Below is a list of my publications from when I was a Ph.D student and post-doc in academia. The titles contain links to the publications themselves, and most are open access.

Peer Review

• Kitchen J. L, Paveley N. D., Van den Bosch F., Helps J., Van den Berg F., (2016) The Evolution of Fungicide Resistance Resulting from Combinations of Foliar-Acting Systemic Seed Treatments and Foliar-Applied Fungicides: A Modeling Analysis. PLoS ONE 11(8): e0161887. doi:10.1371/journal.pone.0161887
• Allaby RG., Kitchen JL., Fuller DQ (2016) Surprisingly low limits of selection in plant domestication. Bioinf (2016): Suppl. 2 41 – 51. Doi: 10.4137/EBO.S33595
• Allaby RG, Kistler L, Gutaker RM, Ware R, Kitchen JL, Smith O, Clarke AC (2014) Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene.  Human Evol (2015): 79. 150 – 157. doi:10.1016/j.jhevol.2014.10.014
• Allaby R.G., Gutaker R., Clarke A.C., Pearson N., Ware R., Palmer S.A., Kitchen J.L., Smith O (2014) Using archaeogenomics and computational approaches to unravel the history of local adaptation in crops. Phil. Trans. Roy. Soc. B (2015): 370(1660). DOI:1098/rstb.2013.0377
• Kitchen J.L., Allaby R. G., (2013) Systems modeling at multiple levels of regulation: Linking systems and genetic networks to spatially explicit plant populations. Plants 2(1): 16-49; doi:10.3390/plants2010016
• Kitchen J. L., Moore J. D., Palmer S. A., Allaby R. G., (2012) MCMC-ODPR: Degenerate primer design using Markov-chain Monte Carlo sampling. BMC Bioinformatics 2012, 13:287 doi:10.1186/1471-2105-13-287
• Kitchen J. L., Allaby R. G., (2012) The limits of mean-field heterozygosity estimates under spatial extension in simulated plant populations. PLoS ONE 7(8): e43254. doi:10.1371/journal.pone.0043254
• Clarkson J. P., Coventry E., Kitchen J., Carter H. E., Whipps J. M., (2012), Population structure of Sclerotinia sclerotiorum in crop and wild hosts in the UK. Plant Pathology. DOI: 10.1111/j.1365-3059.2012.02635.x.
• Palmer S. A., Clapham A. J., Rose P., Freitas F. O., Owen B. D., Beresford-Jones D., Moore J. D., Kitchen J. L., Allaby R. G., (2012) Archaeogenomic evidence of punctuated evolution in Gossypium. Mol Biol Evol 29(8). DOI: 10.1093/molbev/mss070.
• Kitchen J. L., Saunders R. E., Warwicker, J., (2008) Charge environments around phosphorylation sites in proteins, BMC Struct Biol 8(19). DOI:10.1186/1472-6807-8-19.

Conference publications

Poster presentations

• J. L., Fuller D. Q., Brown. T. A., Allaby R. G. (2012) Agrisims: simulating crop domestication using individual-based modelling. SMBE 2012, Convention centre, Dublin, Ireland.
• J., Warwicker. J. (2007) Phosphorylation, charge interactions and effects on conformation. FLS research Symposium, University of Manchester.
• J., Warwicker. J. Protein phosphorylation and structural stabilisation. (2006). Collaborative Computational Project for Biomolecular Simulation (CCPB) annual conference, University of Nottingham.
• J., Bougouffa. S., Bray. T., Greaves. R., Chan. P., Walker. D., Warwicker. J. Structure, function and environment of proteins. (2006). FLS Molecules to Cells departmental poster session, University of Manchester.

 Oral presentations/seminars

• “Quantifying the resistance risks associated with systemic seed treatments: a modelling analysis” (APS conference, Pasadena, August 2015).
• “Quantifying the resistance risks associated with systemic seed treatments: a modelling analysis” (11th conference of the foundation for european plant pathology, Krakow, Poland, September 8^th 2014).
• “Agrisims: Simulating the crop domestication process” (Complexity seminar series, The University of Warwick, 2013).
• “Agrisims: Simulating crop domestication using Individual-based modeling.” (Popgroup annual conference, The University of Glasgow, 2012).
• “Structural Environments around phosphorylation sites.” (Molecular biophysics seminar series, The Indian institute of science, Bangalore, India, 2009).
• Charge environments around phosphorylation sites and their effect on protein-protein interactions. (Bioinformatics departmental symposium, The University of Manchester, 2008).
• A continuum electrostatics approach to prediction of protein phosphorylation. (FLS Bioinformatics seminar series, The University of Manchester, 2006).