Selected PublicationsGrants with Polyomics
- Vincent IM, Daly R, Courtioux B, Cattanach AM, Biéler S, Ndung’u JM, Bisser S, Barrett MP (2016) Metabolomics Identifies Multiple Candidate Biomarkers to Diagnose and Stage Human African Trypanosomiasis. PLOS Neglected Tropical Diseases.
- Vincent IM, Ehmann DE, Mills SD, Perros M, Barrett MP (2016) Untargeted Metabolomics To Ascertain Antibiotic Modes of Action. Antimicrobial Agents and Chemotherapy.
- Grewal JS, McLuskey K, Das D, Myburgh E, Wilkes J, Brown E, Lemgruber L, Gould MK, Burchmore RJ, Coombs GH, Schnaufer A, Mottram JC (2016) PNT1 is a C11 Cysteine Peptidase Essential for Replication of the Trypanosome Kinetoplast. The Journal of Biological Chemistry.
- Cheah BC, Macdonald AI, Martin C, Streklas AJ, Campbell G, Al-Rawhani MA, Nemeth B, Grant JP, Barrett MP, Cumming DR (2016) An Integrated Circuit for Chip-Based Analysis of Enzyme Kinetics and Metabolite Quantification. IEEE Transactions on Biomedical Circuits and Systems.
- Stipetic LH, Dalby MJ, Davies RL, Morton F, Ramage G, and Burgess KE (2016) A novel metabolomic approach used for the comparison of Staphylococcus aureus planktonic cells and biofilm samples. Metabolomics.
- Merlet B, Paulhe N, Vinson F, Frainay C, Chazalviel M, Poupin N, Gloaguen Y Giacomoni F, Jourdan F (2016) A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. Metabolomics.
- Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM, Cotton JA, Sanders M, Blackburn G Dujardin JC, Rijal S, Khanal B, Illingworth CJR, Coombs GH, Carter KC (2016) In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization. Molecular Microbiology.
- Baker N, Hamilton G, Wilkes JM, Hutchinson S, Barrett MP, Horn D (2015) Vacuolar ATPase depletion affects mitochondrial ATPase function, kinetoplast dependency, and drug sensitivity in trypanosomes. PNAS 112: 29.
- Connolly JP, Goldstone RJ, Burgess KE, Cogdell RJ, Beatson SA, Vollmer W, Smith DG, Roe AJ (2015) The host metabolite D-serine contributes to bacterial niche specificity through gene selection. The ISME journal 9: 1052.
- Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt SK, Burgess KE, Breitling R, Watson DG, Bringaud F, Barrett MP (2015) Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose. PLoS pathogens 11: e1004689.
- Kim DH, Achcar F, Breitling R, Burgess KE, Barrett MP (2015) LC-MS-based absolute metabolite quantification: application to metabolic flux measurement in trypanosomes. Metabolomics: DOI 10.1007/s11306-015-0827-2.
- Lindner M, Thummler K, Arthur A, Brunner S, Elliott C, McElroy D, Mohan H, Williams A, Edgar JM, Schuh C, Stadelmann C, Barnett SC, Lassmann H, Mucklisch S, Mudaliar M, Schaeren-Wiemers N, Meinl E, Linington C (2015) Fibroblast growth factor signalling in multiple sclerosis: inhibition of myelination and induction of pro-inflammatory environment by FGF9. Brain: a journal of neurology 138: 1875-1893
- Recknagel H, Jacobs A, Herzyk P, Elmer KR (2015) Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms. Molecular ecology resources DOI: 10.1111/1755-0998.12406.
- Srivastava A, Creek DJ, Evans KJ, De Souza D, Schofield L, Muller S, Barrett MP, McConville MJ, Waters AP (2015) Host reticulocytes provide metabolic reservoirs that can be exploited by malaria parasites. PLoS pathogens 11: e1004882.
- van der Hooft JJ, Ridder L, Barrett MP, Burgess KE (2015) Enhanced acylcarnitine annotation in high-resolution mass spectrometry data: fragmentation analysis for the classification and annotation of acylcarnitines. Frontiers in bioengineering and biotechnology 3: 26.
- Vincent IM, Barrett MP (2015) Metabolomic-based strategies for anti-parasite drug discovery. Journal of biomolecular screening 20: 44-55.
- Haggarty J, Oppermann M, Dalby MJ, Burchmore RJ, Cook K, Weidt S, Burgess KE. (2015) Serially coupling hydrophobic interaction and reversed-phase chromatography with simultaneous gradients provides greater coverage of the metabolome. Metabolomics11: 5./li>
- Daly R, Rogers S, Wandy J, Jankevics A, Burgess KE, Breitling R (2014) MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach. Bioinformatics 30: 2764-2771
- Huser CA, Gilroy KL, de Ridder J, Kilbey A, Borland G, Mackay N, Jenkins A, Bell M, Herzyk P, van der Weyden L, Adams DJ, Rust AG, Cameron E, Neil JC (2014) Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis. PLoS genetics 10: e1004167
- Rankin NJ, Preiss D, Welsh P, Burgess KE, Nelson SM, Lawlor DA, Sattar N (2014) The emergence of proton nuclear magnetic resonance metabolomics in the cardiovascular arena as viewed from a clinical perspective. Atherosclerosis 237: 287-300.
- Beckham KS, Connolly JP, Ritchie JM, Wang D, Gawthorne JA, Tahoun A, Gally DL, Burgess KE, Burchmore RJ, Smith BO, Beatson SA, Byron O, Wolfe AJ, Douce GR, Roe AJ (2014) The metabolic enzyme AdhE controls the virulence of Escherichia coli O157:H7. Molecular microbiology 93: 199-211
- Robinson SW, Herzyk P, Dow JA, Leader DP (2013) FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster. Nucleic acids research 41: D744-750.
- Sani E, Herzyk P, Perrella G, Colot V, Amtmann A (2013) Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome biology 14: R59
- Tsimbouri PM, Murawski K, Hamilton G, Herzyk P, Oreffo RO, Gadegaard N, Dalby MJ (2013) A genomics approach in determining nanotopographical effects on MSC phenotype. Biomaterials 34: 2177-2184
- Chintapalli VR, Terhzaz S, Wang J, Al Bratty M, Watson DG, Herzyk P, Davies SA, Dow JA (2012) Functional correlates of positional and gender-specific renal asymmetry in Drosophila. PloS one 7: e32577.
- Lee CM, Mudaliar MA, Haggart DR, Wolf CR, Miele G, Vass JK, Higham DJ, Crowther D (2012) Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology. PloS one 7: e48238.
- Zhang T, Creek DJ, Barrett MP, Blackburn G, Watson DG (2012) Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. Analytical chemistry 84: 1994-2001.
Plese click the link to obtain a copy of all the publications airising from Polyomics research, as of June 2015.
- RTMet, Real Time Metabolomics. PI: Karl Burgess (III and Polyomics). IBIOIC. Includes metabolomics, technologist and informatics support.
- BoneMalar. PI: Matthias Marti (WTCMP, III). European Research Council. Includes NGS experiments and bioinformatic support.
- Discovery of new drug candidate(s) for the treatment of Human African Trypanosomiasis (HAT). PI: Michael Barrett (WTCMP, III and Polyomics). Wellcome Trust. Includes metabolomics and NGS experiments.
- Elucidating mechanisms of extracellular vesicle mediated cellular communication and stage conversion in malaria parasites. PI: Matthias Marti (WTCMP, III). Wellcome TrustIncludes proteomics and NGS experiments.
- Parasite induced changes to the metabolome of insect vectors of disease. PI: Michael Barrett (WTCMP, III and Polyomics). Royal Society, Newton. Includes metabolomics experiments.
- Developing the NanoKick bioreactor to enable tissue engineered bone graft and use of metabolomics to identify bone specific drug candidates. PI: Matt Dalby (CCE, MCSB). EPSRC. Includes metabolomics experiments.
- Dissection of the unusual mitochondrial tRNA import translocon of Toxoplasma gondii. PI: Lilach Sheiner (WTCMP, III). BBSRC. Includes proteomics experiments.
- Enhanced interpretation of metabolomics data to accelerate microbial engineering. PI: Karl Burgess (III and Polyomics). Innovate UK. Includes a new informatician.
- Transcriptional regulation of plant growth in nuclear micro domains. PI: Dr Eirini Kaiserli (MCSB). BBSRC. Includes NGS experiments as well as bioinformatics support.
- Regulation of anti-inflammatory gene expression in vascular endothelial Cells by EPAC1. PI: Dr Stephen Yarwood (MCSB now Heriot Watt). BHF. Includes NGS experiments as well as bioinformatics support.
- Where and Why? The influence of host metabolism on bacterial niche specificity. PI: Dr Andrew Roe (III). BBSRC. Includes NGS experiments as well as bioinformatics support.
- Combined suppression of cholesterol bioavailability and androgen de novo synthesis to treat castrate resistant prostate cancer. PI: Prof Hing Leung (ICS). PCF. Includes large scale NGS experiments.
- Optimising the use of chemotherapy in prostate cancer. PI: Prof Hing Leung (ICS). PCF. Includes large scale NGS experiments.
- Glasgow Molecular Pathology (GMP) Node. PI: Dr Karin Oien (ICS). MRC. Includes a new informatician and software provisions.
- Situating Pacific barkcloth production in time and place. PI: Ms Frances Lennard (CoA). AHRC. Includes NGS experiments, proteomics as well as bioinformatics support.