformatics and experimentation to discover how photosynthesis is regulated, how this regulation has evolved in different species, and use this knowledge to help engineer higher yielding crops for the future.

Publications

Emms, D.M., and Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology. 16:157

Kelly, S., Georgomanolis, T., Zirkel, A., Diermeier, S., O’Reilly, D., Murphy, S., Längst, G. Cook, P., and Papantonis A. Splicing of many human genes involves sites embedded within introns. Nucleic Acids Research. 43(9), 4721-32.

Rizal, G., Thakur, V., Dionora, J., Karki, S., Wanchana, S., Acebron, K., Larazo, N., Garcia, R., Mabilangan, A., Montecillo, F., danila, F., Mogul, R., Pablico, P., Leung, H., Langdale, J.A., Sheehy, J., Kelly, S., Quick, W.P. Two forward genetic screens for vein density mutants in sorghum converge on a Cytochrome P450 gene in the brassinosteroid pathway. The Plant Journal. 84(2), 257-66

Fiebig, M., Kelly, S., Gluenz, E. Comparative life cycle transcriptomics revises Leishmania mexicana genome annotation and links a chromosome duplication with parasitism of vertebrates. PLoS Pathogens. 11(10): e1005186

Yasumura, Y., Pierik, R., Kelly, S., Sakuta, M., Voesenek, L.A.C.J., Harberd, N.P. An Ancestral Role for Constitutive Triple Response 1 (CTR1) Proteins in Both Ethylene and Abscisic Acid Signaling Plant Physiology. 169(1), 283-98

Lyu M.J., Gowik, U., Kelly, S., Covshoff, S., Mallmann, J., Westhoff, P., Hibberd, J.M., Stata, M., Sage, R.F., Lu, H., Wei, X., Wong G.K., Zhu, X.G. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evolutionary Biology. 15:116

Kelly, S., Greenman, C., Cook, P., and Papantonis A. Exon skipping is correlated with exon circularization. Journal of Molecular Biology. 427(15), 2414-7

Jaskowska, E.C., Butler, C.E, Preston, G.M., and Kelly, S., Phytomonas: trypanosomatids adapted to plant environments. PLoS Pathogens. DOI: 10.1371/journal.ppat.1004484.

Hughes, T.E., Langdale, J.A., and Kelly, S., The impact of widespread regulatory neofunctionalisation on homeolog gene evolution following whole genome duplication in maize. Genome Research. 24(8), 1348-55.

Kelly, S., Ivens, A., Manna, P.T., Gibson, W.C., and Field, M.C., A draft genome for the African crocodilian trypanosome Trypanosoma grayi. Nature Scientific Data. doi:10.1038/sdata.2014.24

Li, F.W., Villarreal, J.C., Kelly, S., et al. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. PNAS. 111(18), 6672-7.

Fiebig, M., Gluenz, E., Carrington, M., and Kelly, S., SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Molecular and Biochemical Parasitology. 196(2), 71-74.

Kelly, S., Aubrey, S., Kümpers, B.M.C., Smith-Unna, R.D., and Hibberd, J.M. Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS Genetics. 10(6):e1004365.

Christin, P.A., Arakaki, M., Osborne, C.P., Bräutigam, A., Sage, R.F., Hibberd, J.M., Kelly, S., Covshoff, S., Wong, G.K., Hancock, L., Edwards, E.J., Shared origins of a key enzyme during the evolution of C4 and CAM metabolism. Journal of Experimental Botany. DOI: 10.1093/jxb/eru087

Kelly, S., Grenyer, R., and Scotland, R.W., Phylogenetic trees do not reliably predict feature diversity. Diversity and Distributions. DOI: 10.1111/ddi.12188

Holden, J.M., Koreny, l., Kelly, S., Chait, B.T., Rout, M.P., Field, M.C and Obado, S.O. Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle. Nucleus. 5(4) DOI:10.4161/nucl.32228

Holden, J.M., Koreny, L., Obado, S., Ratushny, A.V., Chen, W.M., Chiang, J.H., Kelly, S., Chait, B.T., Aitchison, J.D., Rout, M.P. and Field, M.C. Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular Biology of the Cell. DOI:10.1091/mbc.E13-12-0750

Kelly, S., Wang, P., Fouracre, J.P. and Langdale, J.A., Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy. The Plant Journal. 75, 656-670

§ Kelly, S., and Maini, P.K., DendroBLAST: Approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS One. DOI:10.1371/journal.pone.0054004

Mana, P.T., Kelly, S. and Field, M.C. Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids Molecular Phylogenetics and Evolution. 67, 123-128

Kramer, S., Bannerman-Chukualim, B., Ellis, L., Boulden, E.A, Kelly, S., Field,MC., Carrington, M., Differential localisation of the two T. brucei poly(A) binding proteins to the nucleus and RNA granules suggests binding to two different RNA pools. PLoS One. DOI:10.1371/journal.pone.0054004

Samalova, M., Johnson, J., Illes, M., Kelly, S., Fricker, M., and Gurr, S., Nitric oxide generated by the rice blast fungus Magnaporthe oryzae drives infection New Phytologist. 197, 207-222

Wang, P., Fouracre, J., Kelly, S., Karki, S., Gowik, U., Aubrey, S., Shaw, MK., Westhoff, P., Quick, WP., Hibberd, JM., Langdale, JA., Evolution of golden2-like gene function in C3 and C4 plants Planta. 237, 481-495

Tiengwe, C., Marcello, M., Farr, H., Dickens, N., Kelly, S., Swiderski, M., Vaughan, D., Gull, K., Barry, D.J., Bell, S.D. and McCulloch, R. Interplay between DNA replication and transcription in the Trypanosoma brucei genome. Cell reports. 2, 185-197

Collingridge, P., and Kelly, S., MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC bioinformatics. 10.1186/1471-2105-13-117  

 Kelly, S., Kramer, S., Schwede, A., Maini, P.K., Gull, K., and Carrington M., Genome organisation is a major component of gene expression control in response to stress and during the cell-division cycle in trypanosomes. OpenBiology. 10.1098/rsob.120033.

 Poon, S.K., Peacock, L., Gibson, W., Gull, K., and Kelly, S.. A modular and optimised single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor. OpenBiology. 10.1098/rsob.110037.

 Kelly, S., Maini, P.K., and Gull, K., (2011) Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation PLoS One. 10.1371/journal.pone.0025666.

Kelly, S., Wickstead, B., and Gull, K. (2011) Archaeal phylogenomics provides evidence for a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proceedings of the Royal Society B. 278, 1009-1018.

Daniels, J.P., Kelly, S., Wickstead, B., and Gull, K., (2009) Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea. Biology Direct 154, 103-9.

Kelly, S., Reed, J., Kramer, S., Ellis, L., Webb, H., Sunter, J., Salje, J., Marinsek, N., Gull, K., Wickstead, B., and Carrington, M. (2007). Functional genomics in Trypanosoma brucei: a collection of vectors for the expression of tagged proteins from endogenous and ectopic gene loci. Molecular and Biochemical Parasitology. 154, 103-9.

Kelly, S., Devaux, S., Lecordier, L., Wickstead, B., Perez-Morga, D., Pays, E., Vanhamme, L., and Gull, K. (2007). Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. Molecular Biology of the Cell. 18, 1293-1301.

Kelly, S., Singleton, W., Wickstead, B., Ersfeld, K., and Gull, K. (2006). Characterization and differential nuclear localization of Nopp140 and a novel Nopp140-like protein in trypanosomes. Eukaryotic Cell. 5, 876-879.

Kelly, S., Wickstead, B., and Gull, K. (2005). An in silico analysis of trypanosomatid RNA polymerases: insights into their unusual transcription. Biochemical Society Transactions 33, 1435-1437.