Tim Downing - Publications

Affiliations: 
Dublin City University, Dublin, County Dublin, Ireland 
Area:
bioinformatics, population genetics, bacterial evolution, parasite genomics
Website:
https://www.dcu.ie/biotechnology/people/tim-downing.shtml

32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Decano AG, Tran N, Al-Foori H, Al-Awadi B, Campbell L, Ellison K, Mirabueno LP, Nelson M, Power S, Smith G, Smyth C, Vance Z, Woods C, Rahm A, Downing T. Plasmids shape the diverse accessory resistomes of ST131. Access Microbiology. 3: acmi000179. PMID 33997610 DOI: 10.1099/acmi.0.000179  0.52
2020 Ludden C, Decano AG, Jamrozy D, Pickard D, Morris D, Parkhill J, Peacock SJ, Cormican M, Downing T. Genomic surveillance of ST131 identifies local expansion and serial replacement of subclones. Microbial Genomics. PMID 32213258 DOI: 10.1099/mgen.0.000352  0.52
2020 Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, et al. Global genome diversity of the complex. Elife. 9. PMID 32209228 DOI: 10.7554/Elife.51243  1
2020 Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin J, Sanders MJ, Mauricio I, Miles MA, Schnur LF, Jaffe CL, Nasereddin A, Schallig H, Yeo M, et al. Author response: Global genome diversity of the Leishmania donovani complex Elife. DOI: 10.7554/Elife.51243.Sa2  1
2019 Decano AG, Downing T. An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates. Scientific Reports. 9: 17394. PMID 31758048 DOI: 10.1038/S41598-019-54004-5  0.52
2019 Shaw CD, Imamura H, Downing T, Blackburn G, Westrop GD, Cotton JA, Berriman M, Sanders M, Rijal S, Coombs GH, Dujardin JC, Carter KC. Genomic and metabolomic polymorphism among experimentally selected paromomycin-resistant strains. Antimicrobial Agents and Chemotherapy. PMID 31658971 DOI: 10.1128/Aac.00904-19  1
2019 Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J, Downing T. Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts. Msphere. 4. PMID 31068432 DOI: 10.1128/mSphere.00130-19  0.52
2019 Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O'Connell MJ, Spillane C. Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Molecular Biology and Evolution. PMID 30913563 DOI: 10.1093/Molbev/Msz063  1
2018 Coughlan S, Taylor AS, Feane E, Sanders M, Schonian G, Cotton JA, Downing T. and reference genomes highlight genome structure and gene evolution in the subgenus. Royal Society Open Science. 5: 172212. PMID 29765675 DOI: 10.1098/Rsos.172212  1
2017 Gallagher LA, Coughlan S, Black NS, Lalor P, Waters EM, Wee B, Watson M, Downing T, Fitzgerald JR, Fleming GTA, O'Gara JP. Tandem amplification of SCCmec can drive high level methicillin resistance in MRSA. Antimicrobial Agents and Chemotherapy. PMID 28717043 DOI: 10.1128/Aac.00869-17  0.48
2017 Coughlan S, Mulhair P, Sanders M, Schonian G, Cotton JA, Downing T. The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania. Scientific Reports. 7: 43747. PMID 28256610 DOI: 10.1038/Srep43747  1
2017 Waters EM, Rudkin JK, Coughlan S, Clair GC, Adkins JN, Gore S, Xia G, Black NS, Downing T, O'Neill E, Kadioglu A, O'Gara JP. Redeploying β-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections. The Journal of Infectious Diseases. 215: 80-87. PMID 28077586 DOI: 10.1093/Infdis/Jiw461  0.48
2016 Tabib A, Vishwanathan S, Seleznev A, McKeown PC, Downing T, Dent C, Sanchez-Bermejo E, Colling L, Spillane C, Balasubramanian S. A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions of Arabidopsis thaliana. Frontiers in Plant Science. 7: 1311. PMID 27630650 DOI: 10.3389/Fpls.2016.01311  1
2016 Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, et al. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. Elife. 5. PMID 27003289 DOI: 10.7554/Elife.12613  1
2016 Kitavi M, Downing T, Lorenzen J, Karamura D, Onyango M, Nyine M, Ferguson M, Spillane C. The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 26743524 DOI: 10.1007/S00122-015-2647-1  1
2016 Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM, Cotton JA, Sanders M, Blackburn G, Dujardin JC, Rijal S, Khanal B, Illingworth CJ, Coombs GH, Carter KC. In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology. 99: 1134-48. PMID 26713880 DOI: 10.1111/Mmi.13291  1
2016 Imamura H, Downing T, Broeck FVd, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, Muylder GD, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, et al. Author response: Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent Elife. DOI: 10.7554/Elife.12613.031  1
2015 Kelly H, Downing T, Tuite NL, Smith TJ, Kerin MJ, Dwyer RM, Clancy E, Barry T, Reddington K. Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs. Plos One. 10: e0137389. PMID 26355751 DOI: 10.1371/Journal.Pone.0137389  1
2014 Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, Volf P, Berriman M, Cotton JA, Smith DF. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. Plos Genetics. 10: e1004092. PMID 24453988 DOI: 10.1371/Journal.Pgen.1004092  1
2014 Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodová M, Volf P, Berriman M, Cotton JA, Smith DF. Changes in SNP coverage depth pinpoint recombination breakpoints. Plos Genetics. DOI: 10.1371/Journal.Pgen.1004092.G005  1
2013 Connell S, Meade KG, Allan B, Lloyd AT, Downing T, O'Farrelly C, Bradley DG. Genome-wide association analysis of avian resistance to Campylobacter jejuni colonization identifies risk locus spanning the CDH13 gene. G3 (Bethesda, Md.). 3: 881-90. PMID 23550144 DOI: 10.1534/G3.113.006031  1
2012 Mannaert A, Downing T, Imamura H, Dujardin JC. Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania. Trends in Parasitology. 28: 370-6. PMID 22789456 DOI: 10.1016/J.Pt.2012.06.003  1
2012 Vanaerschot M, Decuypere S, Downing T, Imamura H, Stark O, De Doncker S, Roy S, Ostyn B, Maes L, Khanal B, Boelaert M, Schönian G, Berriman M, Chappuis F, Dujardin JC, et al. Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent. The Journal of Infectious Diseases. 206: 752-5. PMID 22753945 DOI: 10.1093/Infdis/Jis424  1
2012 Downing T. The battle of the SNPs. Nature Reviews. Microbiology. 10: 6. PMID 22138960 DOI: 10.1038/Nrmicro2716  0.01
2012 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, Schönian G. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 12: 149-59. PMID 22119748 DOI: 10.1016/J.Meegid.2011.11.005  1
2011 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, Schönian G, Stark O, et al. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Research. 21: 2143-56. PMID 22038251 DOI: 10.1101/Gr.123430.111  1
2010 Downing T, Lloyd AT, O'Farrelly C, Bradley DG. The differential evolutionary dynamics of avian cytokine and TLR gene classes. Journal of Immunology (Baltimore, Md. : 1950). 184: 6993-7000. PMID 20483729 DOI: 10.4049/Jimmunol.0903092  1
2010 Downing T, O'Farrelly C, Bhuiyan AK, Silva P, Naqvi AN, Sanfo R, Sow RS, Podisi B, Hanotte O, Bradley DG. Variation in chicken populations may affect the enzymatic activity of lysozyme. Animal Genetics. 41: 213-7. PMID 19845599 DOI: 10.1111/J.1365-2052.2009.01974.X  1
2009 Downing T, Cormican P, O'Farrelly C, Bradley DG, Lloyd AT. Evidence of the adaptive evolution of immune genes in chicken. Bmc Research Notes. 2: 254. PMID 20003477 DOI: 10.1186/1756-0500-2-254  1
2009 Cormican P, Lloyd AT, Downing T, Connell SJ, Bradley D, O'Farrelly C. The avian Toll-Like receptor pathway--subtle differences amidst general conformity. Developmental and Comparative Immunology. 33: 967-73. PMID 19539094 DOI: 10.1016/J.Dci.2009.04.001  1
2009 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, Bradley DG. Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus. Bmc Evolutionary Biology. 9: 136. PMID 19527513 DOI: 10.1186/1471-2148-9-136  1
2009 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, Bradley DG. Contrasting evolution of diversity at two disease-associated chicken genes. Immunogenetics. 61: 303-14. PMID 19247647 DOI: 10.1007/S00251-009-0359-X  1
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