Publications

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2017

De Pablos, L.M., Kelly, S., de Freitas Nascimento, J., Sunter, j., Carrington, M. (2017). Characterization of RBP9 and RBP10, two developmentally regulated RNA-binding proteins in Trypanosoma brucei. Open BiologyPDF

Butler, C.E., Jaskowska, E., Kelly, S. (2017). Genome Sequence of Phytomonas françai, a Cassava (Manihot esculenta) Latex Parasite. Genome AnnouncementsPDF

Seward, E.A., Votýpka, J., Kment, P., Lukeš, J., Kelly, S. (2017). Description of Phytomonas oxycareni n. sp. from the Salivary Glands of Oxycarenus lavaterae. ProtistPDF

Carrington, M., Dóró, E., Forlenza, M., Wiegertjes, G.F., Kelly, S. (2017). Transcriptome Sequence of the Bloodstream Form of Trypanoplasma borreli, a Hematozoic Parasite of Fish Transmitted by Leeches. Genome AnnouncementsPDF

Venkatesh, D., Boehm, C., Barlow, L.D., Nankissoor, N.N., O’Reilly, A., Kelly, S., Dacks, J.B., Field, M.C. (2017). Evolution of the endomembrane systems of trypanosomatids: conservation and specialisation. Journal of Cell SciencePDF

2016

Seward, E.A., Kelly, S. (2016). Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome BiologyPDF

Suvi Honkanen, S., Jones, V.A.S., Morieri, G., Champion, C., Hetherington, A.J., Kelly, S., Proust, H., Saint-Marcoux, D., Prescott, H., Dolan, L. (2016). The Mechanism Forming the Cell Surface of Tip-Growing Rooting Cells Is Conserved among Land Plants. Current BiologyPDF

Emms, D.M., Covshoff, S., Hibberd, J.M., Kelly, S. (2016). Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species. Molecular Biology and EvolutionPDF

Brackley, C.A., Michieletto, D., Mouvet, F., Johnson, J., Kelly, S., Cook, P.R., Marenduzzo, D. (2016). Simulating topological domains in human chromosomes with a fitting-free model. NucleusPDF

O’Neill, E.C., Kelly, S. (2016). Engineering biosynthesis of high-value compounds in photosynthetic organisms Critical Reviews in BiotechnologyPDF

Catarino, B., Hetherington, A.J., Emms, D.M., Kelly, S. Dolan, L. (2016). The stepwise increase in the number of transcription factor families in the Precambrian predated the diversification of plants on land. Molecular Biology and EvolutionPDF

Smith Unna, R., Boursnell, C.R., Patro, R., Hibberd, J.M., Kelly, S. (2016). TransRate: reference free quality assessment of de novo transcriptome assemblies. Genome ResearchPDF

Brackley, C.A., Johnson, J., Kelly, S., Cook, P.R., Marenduzzo, D. (2016). Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids ResearchPDF

Flegontov, P., Butenko, A., Firsov, S., Kraeva, N., Eliáš, M., Field, M.C., Filatov, D., Flegontova, O., Gerasimov, E.S., Hlaváčová, J., Ishemgulova, A., Jackson, A.P., Kelly, S., Kostygov, A.Y., Logacheva, A.D., Maslov, A.D., Opperdoes, F.R., O’Reilly, A., Sádlová, J., Ševčíková, T,. Venkatesh, Vlček, C., Volf, P., Votýpka, J., Záhonová, K., Yurchenko, V., Lukeš, J. (2016). Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Scientific ReportsPDF

Covshoff, S., Szecowka, M., Hughes, T.E., Smith-Unna, R., Kelly, S., Bailey, K.J., Sage, T.L., Pachebat, J.A., Leegood, R.C., Hibberd, J.M., (2016). C4 photosynthesis in the rice paddy: insights from the noxious weed Echinochloa glabrescens. Plant PhysiologyPDF

van Campen, J., Yaapar, M.N., Narawatthana, S., Lehmeier, C., Wanchana, S., Thakur, V., Chater, C., Kelly, S., Rolfe, S.A., Quick, W.P., Fleming, A.J., (2016). Combined Chlorophyll Fluorescence and Transcriptomic Analysis Identifies the P3/P4 Transition as a Key stage in Rice Leaf Photosynthetic Development. Plant PhysiologyPDF

Proust, H., Honkanen, S., Jones, V.A.S., Morieri, G., Prescott, H., Kelly, S., Ishizaki, K., Kohchi, T., Dolan, L. (2016). RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants. Current BiologyPDF

2015

Emms, D.M., and Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome BiologyPDF

Kelly, S., Georgomanolis, T., Zirkel, A., Diermeier, S., O’Reilly, D., Murphy, S., Längst, G. Cook, P., and Papantonis A. (2015). Splicing of many human genes involves sites embedded within introns. Nucleic Acids ResearchPDF

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. (2015). Two forward genetic screens for vein density mutants in sorghum converge on a Cytochrome P450 gene in the brassinosteroid pathway. The Plant JournalPDF

Fiebig, M., Kelly, S., Gluenz, E. (2015). Comparative life cycle transcriptomics revises Leishmania mexicana genome annotation and links a chromosome duplication with parasitism of vertebrates. PLoS PathogensPDF

Yasumura, Y., Pierik, R., Kelly, S., Sakuta, M., Voesenek, L.A.C.J., Harberd, N.P. (2015). An Ancestral Role for Constitutive Triple Response 1 (CTR1) Proteins in Both Ethylene and Abscisic Acid Signaling Plant PhysiologyPDF

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. (2015). RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evolutionary BiologyPDF

Kelly, S., Greenman, C., Cook, P., and Papantonis A. (2015). Exon skipping is correlated with exon circularization. Journal of Molecular BiologyPDF

Jaskowska E, Butler C, Preston G, and Kelly S. (2015). Phytomonas: Trypanosomatids Adapted to Plant Environments. PLoS PathogensPDF

2014

Hughes, T.E., Langdale, J.A., and Kelly, S. (2014). The impact of widespread regulatory neofunctionalisation on homeolog gene evolution following whole genome duplication in maize. Genome ResearchPDF

– Link to comment on Oxford University science blog

Kelly, S., Ivens, A., Manna, P.T., Gibson, W.C. and Filed, M.C. (2014). A draft genome for the African crocodilian trypanosome Trypanosoma grayi. Nature Scientific DataPDF

Aubry, S., Kelly, S., Kümpers, B.M.C., Smith-Unna, R.D., Hibberd, J.M. (2014). Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS GeneticsPDF

Li, F.W., Villarreal, J.C., Kelly, S., Rothfels, C.J., Melkonian, M., Frangedakis, E., Ruhsam, M., Sigel, E.M., Der, J.P., Pittermann, J., Burge, Pokorny, L., Larsson, A., Chen, T., Weststrand, S., Thomas, P., Carpenter, E., Zhang, Y., Tian, Z., Chen, L., Yan, Z., Zhu, Y., Sun, X., Wang, J., Stevenson, D., Crandall-Stotler, B., Shaw, A.J., Deyholos, M.K., Soltis, D.E., Graham, S., Windham, M.D., Langdale, J.A., Wong, G.K., Mathews, S., and Pryer, K.M. (2014). Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. PNASPDF

– Link to comment in the New York Times
– Link to comment in The Economist
– Link to comment in National Geographic

Kelly, S., Grenyer, R., and Scotland, R.W. (2014) Phylogenetic trees do not reliably predict feature diversity. Diversity and DistributionsPDF

– Link to comment on Oxford University science blog

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. (2014) Shared origins of a key enzyme during the evolution of C4 and CAM metabolism Journal of Experimental BotanyPDF

Holden, J.M., Koreny, l., Kelly, S., Chait, B.T., Rout, M.P., Field, M.C and Obado, S.O. (2014) Touching from a distance: Evolution of interplay between the nuclear pore complex, nuclear basket, and the mitotic spindle. NucleusPDF

Fiebig, M., Gluenz, E., Carrington, M., and Kelly, S. (2014). SLaP mapper: A webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Molecular and Biochemical ParasitologyPDF

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 (2014) Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular Biology of the CellPDF

2013

Kelly, S., Wang, P., Fouracre, J.P. and Langdale, J.A., (2013). Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy. The Plant JournalPDF

Kelly, S. and Maini P.K. (2013). DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS OnePDF

Manna, P.T., Kelly, S. and Field, M.C. (2013). Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids Molecular Phylogenetics and EvolutionPDF

Kramer, S., Chukualim, B., Ellis, L., Boulden, E.A., Kelly, S., Field, M.C., and Carrington, M. (2013). Differential localization of the two T. brucei Poly(A) binding proteins to the nucleus and RNP granules suggests binding to distinct mRNA pools. PLoS OnePDF

2012

Wang, P., Fouracre, J., Kelly, S., Karki, S., Gowick, U., Aubry, S., Shaw, M.K., Westhoff, P., Slamet-Loedin, I.H., Quick, W.P., Hibberd, J.M., and Langdale, J.A. (2012). Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants. PlantaPDF

Samalova, M., Johnson, J., Illes, M., Kelly, S., Fricker, M., and Gurr, S. (2012). Nitric oxide generated by the rice blast fungus Magnaporthe oryzae drives plant infection. New PhytologistPDF

Tiengwe, C., Marcello, L., Farr, H., Dickens, N., Kelly, S., Swiderski, M., Vaughan, D., Gull, K., Barry J.D., Bell, S.D. and McCulloch, R. (2012). Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei. Cell reportsPDF

Collingridge, P.W. and Kelly, S. (2012). MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC BioinformaticsPDF

Kelly, S., Kramer, S., Schwede, A., Maini, P.K., Gull, K., and Carrington, M. (2012). Genome organization is a major component of gene-expression control in response to stress and during the cell-division cycle in trypanosomes. OpenBiologyPDF

Poon, S,K., Peacock, L., Gibson, W., Gull, K., and Kelly, S. (2012). A modular and optimised single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor. OpenBiologyPDF

2011

Kelly, S., Wickstead, B., 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 OnePDF

Kelly, S., Wickstead, B., and Gull, K. (2011). Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.Proc Biol Sci.PDF

– Link to comment in Science
– Link to comment on Wellcome Trust science blog
– Link to comment on Oxford University science blog

2009

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

2007

Kelly, S. (2007). Regulation of Gene Expression in Trypanosomes. D.Phil thesisPDF

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. Mol Biochem Parasitol 154, 103-9. – PDF

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. Mol Biol Cell 18, 1293-1301. – PDFSupplemental data

2006

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. Eukaryot Cell 5, 876-879. – PDFSupplemental data

2005

Kelly, S., Wickstead, B., and Gull, K. (2005). An in silico analysis of trypanosomatid RNA polymerases: insights into their unusual transcription. Biochem Soc Trans 33, 1435-1437. – PDF