Senior Research Fellow in the Plant Sciences Department
Departments and Institutes
- Department of Plant Sciences:
- Bioinformatics Group Leader
Statistical and bioinformatic analysis of high throughput sequencing data, particularly small RNA data; genomics and other 'omics; genetic recombination
Identifying small interfering RNA loci from high-throughput sequencing data. Hardcastle TJ, Kelly KA, Baulcombe DC. Bioinformatics, 2011 Dec 9 [Epub ahead of print]
RNAcentral: A vision for an international database of RNA sequences. RNA 2011; 17: 1941-1946. Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang H, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel J, Williams KP, Wright MW, Zwieb C.
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010; 11(1): 422. Hardcastle TJ, Kelly KA.
The DRM2 cytosine methyltransferase requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genetics 2010; 6(10): e1001182. Henderson IR, Deleris A, Wong W, Chin H, Horwitz G, Zhong X, Kelly KA, Pradhan S, Jacobsen SE.
A putative Arabidopsis THO/TREX export complex is involved in transgene and endogenous siRNA biosynthesis. Proceedings of the National Academy of Sciences 2010; 107(31): 13948-13953. Yelina NE, Smith LM, Jones AM, Patel K, Kelly KA, Baulcombe DC
The Arabisopsis RNA-directed DNA methylation argonautes functionally diverge based on their expresson and interaction with target loci. Plant Cell 2010; 22(2): 321-324. Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Studholme DJ, Schwach F, Doonan JH, Baulcombe DC
Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009; 460: 283-286. Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC.
Neurological and behavioral abnormalities, ventricular dilatation, altered cellular functions, inflammation, and neuronal injury in brains of mice due to common, persistent, parasitic infection. Journal of Neuroinflammation 2008; 5: 48. Hermes G, Ajioka JW, Kelly KA, Mui E, Roberts F, Kasza K, Mayr T, Kirisits MJ, Wollman R, Ferguson DJP, Roberts CW, Hwang J, Trendler T, Kennan RP, Suzuki Y, Reardon C, Hickey AW, Chen L, McLeod R.
Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. PLOS Pathogens 2007; 3(6): e77. Gissot M, Kelly KA, Ajioka JW, Greally JM, Kim K.
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii. Genome Research 2006; 16: 1119-1125. Khan A, Boehme U, Kelly KA et al.
Characterization of conserved non-coding sequences in vertebrate genomes using bioinformatics, statistics and functional studies. Comparative Biochemistry and Physiology Part D 2006; 1: 46-58. Edwards YJK, Walter K, McEwen G, Vavouri T, Kelly KA, Abnizova I, Woolfe A, Goode DK, Goodson M, North P, Snell P, Callaway H, Smith SF, Gilks WR, Cooke JE, Elgar G.
Highly conserved non-coding sequences are associated with vertebrate development. PloSBiology 2005; 3(1): e7. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W, Edwards YJK, Cooke JE, Elgar G.