Pathogen population and evolutionary genomics:

Tackling drug resistant infection outbreaks of global pandemic Escherichia coli ST131 using evolutionary and epidemiological genomics
Downing T arXiv link

Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population
Downing T, Rogers MB, Smith BA, Imamura H, Sanders S, Svobodova M, Volf P, Berriman M, Cotton JA, Smith DF
Plos Genetics 2014 10(1):e1004092 Plos Genetics link PMID: 24453988 York University press release

Genome-wide variant discovery using sequence assembly, mapping and population-wide analysis
Coughlan S, Barreira S, Seoighe C and Downing T
Chapter 3 in book "Bioinformatics and Data Analysis in Microbiology" (Ed: Ozlem Tastan Bishop) Horizon Press 2013

Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania
Mannaert A, Downing T, Imamura H and Dujardin JC
Trends Parasitol. 2012 28(9):370-6 Trends in Parasitology link PMID: 22789456

Genetic markers for SSG-resistance in Leishmania donovani and SSG-treatment failure of visceral leishmaniasis patients in the Indian subcontinent
Vanaerschot M, Decuypere S, Downing T, Imamura H, Stark O, De Doncker S, Roy S, Ostyn B, Maes L, Khanal B, Boelaert M, Schonian G, Berriman M, Chappuis F, Dujardin JC, Sundar S and Rijal S
Journal of Infectious Diseases 2012 206(5):752-5 Journal of Infectious Disease link PUBMED Central PMID: 22753945

Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex
Downing T, Stark O, Vanaerschot M, Imamura H, Sanders M, Decuypere S, de Doncker S, Maes I, Rijal S, Sundar S, Dujardin JC, Berriman M and Schonian G
Infection, Genetics and Evolution 2012 12(1):149-159 DOI link to Infection, Genetics and Evolution PUBMED Central PMID: 22119748

The battle of the SNPs
Downing T
Nature Reviews Microbiology 2012 10(1):6 DOI link to Nature Reviews Microbiology PUBMED Central PMID: 22138960

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton JA, Hilley JD, de Doncker S, Maes I, Mottram JC, Quail MA, Rijal S, Sanders M, Schonian G, Stark O, Sundar S, Vanaerschot M, Hertz-Fowler C, Dujardin JC and Berriman M
Genome research 2011 21(12):2143-2156 Faculty of 1000 review DOI link to Genome Research Full text on PUBMED Central PMID: 22038251

Livestock and plant population and evolutionary genetics:

Genome-Wide Association Analysis of Avian Resistance to Campylobacter jejuni Colonization Identifies Risk Locus Spanning the CDH13 Gene
Connell S, Meade KG, Allan B, Lloyd AT, Downing T, O'Farrelly C and Bradley DG
G3: Genes. Genomes, Genetics. epub 27th March. G3: Genes. Genomes, Genetics link PMID: 23550144

The differential evolutionary dynamics of avian cytokine and TLR gene classes
Downing T, Lloyd AT, O'Farrelly C and Bradley DG
Journal of Immunology 2010 184(12):6993-7000 Journal of Immunology link PMID: 20483729

Evidence of the adaptive evolution of immune genes in chicken
Downing T, Cormican P, O'Farrelly C, Bradley DG and Lloyd AT
BMC Res Notes. 2009 2:254 BMC Res Notes link Full text on PUBMED Central PMID: 20003477

The avian Toll-Like receptor pathway--subtle differences amidst general conformity
Cormican P, Lloyd AT, Downing T, Connell SJ, Bradley D and O'Farrelly C
Dev Comp Immunol. 2009 33(9):967-73 Dev Comp Immunol link PMID: 19539094

Variation in chicken populations may affect the enzymatic activity of lysozyme
Downing T, O'Farrelly C, Bhuiyan AK, Silva P, Naqvi AN, Sanfo R, Sow RS, Podisi B, Hanotte O and Bradley DG
Anim Genet. 2010 41(2):213-7 Animal Genetics link PMID: 19845599

Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus
Downing T, Lynn DJ, Connell S, Lloyd AT, Bhuiyan AK, Silva P, Naqvi AN, Sanfo R, Sow RS, Podisi B, Hanotte O, O'Farrelly C and Bradley DG
BMC Evol Biol. 2009 9:136 BMC Evol Biol link Full text on PUBMED Central PMID: 19527513

Contrasting evolution of diversity at two disease-associated chicken genes
Downing T, Lynn DJ, Connell S, Lloyd AT, Bhuiyan AK, Silva P, Naqvi AN, Sanfo R, Sow RS, Podisi B, O'Farrelly C, Hanotte O and Bradley DG
Immunogenetics 2009 61(4):303-14 Immunogenetics link Immunogenetics erratum DOI link PMID: 19247647

Sport:
Time to try a tri. Downing T. Health Matters 2011 7(2):114-115 Health Matters link