SYNBIOCHEM – Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals

SYNBIOCHEM - Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals

Publications

Latest Highlights

Members of SYNBIOCHEM have published a total of 455 publications in the last 5 years. Most have used infrastructure and resources available in the SYNBIOCHEM Centre. Recent highlights:

Dunstan MS, Robinson CJ, Jervis AJ, Yan C, Carbonell P,  Hollywood KA, Currin A, Swainston N, Le Feuvre R, Micklefield J, Faulon J-L, Breitling R, Turner N, Takano E,  Scrutton N. S. (2020). Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol. Synthetic Biology, In Press, DOI: 10.1093/synbio/ysaa012 Open Access

Carbonell P, Le Feuvre R, Takano E & Scrutton N. (2020) In silico design and automated learning to boost next-generation smart biomanufacturing. Synthetic Biology, Sep 28.

Jervis AJ, Hanko EKR, Dunstan MS, Robinson CJ, Takano E, Scrutton NS. (2021). A plasmid toolset for CRISPR-mediated genome editing and CRISPRi gene regulation in Escherichia coli. Microbial Biotechnology In Press, DOI: 10.1111/1751-7915.13780

Robinson CJ, Carbonell P, Jervis AJ, Yan C, Hollywod KA, Dunstan MS, Currin A, Swainston N, Speiss R, Taylor S, Mulherin P, Parker S, Matthews NE, Malone KJ, Le Feuvre R, Shapira P, Barran P, Turner NJ, Micklefield J, Breitling R, Takano E, Scrutton NS. (2020). Rapid prototyping of microbial production strains for the biomanufacture of materials monomers. Metab. Eng. https://doi.org/10.1016/j.ymben.2020.04.008

Scrutton N, Malone K. (2020). Biomanufacturing; a path to sustainable economic recovery. New Statesman Biotechnology Special Edition. (https://tinyurl.com/yxvdkhtq).

YEAR 5 PUBLICATIONS

  1. Ahmed S, Leferink N, Scrutton N. (2019). Chemo-enzymatic Routes Towards the Synthesis of Bio-based Monomers and Polymers. Molecular Catalysis, 467: 95-110.
  2. Alvarez Gonzalez G, Dixon N. (2019). Genetically encoded biosensors for lignocellulose valorization. In: Biotechnology for Biofuels. 12: 246.
  3. Arora SK, Li Y, Youtie J, Shapira, P. (2019). Measuring dynamic capabilities in new ventures: Exploring strategic change in US green goods manufacturing using website data. J. Tech. Transfer.
  4. Auxillos JY, Garcia-Ruiz E, Jones S, Li T, Jiang S, Dai J, Cai Y. (2019). Multiplex genome engineering for optimizing bio-production in Saccharomyces cerevisiae. ACS Biochemistry. 58: 1492-500.
  5. Bailey S, Payne K, Saaret A, Marshall S, Gostimskaya I, Kosov I, Fisher K, Hay S & Leys D. (2019). Enzymatic control of cycloadduct conformation ensures reversible 1,3 dipolar cycloaddition in a prFMN dependent decarboxylase. Nat. Chem. 11: 1049-57.
  6. Berepiki, A., Kent, R., Machado, L. F. M. & Dixon N. (2020). Development of high-performance whole cell biosensors aided by statistical modelling. ACS Synth. Biol. 9: 576-589.
  7. Beveridge R, Migas LG, Das RK, Pappu RV, Kriwacki RW, Barran PE. (2019). Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins. J. Am. Chem. Soc. 141: 4908-18.
  8. Bornadel A, Bisagni S, Pushpanath A, Montgomery SL, Turner NJ, Dominguez B. (2019). Technical Considerations for Scale-Up of Imine-Reductase-Catalyzed Reductive Amination: A Case Study. Organic Proc. Res. and Dev. 23: 1262-68.
  9. Bozhüyük KA, Micklefield J, Wilkinson B. (2019). Engineering enzymatic assembly lines to produce new antibiotics. Curr. Opin. Microbiol. 51: 88-96.
  10. Burke A, Lovelock S, Frese A, Crawshaw R, Ortmayer M, Dunstan M, Levy C, Green AP. (2019). Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature. 570: 219-23.
  11. Carballo-Amador MA, McKenzie EA, Dickson AJ, Warwicker J. (2019). Surface patches on recombinant erythropoietin predict protein solubility: Engineering proteins to minimise aggregation. BMC Biotechnology 19: 26.
  12. Carbonell, P. (2019). Metabolic Pathway Design. A Practical Guide. Learning Materials in Biosciences. ISBN 978-3-030-29865-4 (Print).
  13. Carbonell P, Faulon JL, Breitling R. (2019). Efficient learning in metabolic pathway designs through optimal IFAC-PapersOnLine. 52: 7-12.
  14. Carbonell P, Radivojevic T, García Martín H. (2019). Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation. ACS Synth Biol. 8: 1474-7.
  15. Castaño-Cerezo S, Fournié M, Urban P, Faulon JL, Truan G. (2020). Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae. Frontiers in Bioengineering and Biotechnology. 7: 372.
  16. Cojocariu C, Vinaixa M, Dunstan M, Jervis A, Silcock P, Rattray NJW. Understanding synthetic biology using the Q Exactive GC, Orbitrap GC-MS/MS and high-resolution accurate mass metabolomics library for untargeted metabolomics. ThermoFisher Application note.
  17. Cummings M, Peters AD, Whitehead GFS, Menon BRK, Micklefield J, Webb SJ, Takano E. (2019). Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. PLoS Biol. 18: e3000347.
  18. Currin A, Kwok J, Sadler JC, Bell E, Swainston N, Ababi M, Day P, Turner NJ, Kell DB. (2019). GeneORator: an effective strategy for navigating protein sequence space more efficiently through Boolean OR-type DNA libraries. ACS Synth Biol. 8: 1371-78.
  19. Currin A, Swainston N, Dunstan MS, Jervis AJ, Mulherin P, Robinson CJ, Taylor S, Carbonell P, Hollywood KA, Yan C, Takano E, Scrutton NS, Breitling R. (2019). Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries. Synthetic Biology. 4: 1 ysz025, DOI: 10.1093/synbio/ysz025.
  20. Del Carratore F, Zych K, Cummings M, Takano E, Medema MH, Breitling R. (2019). Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters. Commun Biol. 2: 83.
  21. Del Carratore F, Schmidt K, Vinaixa M, Hollywood KA, Greenland-Bews C, Takano E, Rogers S, Breitling R. (2019). Integrated Probabilistic Annotation: A Bayesian-Based Annotation Method for Metabolomic Profiles Integrating Biochemical Connections, Isotope Patterns, and Adduct Relationships. Analytical chemistry. 91: 12799-807.
  22. Faber K, Fessner WD, Turner NJ. (2019). Biocatalysis: Ready to Master Increasing Complexity. Advanced Synthesis and Catalysis. 361: 2373-76.
  23. Gaffney CE, Dickson AJ, Elvin M. (2019). Metabolite profiling of mammalian cells in Cell Culture Engineering: Recombinant Protein Production. Advanced Biotechnology Series (eds Lee GM, Lee SY, Nielsen J, Stephanopolous G) 251-77.
  24. Garcia-Ruiz E, Auxillos J, Li T, Dai J, Cai Y. (2018). YeastFab: High-Throughput Genetic Parts Construction, Measurement, and Pathway Engineering in Yeast. Methods Enzymol. 608: 277-306.
  25. Grozinger L, Amos M, Gorochowski TE, Carbonell P, Oyarzún DA, Stoof R, Fellermann H, Zuliani P, Tas H, Goñi-Moreno A. (2019). Pathways to cellular supremacy in biocomputing. Nat Commun. 10: 5250.
  26. Hedison TM, Scrutton NS. (2019). Tripping the light fantastic in membrane redox biology: Linking dynamic structures to function in ER electron transfer chains. FEBS J. 286: 2004-17.
  27. Hedison T, Shenoy R, Iorgu AI, Heyes D, Fisher K, Wright G, Hay S, Eady RR, Antonyuk S, Hasnain SS, Scrutton NS. (2019). Unexpected roles of a tether harboring a tyrosine gatekeeper residue in modular nitrite reductase catalysis. ACS Catal. 9: 6087-99.
  28. Henderson F, Johnston HR, Badrock AP, Jones EA, Forster D, Nagaraju RT, Evangelou C, Kamarashev J, Green M, Fairclough M, Ramirez IB, He S, Snaar-Jagalska BE, Hollywood K, Dunn WB, Spaink HP, Smith MP, Lorigan P, Claude E, Williams KJ, McMahon AW, Hurlstone A. (2019). Enhanced Fatty Acid Scavenging and Glycerophospholipid Metabolism Accompany Melanocyte Neoplasia Progression in Zebrafish. Cancer Res. 79: 2136-51.
  29. Hillson et al, Le Feuvre R. Scrutton N. Freemont P. (2019). Building a global alliance of biofoundries. Nature Communciation, 9: 2040.
  30. Howell E, Scheufele D, Brossard D, Xenos M, Kwon S, Youtie J, Shapira P. (2020). Scientists’ and the Publics’ Views of Synthetic Biology. Synthetic Biology 2020: Frontiers in Risk Analysis and Governance. 371-87.
  31. Iorgu AI, Hedison T, Hay S, Scrutton N. (2019). Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases. FEBS J. 286: 3117-28.
  32. Iorgu AI, Cliff M, Waltho J, Scrutton N & Hay S. (2019). Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods in Enzymology. 620: 145-66.
  33. Issa IS, Toogood HS, Johannissen LO, Raftery J, Scrutton NS, Gardiner JM. (2019). C3 and C6 Modification-Specific OYE Biotransformations of Synthetic Carvones and Sequential BVMO Chemoenzymatic Synthesis of Chiral Caprolactones. Chemistry. 25: 2983-8.
  34. Jeffreys LN, Poddar H, Golovanova M, Levy CW, Girvan HM, McLean KJ, Voice MW, Leys D, Munro (2019). Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs. Sci Rep. 9:1577.
  35. Jeffreys LN, Pacholarz KJ, Johannissen LO, Girvan HM, Barran PE, Voice MW, Munro AW. (2020). Characterization of the structure and interactions of P450 BM3 using hybrid mass spectrometry approaches.J Biol Chem. doi: 10.1074/jbc.RA119.011630.
  36. Jervis A, Carbonell P, Taylor S, Sung R, Dunstan M, Breitling, Takano E, Scrutton N. SelProm: a queryable and predictive expression vector selection tool for Escherichia coli. ACS SynBio. 8: 1478-83.
  37. Kempa EE, Hollywood KA, Smith CA, Barran PE. (2019). High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis. The Analyst. 144: 872-91.
  38. Kearsey LJ, Prandi N, Karuppiah V, Yan C, Leys D, Toogood H, Takano E, Scrutton NS. (2019). Structure of the Cannabis sativa olivetol-producing enzyme reveals cyclization plasticity in type III polyketide synthases. FEBS J.  287: 1511-24.
  39. Kent R, Dixon N. (2019). Contemporary Tools for Regulating Gene Expression in Bacteria. Trends Biotechnol. 38: 316-33.
  40. Kent R, Dixon N. (2019). Systematic evaluation of genetic and environmental factors affecting performance of translational riboswitches. ACS Synthetic Biology. 8: 884-901.
  41. Koch M, Pandi A, Borkowski O, Batista AC, Faulon JL. (2019). Custom-made transcriptional biosensors for metabolic engineering. Curr Opin Biotechnol. 59: 78-84.
  42. Koch M, Duigou T, Faulon JL. (2020). Reinforcement Learning for Bioretrosynthesis. ACS Synth Biol. 19: 157-168.
  43. Kurgan G, Kurgan L, Schneider A, Onyeabor M, Rodriguez-Sanchez Y, Taylor E, Martinez R, Carbonell P, Shi X, Gu H, Wang X. (2019). Identification of major malate export systems in an engineered malate-producing Escherichia coli aided by substrate similarity search. Appl Microbiol Biotechnol. 103: 9001-11.
  44. Leferink NGH, Dunstan MS, Hollywood KA, Swainston N, Currin A, Jervis AJ, Takano E, Scrutton NS. (2019). An automated pipeline for the screening of diverse monoterpene synthase libraries. Sci Rep. 9: 11936.
  45. Leferink NGH,  Ranaghan KE,  Battye J, Johannissen LO,  Hay S,  van der Kamp M,  Mulholland AJ,   Scrutton NS. (2019). Taming the Reactivity of Monoterpene Synthases To Guide Regioselective Product Hydroxylation. Chem Bio Chem. 20: 1-7.
  46. Lin Y, Zou X, Zheng Y, Cai Y, Dai J (2019). Improving Chromosome Synthesis with a Semiquantitative Phenotypic Assay and Refined Assembly Strategy. ACS Synth Biol. 18: 2203-2211.
  47. Machado L, Currin A, Dixon N. (2019). Directed evolution of the PcaV allosteric transcription factor to generate a biosensor for aromatic aldehydes. J Biol Eng. 13: 91.
  48. Manning J, Tavanti M, Porter J, Kress N, De Visser S, Turner N, Flitsch S. (2019). Regio- and Enantio-selective Chemo-enzymatic C-H-lactonization of Decanoic Acid to (S)-δ-Decalactone. Ange. Chemie. 131: 5724-27.
  49. Marshall SA, Payne KAP, Fisher K, White MD, Ní Cheallaigh A, Balaikaite A, Rigby SEJ, Leys D. (2019). The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun. 10: 2357.
  50. Martella A, Firth M, Taylor B, Goeppert A, Cuomo E, Roth R, Dickson A, Fisher D. (2019). Systematic evaluation of CRISPRa and CRISPRi modalities enables development of a multiplexed, orthogonal gene activation and repression system. ACS Synthetic Biology 8: 1998-2006.
  51. Mattey A, Birmingham WR, Both P, Kress N, Huang K, Van Munster JM, Bulmer G, Parmeggiani F, Voglmeir J, Reyes Martinez JE, Turner NJ, Flitsch SL. (2019). Selective Oxidation of N-Glycolylneuraminic Acid Using an Engineered Galactose Oxidase Variant. ACS Catalysis. 9: 8208-12.
  52. Matthews S, Pacholarz K, France A, Jowitt T, Hay S, Barran P & Munro A. (2019). MhuD from Mycobacterium tuberculosis – probing a dual role in heme storage and degradation. ACS Infect. Dis. 5: 1855-66.
  53. Matthews N, Stamford L, Shapira P. (2019). Aligning sustainability assessment with responsible research and innovation: Towards a framework for Constructive Sustainability Assessment. Sustainable Production and Consumption. 20: 58-73.
  54. Meckin R. (2019). Changing Infrastructural Practices: Routine and Reproducibility in Automated Interdisciplinary Bioscience. Science, Technology, & Human Values, Doi.org/10.1177/0162243919893757
  55. Matthews NE, Cizauskas CA, Layton DS, Stamford L, Shapira P. (2019). Collaborating constructively for sustainable biotechnology. Sci Rep. 9: 19033.
  56. Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL. (2019). Metabolic perceptrons for neural computing in biological systems. Nat Comm. 10: 3880.
  57. Pandi A, Grigoras I, Borkowski O, Faulon JL. (2019). Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synth Biol. 16: 1952-7.
  58. Ramsden JI, Heath RS, Derrington SR, Montgomery SL, Mangas-Sanchez J, Mulholland KR, Turner NJ. (2019). Biocatalytic N-Alkylation of Amines Using Either Primary Alcohols or Carboxylic Acids via Reductive Aminase Cascades. J. Am. Chem. Soc. 141: 1201-06.
  59. Randles S. (2019). Interview with Piero Bassetti, President of Fondazione Giannino Bassetti, in R. Schomberg & J. Hankins). International Handbook on Responsible Innovation: A Global Resource. Cheltenham: Edward Elgar. 522-528.
  60. Rajput S, McLean KJ, Poddar H, Selvam IR, Nagalingam G, Triccas JA, Levy CW, Munro AW, Hutton CA. (2019) Structure-Activity Relationships of cyclo(l-Tyrosyl-l-tyrosine) Derivatives Binding to Mycobacterium tuberculosis CYP121: Iodinated Analogues Promote Shift to High-Spin Adduct. J Med Chem. 62: 9792-9805.
  61. Ribeiro B, & Shapira P. (2019). Anticipating governance challenges in synthetic biology: Insights from biosynthetic menthol. Technological Forecasting and Social Change. 139: 311-320.
  62. Ribeiro B, & Shapira P. (2019). Private and public values of innovation: Asa patent analysis of synthetic biology. Research Policy. 49: 103875.
  63. Roberts A, Finnigan W, Wolde-Michael E, Kelly P, Blaker J, Hay S, Breitling R, Takano E, Scrutton N. (2019). Synthetic biology for fibres, adhesives and active camouflage materials in protection and aerospace. MRS Commun. 9: 486-504.
  64. Roberts A, Kelly P, Bain J, Morrison J, Wimpenny I, Barrow M, Woodward RT, Gresil M, Blanford CF, Hay S, Blaker J, Yeates S, Scrutton N. (2019). Graphene–aramid nanocomposite fibres via superacid co-processing. Chem. Commun. 55: 11703.
  65. Robinson CJ, Carbonell P, Jervis AJ, Yan C, Hollywod KA, Dunstan MS, Currin A, Swainston N, Speiss R, Taylor S, Mulherin P, Parker S, Matthews NE, Malone KJ, Le Feuvre R, Shapira P, Barran P, Turner NJ, Micklefield J, Breitling R, Takano E, Scrutton NS. (2020). Rapid prototyping of microbial production strains for the biomanufacture of materials monomers. Metab. Eng. https://doi.org/10.1016/j.ymben.2020.04.008
  66. Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI. (2019). Microbial Genes for a Circular and Sustainable Bio-PET Economy. Genes. 10: 373.
  67. Shapira P. (2019). Religion and ideology in public and expert perceptions of Synthetic Biology: The role of values in understanding perceptions of societal risk and benefit of Synthetic Biology. Public Understanding of Science.
  68. Sinclair E, Bachman M, Addison D, Rohman M, Murray DC, Davies G, Mouchet E, Tonge ME, Stearns RG, Ghislain L, Datwani SS, Majlof L, Hall E, Jones GR, Hoyes E, Olechno J, Ellson RN, Barran PE, Pringle SD, Morris MR, Wingfield J. (2019). Acoustic Mist Ionization Platform for Direct and Contactless Ultrahigh-Throughput Mass Spectrometry Analysis of Liquid Samples. Anal Chem. 19: 3790-94.
  69. Sun C, Theodoropoulos C, Scrutton NS. (2019). Techno-economic assessment of microbial limonene production. Bioresource Technology. 300: 122666.
  70. Thompson MP, Derrington SR, Heath RS, Porter JL, Mangas-Sanchez J, Devine PN, Truppo MD, Turner NJ. (2019). A generic platform for the immobilisation of engineered biocatalysts. Tetrahedron. 75: 327-34.
  71. Torres M, Berrios J, Rigual Y, Latorre Y, Vergara M, Dickson AJ, Altamirano C. (2019). Metabolic flux analysis during galactose and lactate co-consumption reveals enhanced energy metabolism in continuous CHO cell cultures. Chem. Eng. Sci. 205: 201-211.
  72. Tramontina R, Galman J, Parmeggiani F, Derrington S, Timothy B, Turner N, Squina FM & Dixon N. (2019). Consolidated production of coniferol and other high-value aromatic alcohols directly from lignocellulosic biomass. Green Chemistry. 22: 144-52.
  73. Trivedi DK, Sinclair E, Xu Y, Sarkar D, Walton-Doyle C, Liscio C, Banks P, Milne J, Silverdale M, Kunath T, Goodacre R, Barran P. (2019).  Discovery of Volatile Biomarkers of Parkinson’s Disease from Sebum. ACS Central Science. 5: 599-606.
  74. Upton R, Migas L, Pacholarz K, Beniston R, Estdale S, Firth D, Barran P. (2019). Hybrid mass spectrometry methods reveal lot-to-lot differences and delineate the effects of glycosylation on the tertiary structure of Herceptin®. Chem. Sci. 10: 2811-20.
  75. Uyarra E, Ribeiro B, Dale-Clough L. (2019). Exploring the normative turn in regional innovation policy: responsibility and the quest for public value. European Planning Studies, 27: 2359-75.
  76. Voyvodic PL, Pandi A, Koch M, Conejero I, Valjent E, Courtet P, Renard E, Faulon JL, Bonnet J. (2019). Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors. Nat Commun. 10: 1697.
  77. Wang Z, Porter A, Kwon S, Youtie J, Shapira P, Carley S & Liu X. (2019). Updating a Search Strategy to Track Emerging Nanotechnologies. J. Nanoparticle Res. 21: 199
  78. Welty R, Rau M, Pabit S, Dunstan MS, Conn GL, Pollack L, Hall KB. (2019). Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain. J Mol Biol. 432: 991-1007.
  79. Zhang L, Stephens AJ, Lemonnier JF, Pirvu L, Vitorica-Yrezabal IJ, Robinson CJ, Leigh DA. (2019). Coordination Chemistry of a Molecular Pentafoil Knot. J. Am. Chem. Soc. 141: 3952-8.
  80. Zhang S, Sakuma M, Deora GS, Levy C, Klausing A, Breda C, Read KD, Ross BP, Wright Muelas M, Day P, O’Hagan S, Kell D, Schwarcz R, Leys D, Heyes D, Giorgini F, Scrutton N. (2019). A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites. Commun Biol. 2: 271.
  81. Zhang S, Heyes DJ, Feng L, Sun W, Johannissen LO, Liu H, Levy CW, Li X, Yang J, Yu X, Lin M, Hardman SJO, Hoeven R, Sakuma M, Hay S, Leys D, Rao Z, Zhou A, Cheng Q, Scrutton NS. (2019). Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis. Nature. 574: 722-25.

YEAR 4 PUBLICATIONS

  1. Acevedo-Rocha C, Gamble C, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau J, Wirtz C, Farès C, Hinrichs H, Deege A, Mulholland A, Nov Y, Leys D, McLean K, Munro A, Reetz M. (2018). P450-catalyzed regio- and diastereoselective steroid hydroxylation: Efficient directed evolution enabled by mutability landscaping. ACS Catal. 8: 3395-410.
  2. Ahmed WM, Geranios P, White IR, Lawal O, Nijsen TM, Bromley MJ, Goodacre R, Read ND, Fowler SJ. (2018). Development of an adaptable headspace sampling method for metabolic profiling of the fungal volatome. Analyst. 143: 4155-62.
  3. AlRabiah H, Allwood JW, Correa E, Xu Y, Goodacre R. (2018). pH plays a role in the mode of action of trimethoprim on Escherichia coli. PLoS One. 13(7):e0200272.
  4. Amara A, Takano E, Breitling R. (2018). Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. BMC Genomics. 9: 519.
  5. Archipowa N, Kutta RJ, Heyes DJ, Scrutton NS. (2018). Stepwise hydride transfer in a biological system: Insights into the reaction mechanism of the light-dependent protochlorophyllide oxidoreductase. Angew. Chem. Int. Ed. Engl. 57: 2682-6.
  6. Ascue Avalos G, Toogood H, Tait S, Messiha H, Scrutton N. (2018). From bugs to bioplastics: Total (+)-dihydrocarvide biosynthesis by engineered Escherichia coli. ChemBioChem: a European journal of chemical biology, ISSN (Print): 1439-4227.
  7. Baker K, Takano E, Breitling R. (2018). The “three c’s” of novel antibiotic discovery and production through synthetic biology: biosynthetic gene clusters, heterologous chassis, and synthetic microbial consortia. Advanced Biosystems,  54:114-20.
  8. Barley MH, Turner NJ, Goodacre R. (2018). Improved descriptors for the quantitative structure-activity relationship modeling of peptides and proteins. J. Chem. Inf. Model. 58: 234-43.
  9. Barran P, Baker E. (2018). Editorial overview: Omics. Curr. Opin. Chem. Biol. 42: A1-2.
  10. Bennett M, Thompson M, Micklefield J, Levy C, Menon B, Cronin V, Smith D, Herbert A, Dunstan M. Shepherd S. (2018). Structure and biocatalytic scope of coclaurine N-Methyltransferase. Angew. Chemie. 57: 10600-04.
  11. Biarnes-Carrera M, Breitling R, Takano E. (2018). Detection and quantification of butyrolactones from Streptomyces. Methods Mol. Biol. 1673: 117-28.
  12. Biarnes-Carrera M, Lee CK, Nihira T, Breitling R, Takano E. (2018). Orthogonal regulatory circuits for E. coli based on the γ-butyrolactone system of Streptomyces coelicolor. ACS Synth. Biol. 7: 1043-55.
  13. Birmingham WR. Turner NJ. (2018). A single enzyme oxidative “cascade” via a dual-functional galactose oxidase. ACS Catalysis. 8: 4025-32.
  14. Çakar MM, Mangas-Sanchez J, Birmingham WR, Turner NJ. Binay B. (2018). Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii. Preparative Biochemistry and Biotechnology. 48: 327-34.
  15. Carbonell P, Jervis AJ, Robinson C, Yan C, Dunstan M, Swainston N, Vinaixa M, Hollywood KA, Currin A, Rattray NJW, Taylor S, Reynard Spiess R, Sung R, Williams AR, Fellows D, Stanford NJ, Mulherin P, Le Feuvre R, Barran P, Goodacre R, Turner NJ, Goble C, Chen GG, Kell DB, Micklefield J, Breitling R, Takano E, Faulon J-L, Scrutton NS. (2018). An automated Design-Build-Test-Learn pipeline for microbial production of fine chemicals. Communications Biology, 1: 66.
  16. Carbonell P, Koch M, Duigou T, Faulon JL. (2018). Enzyme discovery: enzyme selection and pathway design. Methods Enzymol. 608: 3-27.
  17. Carbonell P, Wong J, Swainston N, Takano E, Turner NJ, Scrutton NS, Kell DB, Breitling R, Faulon JL. (2018). Selenzyme: Enzyme selection tool for pathway design. Bioinformatics. 34(12):2153-4.
  18. Chapman MR, Cosgrove SC, Turner NJ, Kapur N, Blacker AJ. (2018). Highly productive oxidative biocatalysis in continuous flow by enhancing the aqueous equilibrium solubility of oxygen. Angew. Chemie, 57: 10535-9.
  19. Charles ED, Muhamadali H, Goodacre R, Pittman J. (2019). Biochemical signatures of acclimation by Chlamydomonas reinhardtii to different ionic stresses. Algal Research, In press.
  20. Cheallaigh AN, Mansell DJ, Toogood HS, Tait S, Lygidakis A, Scrutton NS, Gardiner JM. (2018). Chemoenzymatic synthesis of the intermediates in the peppermint monoterpenoid biosynthetic pathway. J. Nat. Prod. 81: 1546-52.
  21. Chisanga M, Muhamadali H, Ellis DI, Goodacre R. (2018). Surface-Enhanced Raman Scattering (SERS) in microbiology: illumination and enhancement of the microbial world. Appl. Spectrosc. 72: 987-1000.
  22. Choudry U, Heyes DJ, Hardman SJO, Sakuma M, Sazanovich IV, Woodhouse J, De La Mora E, Pedersen MN, Weik M, Schiro G, Scrutton NS. (2018). Photochemical mechanism of an atypical algal phytochrome. ChemBioChem. 19: 1036-43.
  23. Cosgrove SC, Hussain S, Turner NJ, Marsden SP. (2018). Synergistic chemo/biocatalytic synthesis of alkaloidal tetrahydroquinolines. ACS Catalysis, 8: 5570-3.
  24. Cosgrove SC, Brzezniak A, France SP, Ramsden JI, Mangas-Sanchez J, Montgomery SL, Heath RS, Turner NJ. (Jan 2018). Imine reductases, reductive aminases, and amine oxidases for the synthesis of chiral amines: discovery, characterization, and synthetic applications. Methods in Enzymology. 608: 131-49.
  25. Costa BZ, Galman JL, Slabu I, France SP, Marsaioli AJ. Turner NJ. (2018). Synthesis of 2,5-disubstituted pyrrolidine alkaloids via a one-pot cascade using transaminase and reductive aminase biocatalysts. ChemCatChem, In Press.
  26. Cummings M, Peters AD, Whitehead GFS, Menon BRK, Micklefield J, Webb SJ, Takano E. Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. Nature Communications, in revision Jan. 2018.
  27. Currin A, Dunstan MS, Johannissen LO, Hollywood KA, Vinaixa M, Jervis AJ, Swainston N, Rattray NJW, Gardiner JM, Kell DB, Takano E, Toogood HS, and Scrutton NS. (2018). Engineering the “missing link” in biosynthetic (−)-menthol production: bacterial isopulegone isomerase. ACS Catal., 8: 2012–20.
  28. Darbani B, Kell DB, Borodina I. (2018). Energetic evolution of cellular transportomes. BMC Genomics. 19, 1, 418
  29. de Mattos-Shipley KMJ, Greco C, Heard DM, Hough G, Mulholland NP, Vincent JL, Micklefield J, Simpson TJ, Willis CL, Cox RJ, Bailey AM. (2018). The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis. Chem. Sci. 9: 4109-17.
  30. Delépine B, Duigou T, Carbonell P, Faulon JL. (2018). RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-70.
  31. Dhami N, Trivedi DK, Goodacre R, Mainwaring D, Humphreys DP. (2018). Mitochondrial aconitase is a key regulator of energy production for growth and protein expression in Chinese hamster ovary cells. Metabolomics, 14: 10.
  32. Di Lucia L, Ribeiro B. (2018). Enacting Responsibilities in Landscape Design: The Case of Advanced Biofuels. Sustainability, 10: 4016.
  33. Duigou T, du Lac M, Carbonell P, Faulon J. (2018). RetroRules: a database of reaction rules for engineering biology. Nucleic Acids Research, In Press doi: 10.1093/nar/gky940.
  34. El-Wahab HAAA, Accietto M, Marino LB, McLean KJ, Levy CW, Abdel-Rahman HM, El-Gendy MA, Munro AW, Aboraia AS, Simons C. (2018). Design, synthesis and evaluation against Mycobacterium tuberculosis of azole piperazine derivatives as dicyclotyrosine (cYY) mimics. Bioorg. Med. Chem. 26: 161-76.
  35. Fraczek MG, Naseeb S, Delneri D. (2018). History of genome editing in yeast. Yeast. 35(5):361-368. doi: 10.1002/yea.3308.
  36. Girvan HM, Poddar H, McLean KJ, Nelson DR, Hollywood KA, Levy CW, Leys D, Munro AW. (2018). Structural and catalytic properties of the peroxygenase P450 enzyme CYP152K6 from Bacillus methanolicus. J. Inorg. Biochem. 188: 18-28.
  37. Goodacre R, Graham D, Faulds K. (2018). Recent developments in quantitative SERS moving towards absolute quantification. Trends in Analytical Chemistry, 102: 359-68.
  38. Green AP, Hardy S, Lee ATL, Thomas EJ. (2018). Total synthesis of 7-des-O-pivaloyl-7-O-benzylbryostatin 10. Org Biomol Chem. 15:  9497-526.
  39. Hayashi T, Hilvert D, Green AP. (2018).  Engineered metalloenzymes with non-canonical coordination environments. Chemistry. 24: 11821-30.
  40. Hedison TM, Hay S, Scrutton NS. (2018).Trapping methods for probing functional intermediates in nitric oxide synthases and related enzymes. Front Biosci (Landmark Ed). 2018 Jun 1;23:1874-88.
  41. Hernandez-Ortega A, Vinaixa M, Zebec Z, Takano E, Scrutton N. (2018). A toolbox for diverse oxyfunctionalisation of monoterpenes. Sci. Rep. 8, 14396.
  42. Heyes D, Hardman S, Pedersen MN, Woodhouse J, De La Mora E, Wulff M, Weik M, Cammarata M, Scrutton N, Schiro G. (2019). Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering. Communications Biology, 2: 1. 2:1, DOI: 10.1038/s42003-018-0242-0.
  43. Hollywood KA, Schmidt K, Takano E, Breitling R. (2018). Metabolomics tools for the synthetic biology of natural products. Curr. Opin. Biotechnol. 54:114-20.
  44. Horga LG, Halliwell S, Castiñeiras TS, Wyre C, Matos CFRO, Yovcheva DS, Kent R, Morra R,. Williams GS, Smith DC, Dixon N. (2019). Tuning recombinant protein expression to match secretion capacity. Microbial Cell Factories , 17: 199.
  45. Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. (2018). Nonequivalence of second sphere “noncatalytic” residues in pentaerythritol tetranitrate reductase in relation to local dynamics linked to h-transfer in reactions with NADH and NADPH coenzymes. ACS Catal., 8: 11589–99.
  46. Jeffreys LN, Girvan HM, McLean KJ, Munro AW. (2018). Characterization of cytochrome P450 enzymes and their applications in synthetic biology. Methods Enzymol. 608: 189-261.
  47. Jeffreys LN, Poddar H, Golovanova M, Levy CW, Girvan HM, McLean KJ, Voice MW, Leys D, and Munro AW. (2018). Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs. Sci. Rep. In Press.
  48. Jervis A, Carbonell P, Vinaixa M, Dunstan M, Hollywood K, Rattray N, Robinson CJ, Yan C, Swainston N, Currin A, Sung R, Toogood H, Taylor S, Breitling R, Takano E, Scrutton N. (2018). Machine learning of designed translational control allowing predictive pathway optimisation. ACS Synthetic Biology, doi: 10.1021/acssynbio.8b00398.
  49. Jervis AJ, Wood AG, Cain JA, Butler JA, Frost H, Lord E, Langdon R, Cordwell SJ, Wren BW, Linton D. (2018). Functional analysis of the Helicobacter pullorum N-linked protein glycosylation system. Glycobiology. 28: 233-44.
  50. Jones S, Martella A, Cai Y. (2019). EMMA assembly explained: a step-by-step guide to assemble synthetic mammalian vectors. Methods in Enzymology. In Press.
  51. Kent R, Halliwell S, Young K, Swainston N, Dixon N. (2018). Rationalizing context-dependent performance of dynamic rna regulatory devices. ACS Synth. Biol. 7: 1660-8.
  52. Kimber R, Lewis EA, Parmeggiani F, Smith K, Bagshaw H, Starborg T, Joshi N, Figueroa AI, Van der Laan G, Cibin G, Gianolio D, Haigh S, Pattrick RAD, Turner N, Lloyd J. (2019). Biosynthesis and characterization of copper nanoparticles using shewanella oneidensis: application for click chemistry. Small, 14: doi: 10.1002/smll.201703145.
  53. Klumbys E, Zebec Z, Weise N, Turner N. Scrutton N. (2019). Bio-derived production of cinnamyl alcohol via a three step biocatalytic cascade and metabolic engineering. Green Chemistry, 20: 658-63.
  54. Knaus T, Tseliou V, Humphreys LD, Scrutton NS, Mutti FG. (2018). A biocatalytic method for the chemoselective aerobic oxidation of aldehydes to carboxylic acids.  Green Chemistry, 20: 3887-4122.
  55. Koch M, Pandi A, Delépine B, Faulon JL. (2018). A dataset of small molecules triggering transcriptional and translational cellular responses. Data Brief. 17: 1374-8.
  56. Koch M, Faulon JL, Borkowski O. (2018). Models for cell-free synthetic biology: make prototyping easier, better, and faster. Fr. Bioengin. and Biotech., https://doi.org/10.3389/fbioe.2018.00182.
  57. Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. (2018). Development of halogenase enzymes for use in synthesis. Chem. Rev. 118: 232-69.
  58. Law B, Zhuo Y, Winn M, Francis D, Samborskyy M, Murphy A, Ren L, Leadlay P F and Micklefield J. (2018). A vitamin K-dependent carboxylase orthologue is involved in antibiotic biosynthesis. Nature Catalysis,  1: 977-84.
  59. Lawal O, Knobel H, Weda H, Bos LD, Nijsen TME, Goodacre R, Fowler SJ. (2018). Volatile organic compound signature from co-culture of lung epithelial cell line with Pseudomonas aeruginosa. Analyst. 143: 3148-55.
  60. Lawal O, Muhamadali H, Ahmed WM, White IR, Nijsen TME, Goodacre R, Fowler SJ. (2018). Headspace volatile organic compounds from bacteria implicated in ventilator-associated pneumonia analysed by TD-GC/MS. J. Breath Res. 12(2):026002.
  61. Lawal O, Knobel H, Weda H, Nijsen TM, Goodacre R, Fowler SJ, Ahmed WM, Artigas A, Bannard-Smith J, Bos LD, Camprubi M, Coelho L, Dark P, Davie A, Diaz E, Goma G, Felton T, Leopold JH, van Oort PM, Povoa P, Portsmouth C, Rattray NJ, Rijnders G, Schultz MJ, Steenwelle R, Sterk PJ, Valles J, Verhoeckx F, Vink A, White IR, Winters T, Zakharkina T, the BreathDx consortium. (2018). TD/GC–MS analysis of volatile markers emitted from mono- and co-cultures of Enterobacter cloacae and Pseudomonas aeruginosa in artificial sputum. Metabolomics, 14: 66.
  62. Le Feuvre RA. (2018). How Manchester’s SYNBIOCHEM is harnessing the power of synthetic biology to scale up the production of chemicals and materials. https://synbiobeta.com/synbiochem-is-synthetic-biology-chemicals-and-materials/  SynbiCITE sponsored article.
  63. Le Feuvre RA, Scrutton NS. (2018). A living foundry for synthetic biological materials: A synthetic biology roadmap to new advanced materials. Synthetic and Systems Biotechnology. 3: 105-12.
  64. Leferink N, Ranaghan K, Karuppiah V, Currin A, van der Kamp M, Mulholland AJ and Scrutton NS. (2018). Experiment and simulation reveal how mutations in functional plasticity regions guide plant monoterpene synthase product outcome. ACS Catalysis. 8: 3780-91.
  65. Liu W, Luo Z, Wang Y, Pham NT, Tuck L, Pérez-Pi I, Liu L, Shen Y, French C, Auer M, Marles-Wright J, Dai J, Cai Y. (2018) Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nat. Commun. 9: 1936.
  66. Luo Z, Wang L, Wang Y, Zhang W, Guo Y, Shen Y, Jiang L, Wu Q, Zhang C, Cai Y, Dai J. (2018). Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nat. Commun. 9: 1930.
  67. Megraw VE, Brown AR, Boothman C, Goodacre R, Morris K, Sigee D, Anderson L, Lloyd JR, Bailey MJ. (2018). A novel adaptation mechanism underpinning algal colonization of a nuclear fuel storage pond, mBio. 9: 3.
  68. Meckin R, Balmer A. (2018). Everyday uncertainty work: Making sense of biosynthetic menthol. Engaging Science, Technology, and Society. 4: DOI: 10.17351/ests2018.250
  69. Meckin R. Balmer A. (2018). Situating anticipation in everyday life: Using sensory methods to explore public expectations of synthetic biology. Public Understanding of Science. DOI: 10.1177/0963662518808694.
  70. Messiha H, Ahmed S, Karuppiah V, Suardiaz R, Ascue Avalos G, Fey N, Yeates S, Toogood HS, Mulholland AJ and Scrutton NS. (2018). Biocatalytic routes to lactone monomers for polymer production. Biochemistry. 57: 1997-2008.
  71. Micklefield J, Latham J, Brandenburger E, Shepherd S, Menon B. (2018). Development of halogenase enzymes for use in synthesis. Chemical Rev. 118: 232–69.
  72. Mistarz UH, Bellina B, Jensen PF, Brown JM, Barran PE, Rand KD. (2018). UV photodissociation mass spectrometry accurately localize sites of backbone deuteration in peptides. Anal. Chem. 90: 1077-80.
  73. Moraes EC, Alvarez TM, Persinoti GF, Tomazetto G, Brenelli LB, Paixão DAA, Ematsu GC, Aricetti JA, Caldana C, Dixon N, Bugg TDH, Squina FM. (2018). Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization. Biotechnol. Biofuels. 11: 75.
  74. Morra R, Del Carratore F, Muhamadali H, Horga LG, Halliwell S, Goodacre R, Breitling R, Dixon N. (2018). Translation stress positively regulates mscl-dependent excretion of cytoplasmic proteins. MBio. 9: pii: e02118-17.
  75. Morrill C, Jensen C, Just-Baringo X, Grogan G, Turner N. Procter D. (2018). Biocatalytic conversion of cyclic ketones bearing α-quaternary stereocenters to lactones in an enantioselective radical approach to medium-sized carbocycles. Angewandte Chemie,. 57: 3692-6.
  76. Munro AW, McLean KJ, Grant JL, Makris TM. (2018). Structure and function of the cytochrome P450 peroxygenase enzymes. Biochem Soc Trans. 46: 183-96.
  77. Munro AW. (2018). Cytochrome P450 1A1 opens up to new substrates. J. Biol. Chem. 293: 19211-12
  78. Naseeb S, Alsammar H, Burgis T, Donaldson I, Knyazev N, Knight C, Delneri D. (2018). Whole genome sequencing, de novo assembly and phenotypic profiling for the new budding yeast species Saccharomyces jurei. G3 (Bethesda). 8: 2967-77.
  79. Odachowski M, Greaney MF, Turner NJ. (2018). Concurrent biocatalytic oxidation and C–C bond formation via gold catalysis: one-pot alkynylation of N-alkyl tetrahydroisoquinolines. ACS Catalysis, 8: 10032-35.
  80. O’Hagan S, Kell DB. (2018). Analysing and navigating natural products space for generating small, diverse, but representative chemical libraries. Biotechnol. J. 13: 1700503.
  81. Oldham PD, Hall S. (2018). Synthetic biology: Mapping the patent landscape. bioRxiv preprint. https://doi.org/10.1101/483826
  82. Parker S, Fraczek MG, Wu J, Shamsah S, Manousaki A, Dungrattanalert K, de Almeida RA, Invernizzi E, Burgis T, Omara W, Griffiths-Jones S, Delneri D, O’Keefe RT. (2018).  Large-scale profiling of noncoding RNA function in yeast. PLoS Genet. 14(3):e1007253.
  83. Peña A, Del Carratore F, Cummings M, Takano E, Breitling R. (2018). Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery. J. Ind. Microbiol. Biotechnol. 45: 615-9.
  84. Porter JL, Manning J, Sabatini S, Tavanti M, Turner NJ, Flitsch SL. (2018). Characterisation of CYP102A25 from Bacillus marmarensis and CYP102A26 from Pontibacillus halophilus: P450 Homologues of BM3 with Preference towards Hydroxylation of Medium-Chain Fatty Acids. Chembiochem. 19: 513-20.
  85. Porter JL, Sabatini S, Manning J, Tavanti M, Galman JL, Turner NJ, Flitsch SL. (2018). Cloning, expression and characterisation of P450-Hal1 (CYP116B62) from Halomonassp. NCIMB 172: A self-sufficient P450 with high expression and diverse substrate scope. Enzyme Microbial Tech. 113: 1-8.
  86. Pott M, Hayashi T, Mori T, Mittl PRE, Green AP, Hilvert D. (2018). A noncanonical proximal heme ligand affords an efficient peroxidase in a globin fold. J. Am. Chem. Soc. 140: 1535-43.
  87. Pretorius E, Page MJ, Mbotwe S, Kell DB. (2018). Lipopolysaccharide-binding protein (LBP) can reverse the amyloid state of fibrin seen or induced in Parkinson’s disease. PLoS ONE. 13: 3, e0192121.
  88. Ribeiro B, Bengtsson L, Benneworth P, Bührer S, Castro-Martínez E, Hansen M, Jarmai K, Lindner R, Olmos-Peñuela J, Ott C, Shapira P. (2018). Introducing the dilemma of societal alignment for inclusive and responsible research and innovation. J. Resp. Innovation,  DOI: 10.1080/23299460.2018.1495033.
  89. Ribeiro B, Hartley S, Nerlich B, Jaspal R. (2018). Media coverage of the Zika crisis in Brazil: The construction of a “war” frame that masked social and gender inequalities. Social Science & Medicine 200: 137–144.
  90. Ribeiro B, Shapira P. (2018). Anticipating governance challenges in synthetic biology: Insights from biosynthetic menthol, Technological Forecasting & Social Change. In press.
  91. Robinson CJ, Dunstan MS, Swainston N, Titchmarsh J, Takano E, Scrutton NS, Jervis AJ. (2018). Multifragment DNA assembly of biochemical pathways via automated ligase cycling reaction. Methods Enzymol. 608: 369-92.
  92. Rose KM, Howell EL, Scheufele DA, Brossard D, Xenos MA, Shapira P, Youtie J, Kwon S. (2018). The values of synthetic biology: researcher views of their field and participation in public engagement. BioScience, 68: 782–91.
  93. Sabatini M, Comba S, Altabe S, Recio-Balsells AI, Labadie GR, Takano E, Gramajo H, Arabolaza A. (2018). Biochemical characterization of the minimal domains of an iterative eukaryotic polyketide synthase. FEBS J, 285:4494-4511
  94. Sadler JC, Currin A, Kell DB. (2018). Ultra-high throughput functional enrichment of large monoamine oxidase (MAO-N) libraries by fluorescence activated cell sorting. Analyst. 143: 4747-55.
  95. Sadler JC, Green L, Swainston N, Kell DB, Currin A. (2018). Fast and flexible synthesis of combinatorial libraries for directed evolution. Methods Enzymol. 608: 59-79.
  96. Shapira P, Kwon S. (2018). Synthetic biology research and innovation profile 2018: Publications and patents. Manchester Institute of Innovation Research and Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals, University of Manchester. bioRxiv preprint; http://dx.doi.org/10.1101/485805.
  97. Sinclair E, Hollywood KA, Yan C, Blankley R, Breitling R, Barran P. (2018). Mobilising ion mobility mass spectrometry for metabolomics. Analyst. 143: 4783.
  98. Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. (2018). Data management in computational systems biology: exploring standards, tools, databases, and packaging best practices. Yeast Systems Biology, Vol. 2. In Press.
  99. Stuchfield D, Barran P. (2018). Unique insights to intrinsically disordered proteins provided by ion mobility mass spectrometry. Curr. Opin. Chem. Biol. 2:177-85.
  100. Swainston N, Jervis A, Dunstan M, Carbonell P, Williams A, Faulon JL, Kell DB,  Scrutton NS. (2018). PartsGenie: an integrated design tool for optimising and sharing synthetic biology parts. Bioinformatics. Bioinformatics.  34: 2327-9.
  101. Swainston N, Kettner C. (2018). Quality-assured data for enzyme activity. Nature. 556, 309.
  102. Swainston N, et al (2018). STRENDA DB: enabling the validation and sharing of enzyme kinetics data. FEBS J. 285: 2193-204.
  103. Tavanti M, Porter JL, Levy CW, Gómez Castellanos JR, Flitsch SL, Turner NJ. (2018). The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s. Biochem. Biophys. Res. Commun. 501: 846-50.
  104. Theisen A, Black R, Corinti D, Brown JM, Bellina B, Barran PE. (2018). Initial protein unfolding events in ubiquitin, cytochrome c and myoglobin are revealed with the use of 213 nm UVPD coupled to IM-MS. J. Am. Soc. Mass Spectrom. 30: 24-33.
  105. Toogood HS and Scrutton NS. (2018). Discovery, characterisation, engineering and applications of ene reductases for industrial biocatalysis. ACS Catalysis, 8: 3532-49.
  106. Toscani A, Risi C, Black GW, Brown NL, Shaaban A, Turner NJ, Castagnolo D. (2018). Monoamine oxidase (MAO-N) whole cell biocatalyzed aromatization of 1,2,5,6-tetrahydropyridines into pyridines. ACS Catalysis, 8: 8781-7.
  107. Trabelsi H, Koch M, Faulon JL. (2018). Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids. Biotechnol. Bioeng. 115: 2292-304.
  108. Tsigkinopoulou A, Hawari A, Uttley M, Breitling R. (2018). Defining informative priors for ensemble modelling in systems biology. Nature protocols. 13: 2643-63.
  109. Xu J, Green A, Turner NJ. (2018). Chemo-enzymatic synthesis of pyrazine and pyrroles. Ange. Chemie, 57: 16760-63
  110. Ujma J, Kopysov V, Nagornova NS, Migas LG, Lizio MG, Blanch EW, MacPhee C, Boyarkin OV, Barran PE. (2018). Initial steps of amyloidogenic peptide assembly revealed by cold-ion spectroscopy. Angew. Chem. Int. Ed. Engl. 57:213-7.
  111. Weise N, Parmeggiani F, Ahmed S. Turner N. (2018). Discovery and investigation of mutase-like activity in a phenylalanine ammonia lyase from Anabaena variabilis. Topics in Catalysis. DOIs: 10.1007/s11244-018-0898-1
  112. Winn M, Francis D, Micklefield J. (2018). De novo biosynthesis of ‘non‐natural’ thaxtomin phytotoxins. Angew. Chemie, 57: 6830-3.
  113. Wright Muelas M, Ortega F, Breitling R, Bendtsen C, Westerhoff H. (2018). Rational cell culture optimization enhances experimental reproducibility in cancer cells. Scientific Rep. 14: 3029.
  114. You L, Takano E. (2018). Synthetic Biology: Reports from CSHA 2016 and More. Biotechnol. J. 13(5):e1800160.
  115. Zebec Z, Scrutton NS. (2018). Genome editing for the production of natural products in Escherichia coli.  Advanced Biosystems. 2: 1800056.

YEAR 3 PUBLICATIONS

  1. Aitken JF, Loomes KM, Riba-Garcia I, Unwin RD, Prijic G, Phillips AS, Phillips AR, Wu D, Poppitt SD, Ding K, Barran PE, Dowsey AW, Cooper GJ. (2017). Quantitative data describing the impact of the flavonol rutin on in-vivo blood-glucose and fluid-intake profiles, and survival of human-amylin transgenic mice. Data in brief, 10, 298-303.
  2. Barley MH, Turner NJ, Goodacre R. (2017). Recommendations on the implementation of genetic algorithms for the directed evolution of enzymes for industrial purposes. ChemBioChem., 18, 1087-97.
  3. Barran P. (2017). From microsolvation to cell permeation: Novel separation science for drug discovery. ACS central science, 3, 158-60.
  4. Bennett MR, Shepherd SA, Cronin VA, Micklefield J. (2017). Recent advances in methyltransferase biocatalysis. Current opinion in chemical biology, 37, 97-106.
  5. Bennett MR, Thompson M, Dunstan MS, Shepherd SA, Cronin VA, Menon BRK, Levy C, Micklefield J. (2017). Structure and biocatalytic scope of coclaurine N-methyltransferase. Angewandte, In press.
  6. Betts Z, Dickson AJ. (2017). Improved CHO cell line stability and recombinant protein expression during long-term culture. Methods Mol. Biol., 1603: 119-41.
  7. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen, CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH. (2017). AntiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic acids research, 45(W1), W36-41.
  8. Brandariz-de-Pedro G, Heyes DJ, Hardman SJ, Shanmugam M, Jones AR, Weber S, Nohr D, Scrutton NS, Fielding AJ. (2017). Direct evidence of an excited-state triplet species upon photoactivation of the chlorophyll precursor protochlorophyllide. J. Physical Chemistry Letts., 8, 1219-23.
  9. Carbonell P, Lopez O, Amberg A, Pastor M,  Sanz F. (2017). Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data. Altex, 34, 219-34.
  10. Carbonell P, Delépine B, Faulon JL. (2017). Extended metabolic space modeling. Methods in Molecular Biology, volume “Synthetic Metabolic Pathways”, 1671, 83-96.
  11. Currin A, Korovin K, Ababi M, Roper K, Kell DB, Day PJ,  King RD. (2017). Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA. J. Royal Society, Interface, 14(128). pii: 20160990.
  12. Currin A, Swainston N, Day PJ, Kell DB. (2017). SpeedyGenes: Exploiting an improved gene synthesis method for the efficient production of synthetic protein libraries for directed evolution. Methods in molecular biology, 1472, 63-78.
  13. Currin A, Dunstan M, Johannissen L, Hollywood K, Vinaixa M, Jervis AJ, Swainston N, Rattray MJW,  Gardiner JM, Kell DB, Takano E, Toogood HS, Scrutton NS. (2018). Engineering the ‘missing link’ in biosynthetic (–)-menthol production: Bacterial isopulegone isomerase. ACS Catalysis, 8: 2012-2020.
  14. Czarnota S, Baxter NJ, Cliff MJ, Waltho JP, Scrutton NS, Hay S. (2017). 1H, 15N, 13C backbone resonance assignments of human soluble catechol O-methyltransferase in complex with S-adenosyl-L-methionine and 3,5-dinitrocatechol. Biomolecular NMR assignments, 11, 57-61.
  15. Delépine B, Duigou T, Carbonell P, Faulon JL. (2017). RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45, 158-70.
  16. Driver T, Trivedi DK, McIntosh O, Dea, AP, Goodacre R. & Pittman JK. (2017). Two glycerol-3-phosphate dehydrogenases from Chlamydomonas have distinct roles in lipid metabolism. Plant Physiology, 174, 2083-97.
  17. Evie IM, Dickson AJ, Elvin M. (2017). Metabolite profiling of mammalian cell culture processes to evaluate cellular viability. Methods Mol. Biol. 1601: 137-52.
  18. Fisk H, Xu Y, Westley C, Turner NJ. Micklefield J, Goodacre R. (2017). From multistep enzyme monitoring to whole-Cell biotransformations: Development of real-time ultraviolet resonance raman spectroscopy. Analytical chemistry, 89, 12527-32.
  19. France SP, Hepworth LJ, Turner NJ, Flitsch SL. (2017). Constructing biocatalytic cascades: In vitro and in vivo approaches to de novo multi-enzyme pathways. ACS Catal., 7, 710-24.
  20. Francis D, Winn M, Latham J, Greaney MF, Micklefield J. (2017). An engineered tryptophan synthase opens new enzymatic pathways to beta-methyltryptophan and derivatives. Chembiochem, 18, 382-6.
  21. Gahloth D, Dunstan MS, Quaglia D, Klumbys E, Lockhart-Cairns MP, Hill AM, Derrington SR, Scrutton NS, Turner NJ, Leys D. (2017). Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis. Nature Chemical Biology, 13, 975-81.
  22. Galman JL, Slabu I, Weise NJ, Iglesias C, Parmeggiani F, Lloyd RC, Turner NJ. (2017). Biocatalytic transamination with near-stoichiometric inexpensive amine donors mediated by bifunctional mono-and di-amine transaminases. Green Chem., 19, 361-66.
  23. Goodacre R, Kell DB. (2017). Commentary on: Rapid identification of Streptococcus and Enterococcus species using diffuse reflectance-absorbance Fourier transform infrared spectroscopy and artificial neural networks. FEMS microbiology letts., 364. nx018.
  24. Gray CJ, Schindler B, Migas LG, Picmanova M, Allouche AR, Green AP, Mandal S, Motawia MS, Sanchez-Perez R, Bjarnholt N, Moller BL, Rijs AM, Barran PE, Compagnon I, Eyers CE, Flitsch SL. (2017). Bottom-up elucidation of glycosidic bond stereochemistry. Analytical Chem., 89, 4540-49.
  25. Grixti JM, O’Hagan S, Day PJ, Kell DB. (2017). Enhancing drug efficacy and therapeutic index through cheminformatics-based selection of small molecule binary weapons that improve transporter-mediated targeting: A cytotoxicity system based on gemcitabine. Frontiers in Pharmacology, 8, 155.
  26. Hedison TM, Hay S, Scrutton NS. (2017). A perspective on conformational control of electron transfer in nitric oxide synthases. Nitric oxide: biology and chemistry, 63, 61-67.
  27. Hepworth LJ, France SP, Hussain S, Both P, Turner NJ, Flitsch SL. (2017). Enzyme cascades in whole cells for the synthesis of chiral cyclic amines. ACS Catal., 7, 2920-25.
  28. Herter SF, Medina S, Wagschal C, Benhaim F, Leipold F, Turner NJ. (2017). Mapping the substrate scope of monoamine oxidase (MAO-N) as a synthetic tool for the enantioselective synthesis of chiral amines. Bioorg. Med. Chem., pii: S0968-0896(17)30391-7.
  29. Heyes DJ, Hardman SJ, Mansell D, Ni Cheallaigh A, Gardiner JM, Johannissen LO, Greetham GM, Towrie M, Scrutton NS. (2017). Excited-state properties of protochlorophyllide analogues and implications for light-driven synthesis of chlorophyll. J. Physical Chemistry, B 121, 1312-20.
  30. Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers, B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. (2017). Systems biology guided by XCMS online metabolomics. Nature Methods, 14, 461-62.
  31. Hussain H, Fisher DI, Abbott WM, Roth RG, Dickson AJ. (2017). Use of a protein engineering strategy to overcome limitations in the production of ‘difficult to express’ recombinant proteins. Biotechnol. Bioeng., 114: 2348-59.
  32. Iorgu AI, Baxter NJ, Cliff MJ, Waltho JP, Hay S, Scrutton NS. (2017). (1)H, (15)N and (13)C backbone resonance assignments of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2. Biomolecular NMR assignments. doi: 10.1007/s12104-017-9791-2.
  33. Jhingree JR, Bellina B, Pacholarz KJ, Barran PE. (2017). Charge mediated compaction and rearrangement of gas-phase proteins: A case study considering two proteins at opposing ends of the structure-disorder continuum. J. American Society for Mass Spectrometry, 28, 1450-61.
  34. Johannissen LO, Leys D, Hay S. (2017). A common mechanism for coenzyme cobalamin-dependent reductive dehalogenases. Physical Chemistry Chemical Physics, 19, 6090-94.
  35. Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ni Cheallaigh A, Bennett, NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS. (2017). Structural basis of catalysis in the bacterial monoterpene synthases linalool synthase and 1,8-cineole synthase. ACS catalysis, 7, 6268-82.
  36. Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. (2017). Fragment profiling approach to inhibitors of the orphan M. tuberculosis P450 CYP144A1. Biochemistry, 56, 1559-72.
  37. Kavanagh ME, Gray JL, Gilbert SH, Coyne AG, McLean KJ, Davis HJ, Munro AW, Abell C. (2017). Corrigendum: substrate fragmentation for the design of M. tuberculosis CYP121 inhibitors. ChemMedChem. 12, 194-95.
  38. Kekilli D, Petersen CA, Pixton DA, Ghafoor DD, Abdullah GH, Dworkowski FSN, Wilson MT, Heyes D J, Hardman SJO, Murphy LM, Strange RW, Scrutton NS, Andrew CR, Hough MA. (2017). Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design. Chemical science, 8, 1986-94.
  39. Kell DB. (2017). Evolutionary algorithms and synthetic biology for directed evolution: commentary on “on the mapping of genotype to phenotype in evolutionary algorithms” by Peter A. Whigham, Grant Dick, and James Maclaurin, Genetic programming and evolvable machines, 18, 373-78.
  40. Klumbys E, Ziga Z, Weise NJW, Turner NJ, Scrutton NS. (2018). Bio-derived production of cinnamyl alcohol via a three step biocatalytic cascade and metabolic engineering. Green Chemistry, 20: 658-663.
  41. Koch M, Duigou T, Carbonell P, Faulon JL. (2017). Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9(1):64.
  42. Kutta RJ, Archipowa N, Johannissen LO, Jones AR, Scrutton NS. (2017). Vertebrate cryptochromes are vestigial flavoproteins. Scientific Reports, 7, 44906.
  43. Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. (2018). Development of halogenase enzymes for use in synthesis. Chemical Reviews, 118, 232-69.
  44. Liu KC, Hughes JMX, Hay S, Scrutton NS. (2017). Liver microsomal lipid enhances the activity and redox coupling of colocalized cytochrome P450 reductase-cytochrome P450 3A4 in nanodiscs, The FEBS Journal, 284, 2302-19.
  45. Lopez O, Pastor M, Sanz F, Carbonell P. (2018). Hepatotoxicity prediction by systems biology modelling of disturbed metabolic pathways using gene expression data. Methods in Molecular Biology, volume “Computational Toxicology”, In press.
  46. Luo Z, Wang L, Wang Y, Zhang W, Guo Yakun, Shen Y, Jiang L, WuQ, Zhang C, Cai Y, Dai J. (2017). Identifying and characterizing SCRaMbLEd synthetic yeast using ReSCuES. Nature Communications, 2017, doi:10.1038/s41467-017-00806-y. In press.
  47. Maldonado-Agurto R, Dickson, AJ (2018). Multiplexed digital mRNA expression analysis profiles system-wide changes in mRNA abundance and responsiveness of UPR-specific gene expression changes during batch culture of recombinant Chinese Hamster Ovary cells. Biotechnol. J., DOI: 10.1002/biot.201700429.
  48. Mangas-Sanchez J, France SP, Montgomery SL, Aleku GA, Man H, Grogan G, Turner NJ, (2017). Imine reductases (IREDs). Curr. Opin. Chem. Biol., 37, 19-25.
  49. Markosova K, Camattari A, Rosenberg M, Glieder A, Turner NJ Rebroš M. (2017). Cloning and upscale production of monoamine oxidase N (MAO-N D5) by Pichia pastoris. Biotechnol. Lett., 40, 127-133.
  50. Matthews S, Belcher JD, Tee K-L., Girvan HM, McLean KJ, Rigby SE, Levy D, Parker DA,  Blankley R T. (2017). Catalytic determinants of alkene production by the cytochrome P450 peroxygnease OleTJE. J. Biological Chemistry, 292, 5128-43.
  51. Matthews S, Tee KL, Rattray NJ, McLean KJ, Leys D, Parker DA, Blankley RT, Munro AW. (2017). Production of alkenes and novel secondary products by P450 OleTJE using novel H2 O2 -generating fusion protein systems. FEBS letters, 591, 737-50.
  52. McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Heriche JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novere N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Muller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. (2017). Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS biology, 15, e200.
  53. Meckin R, Balmer A. (2017). Engaging the senses, understanding publics: Research methods, science engagement, and synthetic biology. Trends Biotechnol., 35(11), 1015-17.
  54. Menon BRK, Brandenburger E, Sharif HH, Klemstein U, Shepherd SA, Greaney MF, Micklefield J. (2017). RadH: A versatile halogenase for integration into synthetic pathways. Angewandte Chemie, 56, 11841-45.
  55. O’Hagan S, Kell DB. (2017). Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. Journal of Cheminformatics, 9, 18.
  56. O’Hagan S, Kell DB. (2017). Consensus rank orderings of molecular fingerprints illustrate the ‘most genuine’ similarities between marketed drugs and small endogenous human metabolites, but highlight exogenous natural products as the most important ‘natural’ drug transporter substrates. ADMET & DMPK, 5, 85-125.
  57. O’Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB. (2018). GeneGini: novel ‘housekeeping’ genes and an unusually heterogeneous distribution of transporter expression profiles in human tissues and cell lines, assessed using the Gini coefficient. Cell Syst 2018:in press.
  58. O’Hagan S,  Kell DB. (2018). Analysing and navigating natural products space for generating small, diverse, but representative chemical libraries. Biotechnol J, 1700503. doi:10.1002/biot.201700503.
  59. Pacholarz KJ, Burnley RJ, Jowitt TA, Ordsmith V, Pisco JP, Porrini M, Larrouy-Maumus G, Garlish RA, Taylor RJ, de Carvalho LPS, Barran PE. (2017). Hybrid mass spectrometry approaches to determine how L-histidine feedback regulates the enzyzme MtATP-phosphoribosyltransferase. Structure, 25, 730-38 e734.
  60. Paciotti R, Corinti D, De Petris A, Ciavardini A, Piccirillo S, Coletti C, Re N, Maitre P, Bellina B, Barran P, Chiavarino B, Elisa Crestoni M, Fornarini S. (2017). Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes. Physical Chemistry Chemical Physics, 19, 26697-707.
  61. Ahmed S T, Weise N, Parmeggiani F, Turner NJ. (2017). Applications of phenylalanine ammonia lyases in synthesis: Access to enantiopure arylalanines from laboratory scale to industrial production. Chim. Oggi, 2017, in press.
  62. Peña A, Carratore FD, Cummings M, Takano E, Breitling R. (2017). An output ordering and prioritisation system (OOPS): Ranking biosynthetic gene clusters to enhance bioactive metabolite discovery. Journal of Industrial Microbiology & Biotechnology, doi.org/10.1007/s10295-017-1993-1
  63. Pisco JP, de Chiara C, Pacholarz KJ, Garza-Garcia A, Ogrodowicz RW, Walker PA, Barran PE, Smerdon SJ, de Carvalho LPS. (2017). Uncoupling conformational states from activity in an allosteric enzyme. Nature communications, 8, 203.
  64. Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ. (2017). Ab initio QM/MM modeling of the rate-limiting proton transfer Step in the deamination of tryptamine by aromatic amine dehydrogenase. J. Physical Chemistry, B 121, 9785-98.
  65. Scrutton NS. (2017). Enzymes make light work of hydrocarbon production. Science, 357, 872-73.
  66. Scrutton NS. (2017). Speeding up enzyme engineering computationally. IUCrJ, 4, 5-6.
  67. Selle K, Goh YJ, Johnson BR, O’Flaherty S, Andersen JM, Barrangou R, Klaenhammer TR. (2017). Deletion of lipoteichoic acid synthase impacts expression of genes encoding cell surface proteins in Lactobacillus acidophilus. Frontiers in Microbiology, 8, 553.
  68. Shapira P, Kwon, S, Youtie J. (2017). Tracking the emergence of synthetic biology. Scientometrics 112, 1439-69.
  69. Slabu I, Galman JL, Iglesias C, Weise NJ, Lloyd RC, Turner NJ. (2017). n-Butylamine as an alternative amine donor for the stereoselective biocatalytic transamination of ketones. Catalysis Today, In press, DOI.org/10.1016/j.cattod.2017.01.025.
  70. Stacey GN, Connon CJ, Coopman K, Dickson AJ, Fuller B, Hunt CJ, Kemp B, Kerby J, Man J, Matejtschuk P, Moore H, Morris J, Ward S, Wiggins C, Zimmermann H. (2017). Preservation and stability of cell therapy products: Recommendations from an expert workshop on developing improved preservation, storage and shipping systems. Regenerative Medicine, 12: DOI 10.2217/rme-2017-0073
  71. Swainston N, Batista-Navarro R, Carbonell P, Dobson PD, Dunstan M, Jervis AJ, Vinaixa M, Williams AR, Ananiadou S, Faulon JL, Mendes P, Kell DB, Scrutton NS, Breitling R. (2017). biochem4j: Integrated and extensible biochemical knowledge through graph databases. PloS one, 12, e0179130.
  72. Swainston N, Currin A, Green L, Breitling R, Day PJ, Kell DB. (2017). CodonGenie: optimised ambiguous codon design tools. PeerJ Computer Science, 7, e120. DOI: 10.7717/peerj-cs.120.
  73. Taban IM, Elshihawy HEAE, Torun B, Zucchini B, Williamson CJ, Altuwairigi D, Ngu AST, McLean KJ, Levy CW, Sood S, Marino LB, Munro AW, de Carvalho LPS, Simons C. (2017). Novel aryl substituted pyrazoles as small molecule inhibitors of cytochrome P450 CYP121A1: synthesis and antimycobacterial evaluation. J. Med. Chem., 60, 10257-67.
  74. Tavanti M, Porter JL, Sabatini S, Turner NJ, Flitsch SL. (2017). A panel of new thermostable CYP116B self-sufficient cytochrome P450 monooxygenases catalysing C-H activation with diverse substrate scope. ChemCatChem., 9, in press, (DOI: 10.1002/cctc.201701510R1).
  75. Toogood HS, Scrutton NS. (2017). Retooling microorganisms for the fermentative production of alcohols. Current Opinion in Biotechnology, 50, 1-10
  76. Tsigkinopoulou A, Baker SM, Breitling R. (2017). Respectful modeling: Addressing uncertainty in dynamic system models for molecular biology. Trends in Biotechnology, 35, 518-29
  77. Waller J, Toogood HS, Karuppiah V, Rattray NJW, Mansell DJ, Leys D, Gardiner JM, Fryszkowska A, Ahmed ST, Bandichhor R, Reddy GP, Scrutton NS. (2017). Structural insights into the ene-reductase synthesis of profens. Organic & Biomolecular Chemistry, 15, 4440-48
  78. Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. (2017). Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy. Metabolomics, 13, 12
  79. Weise NJ, Ahmed ST, Parmeggiani F, Galman JL, Dunstan MS, Charnock SJ, Leys D, Turner NJ. (2017). Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes. Sci Rep. 7, 13691
  80. Westley C, Fisk H, Xu Y, Hollywood KA, Carnell AJ, Micklefield J, Turner NJ, Goodacre R. (2017). Real-Time monitoring of enzyme-catalysed reactions using deep UV resonance Raman spectroscopy. Chemistry, 23, 6983-87
  81. Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, OhEigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ. (2017). A transatlantic perspective on 20 emerging issues in biological engineering. eLife 6. DOI: https://doi.org/10.7554/eLife.30247.001.
  82. Wood AJL, Weise NJ, Frampton JD, Dunstan MS, Hollas MA, Derrington SR, Lloyd RC, Quaglia D, Parmeggiani F, Leys D, Turner NJ, Flitsch SL. (2017). Adenylation activity of carboxylic acid reductases enables the synthesis of amides. Angew. Chem. Int. Ed. Engl., 56, 14498-501
  83. Xie ZX, Liu D, Li BZ, Zhao M, Zeng BX, Wu Y, Shen Y, Lin T, Yang P, Dai J, Cai Y, Yang H, Yuan YJ. (2017). Design and chemical synthesis of eukaryotic chromosomes. Chemical Society Reviews, Nov2. doi: 10.1039/c7cs00208d. [Epub ahead of print]. PMID: 29094136
  84. Yan C, Parmeggiani F, Jones EA, Claude E, Hussain SA, Turner NJ, Flitsch SL, Barran PE. (2017). Real-time screening of biocatalysts in live bacterial colonies. J. Am. Chem. Soc. 139, 1408-11.
  85. Zajkoska P, Cárdenas‐Fernández M, Lye GJ, Rosenberg M, Turner NJ, Rebros M. (2017). Chemo‐biocatalytic one‐pot two‐step conversion of cyclic amine to lactam using whole cell monoamine oxidase. J. Chem. Tech. Biotechnol., 92, 1558-65.
  86. Montgomery SL, Mangas-Sanchez J, Thompson MP, Aleku GA, Dominguez B, Turner NJ. (2017). Direct alkylation of amines with primary and secondary alcohols through biocatalytic hydrogen borrowing. Angew Chem Int Ed Engl. 56, 10491-10494.
  87. Aleku GA, France SP, Man H, Mangas-Sanchez J, Montgomery SL, Sharma M, Leipold F, Hussain S, Grogan G, Turner NJ. (2017). A reductive aminase from Aspergillus oryzae. Nature Chemistry volume 9, 961–969.

YEAR 2 PUBLICATIONS

  1. Ahmed ST, Parmeggiani F, Weise NJ, Flitsch SL, Turner NJ. (2016). Synthesis of enantiomerically pure ring-substituted L-pyridylalanines by biocatalytic hydroamination. Org. Lett. 18: 5466-71.
  2. Aleku GA, Man H, France SP, Leipold F, Hussain S, Toca-Gonzalez L, Marchington R, Hart S, Turkenburg JP, Grogan G, Turner NJ. (2016). Stereoselectivity and structural characterization of an imine reductase (IRED) from Amycolatopsis orientalis. ACS Catalysis, 6: 3880-9.
  3. AlMasoud N, Xu Y, Trivedi DK, Salivo S, Abban T, Rattray NJ, Szula E, AlRabiah H, Sayqal A, Goodacre R. (2016). Classification of Bacillus and Brevibacillus species using rapid analysis of lipids by mass spectrometry. Analytical and bioanalytical chemistry, 408: 7865-78.
  4. Almeida R, Fraczek M, Parker S, Delneri D, O’Keefe R. (2016). Non-coding RNAs and disease: the classical ncRNAs make a comeback. Biochemical Society transactions, 44: 1073-8.
  5. Aslan AS, Birmingham WR, Karaguler NG, Turner NJ, Binay B. (2016). Semi-Rational design of Geobacillus stearothermophilus L-lactate dehydrogenase to access various chiral alpha-hydroxy acids. Applied biochemistry and biotechnology, 179: 474-84.
  6. Bajhaiya AK, Dean AP, Driver T, Trivedi DK, Rattray NJ, Allwood JW, Goodacre R, Pittman JK. (2016). High-throughput metabolic screening of microalgae genetic variation in response to nutrient limitation. Metabolomics, 12: 9.
  7. Balmer AS, Bulpin K, Molyneux-Hodgson M. (2016). Synthetic Biology: A Sociology of Changing Practices, Basingstoke: Palgrave Macmillan. Hardback: ISBN 978-1-137-49541-9; eBook ISBN 978-1-137-49542-6. http://www.palgrave.com/us/book/9781137495419
  8. Balmer AS, Marris C, Calvert J, Molyneux-Hodgson S, Kearnes M, Bulpin K, Frow E, Schyfter P, Mackenzie A, Martin P. (2016). Five Rules of thumb for post-ELSI interdisciplinary collaborations. J. Responsible Research and Innovation, 3: 73-80.
  9. Beveridge R, Migas LG, Payne KA, Scrutton NS, Leys D, Barran PE. (2016). Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nature communications, 7: 12163.
  10. Both P, Busch H, Kelly PP, Mutti FG, Turner NJ, Flitsch SL. (2016). Whole-cell biocatalysts for stereoselective C-H amination reactions. Angew. Chem. 55: 1511-3.
  11. Breitling R, Takano E. (2016). Synthetic biology of natural products. Cold Spring Harbor Perspect. Biol. 8: aD23994.
  12. Carbonell P, Currin A, Dunstan M, Fellows D, Jervis A, Rattray NJ, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Le Feuvre RL, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ. (2016). SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society transactions, 44: 675-7.
  13. Carbonell P, Currin A, Jervis AJ, Rattray NJ, Swainston N, Yan C, Takano E, Breitling R. (2016). Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Natural product reports, 33: 925-32.
  14. Carbonell P, Gök A, Shapira P, Faulon JL. (2016). Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial Biotechnology, 9: 687-95.
  15. Carbonell P, Lopez O, Amberg A, Pastor M, Sanz F. (2016). Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data. ALTEX: 34: 219-234.
  16. Chan S. (2016). Research translation and emerging technologies: synthetic biology and beyond. Health Care Analysis, 1-16
  17. Chenge J, Kavanagh ME, Driscoll MD, McLean KJ, Young DB, Cortes T, Matak-Vinkovic D, Levy CW, Rigby SE, Leys D, Abell C, Munro AW. (2016). Structural characterization of CYP144A1 – a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis. Scientific reports, 6: 26628.
  18. Currie F, Broadhurst DI, Dunn WB, Sellick CA, Goodacre R. (2016). Metabolomics reveals the physiological response of Pseudomonas putida KT2440 (UWC1) after pharmaceutical exposure. Molecular Biosystems, 12: 1367-77.
  19. Currin A, Swainston N, Day PJ, Kell DB. (2017). SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution. Methods in Molecular Biology, 1472: 63-78.
  20. de Graaff C, Oppelaar B, Péruch O, Vande Velde CML, Bechi B, Turner NJ, Ruijter E, Orru RVA. (2016). Stereoselective monoamine oxidase‐catalyzed oxidative aza‐friedel–crafts reactions of meso‐pyrrolidines in aqueous buffer. Adv. Synth. Catal. 358: 1555-60.
  21. Delepine B, Libis V, Carbonell P, Faulon JL. (2016). SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic acids research, 44: W226-231.
  22. Eichler A, Gricman L, Herter S, Kelly PP, Turner NJ, Pleiss J, Flitsch SL. (2016). Enantioselective benzylic hydroxylation catalysed by P450 monooxygenases: Characterisation of a P450cam mutant library and molecular modelling. Chembiochem, 17: 426-32.
  23. Fisk H, Westley C, Turner NJ, Goodacre R. (2016). Achieving optimal SERS through enhanced experimental design. J. Raman Spectrosc. 47: 59-66.
  24. Formisano N, Bhalla N, Heeran M, Reyes Martinez J, Sarkar A, Laabei M, Jolly P, Bowen CR, Taylor JT, Flitsch S, Estrela P. (2016). Inexpensive and fast pathogenic bacteria screening using field-effect transistors. Biosensors & Bioelectronics, 85: 103-9.
  25. France SP, Hussain S, Hill AM, Hepworth LJ, Howard RM, Mulholland KR, Flitsch SL, Turner NJ. (2016). One pot cascade synthesis of mono-and di-substituted piperidines and pyrrolidines using carboxylic acid reductase (CAR), ω-transaminase (ω-TA) and imine reductase (IRED) biocatalysts. ACS Catalysis, 6: 3753-9.
  26. Galman JL, Slabu I, Weise NJ, Iglesias C, Parmeggiani F, Lloyd RC, Turner NJ. (2016). Biocatalytic transamination with near-stoichiometric inexpensive amine donors mediated by bifunctional mono-and di-amine transaminases. Green Chem. 19: 361-366.
  27. Galman J, Willies SC, Slabu I, Turner NJ. (2016). A stereospecific solid phase screening assay for colonies expressing both (R)- and (S)-selective ω-aminotransferases. Phil. Trans. Royal Soc. A, A374: 20150084.
  28. Girvan HM, Bradley JM, Cheesman MR, Kincaid JR, Liu Y, Czarnecki K, Fisher K, Leys D, Rigby SE, Munro AW. (2016). Analysis of heme iron coordination in DGCR8: The heme-binding component of the microprocessor complex. Biochemistry, 55: 5073-83.
  29. Girvan HM, Munro AW. (2016). Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology. Current Opinion in Chemical Biology, 31: 136-45.
  30. Gray CJ, Thomas B, Upton R, Migas LG, Eyers CE, Barran PE, Flitsch SL. (2016). Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochimica et Biophysica Acta, 1860: 1688-709.
  31. Green AP, Turner NJ. (2016). Biocatalytic Retrosynthesis: Redesigning synthetic routes to high-value chemicals. Perspectives in Science, 9: 42-48.
  32. Grogan G, Turner NJ. (2016). InspIRED by Nature: NADPH-dependent imine reductases (IREDs) as catalysts for the preparation of chiral amines. Chemistry, 22: 1900-7.
  33. Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic acids research, 44: D1214-9.
  34. Heath RS, Pontini M, Hussain S, Turner NJ. (2016). Combined imine reductase and amine oxidase catalyzed deracemization of nitrogen heterocycles. Chem. Cat. Chem. 8: 117-20.
  35. Hedison TM, Hay S, Scrutton NS. (2016). A perspective on conformational control of electron transfer in nitric oxide synthases. Nitric oxide, S1089-8603.
  36. Hedison TM, Le Ferink NG, Hay S, Scrutton NS. (2016). Correlating calmodulin landscapes with chemical catalysis in neuronal nitric oxide synthase using time-resolved FRET and a 5-deazaflavin thermodynamic trap. Acs. Catal. 6: 5170-80.
  37. Hoeven R, Hardman SJ, Heyes DJ, Scrutton NS. (2016). Cross-Species analysis of protein dynamics associated with hydride and proton transfer in the catalytic cycle of the light-driven enzyme protochlorophyllide oxidoreductase. Biochemistry, 55: 903-13.
  38. Hooks K, Naseeb S, Parker S, Griffiths-Jones S. Delneri D. (2016). Novel intronic RNA structures contribute to maintenance of phenotype in Saccharomyces cerevisiae. Genetics, 203: 1469-81.
  39. Hugentobler KG, Sharif H, Rasparini M, Heath RS, Turner NJ. (2016). Biocatalytic approaches to a key building block for the anti-thrombotic agent ticagrelor. Organic & biomolecular chemistry, 14: 8064-7.
  40. Kavanagh ME, Coyne AG, McLean KJ, James GG, Levy CW, Marino LB, de Carvalho LP, Chan DS, Hudson SA, Surade S, Leys D, Munro AW, Abell C. (2016). Fragment-based approaches to the development of mycobacterium tuberculosis CYP121 inhibitors. Journal of medicinal chemistry, 59: 3272-302.
  41. Kavanagh ME, Gray JL, Gilbert SH, Coyne AG, McLean KJ, Davis HJ, Munro AW, Abell C. (2016). Substrate fragmentation for the design of tuberculosis CYP121 inhibitors. Chem. Med. Chem. 11: 1924-35.
  42. Kell DB. (2016). Implications of endogenous roles of transporters for drug discovery: hitchhiking and metabolite-likeness. Nature Reviews Drug Discovery, 15: 143.
  43. Knaus T, Paul CE, Levy CW, de Vries S, Mutti FG, Hollmann F, Scrutton NS. (2016). Better than Nature: Nicotinamide biomimetics that outperform natural coenzymes. J. Am. Chem. Soc. 138: 1033-9.
  44. Latham J, Henry JM, Sharif HH, Menon BR, Shepherd SA, Greaney MF, Micklefield J. (2016). Integrated catalysis opens new arylation pathways via regiodivergent enzymatic C-H activation. Nature Communications, 7: 11873.
  45. Law BJ, Bennett MR, Thompson ML, Levy C, Shepherd SA, Leys D, Micklefield J. (2016). Effects of active-site modification and quaternary structure on the regioselectivity of catechol-O-methyltransferase. Angew. Chemie, 55: 2683-7.
  46. Leferink N, Jervis A, Zebec Z, Toogood H, Hay S, Takano E, Scrutton N. (2016). A ‘Plug and Play’ Platform for the Production of Diverse Monoterpene Hydrocarbon Scaffolds in Escherichia coli. Chemistry Select, 9: 1893–1896.
  47. Le Feuvre RA, Carbonell P, Currin A, Dunstan M, Fellows D, Jervis AJ, Rattray NJW, Robinson CJ, Swainston N, Vinaixa M, Williams A, Yan C, Barran P, Breitling R, Chen GG, Faulon JL, Goble C, Goodacre R, Kell DB, Micklefield J, Scrutton NS, Shapira P, Takano E, Turner NJ. (2016). SYNBIOCHEM Synthetic Biology Research Centre, Manchester – A UK foundry for fine and speciality chemicals production. Synthetic and Systems Biotechnology, 1: 271-5.
  48. Leys D, Scrutton NS. (2016). Sweating the assets of flavin cofactors: new insight of chemical versatility from knowledge of structure and mechanism. Current Opinion in Structural Biology, 41: 19-26.
  49. Libis V, Delepine B, Faulon JL. (2016). Sensing new chemicals with bacterial transcription factors. Current Opinion in Microbiology, 33: 105-12.
  50. Libis V, Delepine B, Faulon JL. (2016). Expanding biosensing abilities through computer-aided design of metabolic pathways. ACS Synthetic Biology. 5: 1076-85.
  51. Lindner R, Kuhlmann S, Randles S, Bedsted B, Gorgoni G, Griessler R, Loconto A, Mejlgaard N (Eds.) (2016). Navigating Towards Shared Responsibility in Research and Innovation: Approach, Process and Results of the Res-AGorA project.  Fraunhofer Institute for Systems and Innovation Research ISI: Karlsruhe. http://publica.fraunhofer.de/eprints/urn_nbn_de_0011-n-3829371.pdf
  52. Longbotham JE, Hardman SJ, Gorlich S, Scrutton NS, Hay S. (2016). Untangling heavy protein and cofactor isotope effects on enzyme-catalyzed hydride transfer. J. Am. Chem. Soc. 138: 13693–9.
  53. Lygidakis A, Karuppiah V, Hoeven R, Ni Cheallaigh A, Leys D, Gardiner JM, Toogood HS, Scrutton NS. (2016). Pinpointing a mechanistic switch between ketoreduction and “ene” reduction in short-chain dehydrogenases/reductases. Angew. Chem. 55: 9596-600.
  54. Machado LF, Dixon N. (2016). Development and substrate specificity screening of an in vivo biosensor for the detection of biomass derived aromatic chemical building blocks. Chemical Communications, 52: 11402-5.
  55. Markošová K, Dolejš I, Stloukal R, Rios-Solis L, Rosenberg M, Micheletti M, Lye GJ, Turner NJ, Rebroš M. (2016). Immobilisation and kinetics of monoamine oxidase (MAO-N-D5) enzyme in polyvinyl alcohol gels. Mol. Cat. B: Enzym. 129: 69-74.
  56. McLean KJ, Munro AW. (2016). Azole-class antibiotics for tuberculosis. Future Science Ltd, 72-88.
  57. McLean KJ, Munro AW. (2016). Drug targeting of heme proteins in Mycobacterium tuberculosis. Drug Discovery Today, S1359-6446.
  58. Mellor J, Grigoras I, Carbonell P, Faulon JL. (2016). Semisupervised gaussian process for automated enzyme search. ACS Synthetic Biology, 5: 518-28.
  59. Mendes P, Oliver SG, Kell DB. (2016). Response to ‘The need for speed’, by Matsson et al. Trends in Pharmacological Sciences, 37: 245-6.
  60. Menon BR, Hardman SJ, Scrutton NS, Heyes DJ. (2016). Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR). Journal of Photochemistry and Photobiology B Biology, 161: 236-43.
  61. Menon BR, Latham J, Dunstan MS, Brandenburger E, Klemstein U, Leys D, Karthikeyan C, Greaney MF, Shepherd SA, Micklefield J. (2016). Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Org Biomol Chem. 14: 9354-61.
  62. Muhamadali H, Xu Y, Morra R, Trivedi DK, Rattray NJ, Dixon N, Goodacre R. (2016). Metabolomic analysis of riboswitch containing coli recombinant expression system. Molecular Biosystems, 12: 350-61.
  63. Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, Delneri D. (2016). Widespread impact of chromosomal inversions on gene expression uncovers robustness via phenotypic buffering. Molecular Biology and Evolution, 33: 1679-96.
  64. O’Hagan S, Swainston N, Handl J, Kell DB. (2015). A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics, 11: 323-39.
  65. Ortmayer M, Lafite P, Menon BRK, Tralau T, Fisher K, Denkhaus L, Scrutton NS, Rigby SE, Munro AW, Hay S Leys D. (2016). An oxidative demehtylase reveals PAS transition from ubiquitous sensor to enzyme. Nature, 539: 593-7.
  66. Parmeggiani F, Ahmed ST, Thompson MP, Weise NJ, Galman JL, Gahloth D, Dunstan MS, Leys D, Turner NJ. (2016). Single-biocatalyst synthesis of enantiopure d-arylalanines exploiting an engineered d-amino acid dehydrogenase. Synth. Catal. 358: 3298-3306.
  67. Peers MK, Toogood HS, Heyes DJ, Mansell D, Coe BJ, Scrutton NS. (2016). Light-driven biocatalytic reduction of alpha, beta-unsaturated compounds by ene reductases employing transition metal complexes as photosensitizers. Catal. Sci. Technol. 6: 169-77.
  68. Randles S, Laasch O. (2016). Theorising the normative business model. Organ Environ. 29: 53-73.
  69. Rattray NJ. (2015). Analytical medicine: Citizen Scientists can aid diagnostics. Nature, 528: 193.
  70. Robinson CJ, Medina-Stacey D, Wu MC, Vincent HA, Micklefield J. (2016). Rewiring riboswitches to create new genetic circuits in bacteria. Methods in Enzymology, 575: 319-48.
  71. Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S. (2016). Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics, 12: 1-13.
  72. Roselló JM, Staniland S, Turner NJ, Clayden J. (2016). Substituent effects on axial chirality in 1-aryl-3,4-dihydroisoquinolines: Controlling the rate of bond rotation. Tetrahedron, 72: 5172-7.
  73. Rowles I, Groenendaal B, Binay B, Malone KJ, Willies SC, Turner NJ. (2016). Engineering of phenylalanine ammonia lyase from Rhodotorula graminis for the enhanced synthesis of unnatural l-amino acids. Tetrahedron, 72: 7343-7.
  74. Ruscoe RE, Fazakerley NJ, Huang HM, Flitsch S, Procter DJ. (2016). Copper-catalyzed double additions and radical cyclization cascades in the re-engineering of the antibacterial pleuromutilin. Chem-Eur. J 22: 116-9.
  75. Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Goodacre R. (2016). Metabolic fingerprinting of Pseudomonas putida DOT-T1E strains: Understanding the influence of divalent cations in adaptation mechanisms following exposure to toluene. Metabolites, 6: E14.
  76. Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Muhamadali H, Rattray NJ, Webb C, Goodacre R. (2016). Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry. Metabolomics, 12: 112.
  77. Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Rattray NJ, Goodacre R. (2016). Metabolomics analysis reveals the participation of efflux pumps and ornithine in the response of Pseudomonas putida DOT-T1E cells to challenge with propranolol. PloS one, 11: e0156509.
  78. Shepherd SA, Menon BR, Fisk H, Struck AW, Levy C, Leys D, Micklefield J. (2016). A structure-guided switch in the regioselectivity of a tryptophan halogenase. ChemBioChem. 17: 821-4.
  79. Slabu I, Galman JL, Weise NJ, Lloyd RC, Turner NJ. (2016). Putrescine transaminases for the synthesis of saturated nitrogen heterocycles from polyamines. ChemCatChem. 8: 1038-42.
  80. Staniland S, Adams RW, McDouall JJ, Maffucci I, Contini A, Grainger DM, Turner NJ, Clayden J. (2016). Biocatalytic dynamic kinetic resolution for the synthesis of atropisomeric biaryl n-oxide Lewis base catalysts. Angew. Chem. 55: 10755-9.
  81. Struck AW, Bennett MR, Shepherd SA, Law BJ, Zhuo Y, Wong LS, Micklefield J. (2016). An enzyme cascade for selective modification of tyrosine residues in structurally diverse peptides and proteins. J. Am. Chem. Soc. 138: 3038-45.
  82. Surman AJ, Robbins PJ, Ujma J, Zheng Q, Barran PE, Cronin L. (2016). Sizing and discovery of nanosized polyoxometalate clusters by mass spectrometry. J. Am. Chem. Soc. 138: 3824-30.
  83. Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P. (2016). libChEBI: an API for accessing the ChEBI database. J. Cheminformatics, 8: 11.
  84. Swainston N, Smallbone K, Hefzi H, Dobson PD, Brewer J, Hanscho M, Zielinski DC, Ang KS, Gardiner NJ, Gutierrez JM, Kyriakopoulos S, Lakshmanan M, Li S, Liu JK, Martinez VS, Orellana CA, Quek, LE, Thomas A, Zanghellini J, Borth N, Lee DY, Nielsen LK, Kell DB, Lewis NE, Mendes P. (2016). Recon 2.2: from reconstruction to model of human metabolism. Metabolomics, 12: 109.
  85. Toogood HS, Tait S, Jervis A, Ni Cheallaigh A, Humphreys L, Takano E, Gardiner JM, Scrutton NS. (2016). Natural product biosynthesis in Escherichia coli: mentha monoterpenoids. Methods in enzymology, 575: 247-70.
  86. Turner NJ. (2016). Sustainable catalysis. Beilstein Journal of Organic Chemistry, 12: 1778-9.
  87. van Oosterwijk N, Willies S, Hekelaar J, Terwisscha van Schelting AC, Turner NJ, Dijkstra BW. (2016). Structural basis of the substrate range and enantioselectivity of two (S)-selective omega-transaminases. Biochemistry, 55: 4422-31.
  88. Weise NJ, Ahmed ST, Parmeggiani F, Siirola E, Pushpanath A, Schell U, Turner NJ. (2016). Intensified biocatalytic production of enantiomerically pure halophenylalanines from acrylic acids using ammonium carbamate as the ammonia source. Sci. Tech. 6: 4086-9.
  89. Weissenborn MJ, Notonier S, Lang SL, Otte KB, Herter S, Turner NJ, Flitsch SL, Hauer B. (2016). Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s. Chemical Communications, 52: 6158-61.
  90. Wells AS, Wong JW, Michels PC, Entwistle DA, Fandrick K, Finch GL, Goswami A, Lee H, Mix S, Moody TS, Pang L, Sato RK, Turner NJ, Watson (2016). Case studies illustrating a science and risk-based approach to ensuring drug quality when using enzymes in the manufacture of active pharmaceuticals ingredients for oral dosage form. Org. Proc. Res. Dev. 20: 594-601.
  91. Westley C, Xu Y, Carnell AJ, Turner NJ, Goodacre R. (2016). Label-free surface enhanced Raman scattering approach for high-throughput screening of biocatalysts. Analytical Chemistry, 88: 5898-903.
  92. Willies SC, Galman JL, Slabu I, Turner NJ. (2016). A stereospecific solid-phase screening assay for colonies expressing both (R)- and (S)-selective omega-aminotransferases. Philos. Trans. A. Math. Phys. Eng. Sci. 374: 20150084.
  93. Winn M, Fyans J, Zhuo Y, Micklefield J. (2016). Recent advances in engineering nonribosomal peptide assembly lines. Natural Product Reports, 33: 317-47.
  94. Xu Y, Muhamadali H, Sayqal A, Dixon N, Goodacre R. (2016). Partial least squares with structured output for modelling the metabolomics data obtained from complex experimental designs: A study into the Y-block coding. Metabolites, 6: E38.
  95. Yan C, Schmidberger JW, Parmeggiani F, Hussain SA, Turner NJ, Flitsch SL, Barran P. (2016). Rapid and sensitive monitoring of biocatalytic reactions using ion mobility mass spectrometry. The Analyst, 141: 2351-5.
  96. Zabala D, Cartwright JW, Roberts DM, Law B, Song L, Samborskyy M Leadlay PF. Micklefield J. Challis GL. (2016). A Flavin-dependent decarboxylase-dehydrogenase-monooxygenase assembles the warhead of α,β-epoxyketone proteasome inhibitors. J. Am. Chem. Soc., 138: 4342−5.
  97. Zebec Z, Wilkes J, Jervis AJ, Scrutton NS, Takano E, Breitling R. (2016). Towards synthesis of monoterpenes and derivatives using synthetic biology. Current Opinion in Chemical Biology, 34: 37-43.

YEAR 1 PUBLICATIONS

  1. Ahmed ST, Parmeggiani F, Weise NJ, Flitsch SL, Turner NJ. (2015). Chemo-Enzymatic Synthesis of Optically Pure L-and D-Biarylalanines through Biocatalytic Asymmetric Amination and Palladium-Catalysed Arylation. ACS Catalysis, 5: 5410-5413.
  2. Balmer AS, Marris C, Calvert J, Molyneux-Hodgson S, Kearnes M, Bulpin K, Frow E, Schyfter P, Mackenzie A, and Martin P. (2015). Taking Roles in Interdisciplinary Collaborations: Reflections on Working in Post-ELSI Spaces in the UK Synthetic Biology Community.  Science and Technology Studies, 28(3).
  3. Barran P, and Ruotolo B. (2015). Ion Mobility Mass Spectrometry. Analyst, 14(20): 6772-6774.
  4. Barran P, Cooper H, and Eyers C. (2015). Protein Structure. Proteomics, 15(16): p. 2731-2732.
  5. Berezovskaya Y, Porrini M, Nortcliffe C, and Barran PE. (2015). The use of ion mobility mass spectrometry to assist protein design: a case study on zinc finger fold versus coiled coil interactions. Analyst, 140(8): 2847-2856.
  6. Beveridge R, Phillips AS, Denbigh L, Saleem HM, MacPhee CE and Barran PE. (2015). Relating gas phase to solution conformations: Lessons from disordered proteins. Proteomics, 15(16): 2872-2883.
  7. Biarnes-Carrera M, Breitling R, Takano E, Micklefield J. (2015). Butyrolactone signalling circuits for synthetic biology. Curr. Opin. Chem. Biol. 28: 91-98.
  8. Breitling R, Takano E, Gardner TS. (2015). Judging synthetic biology risks. Science, 347: 107.
  9. Breitling R, Takano E. (2015). Synthetic biology advances for pharmaceutical production. Curr. Opin. Biotechnol. 35: 46-51.
  10. Ceroni F, Carbonell P, François JM, Haynes KA. (2015). Editorial – Synthetic Biology: engineering complexity and refactoring cell capabilities. Frontiers in Synthetic Biology. 3: 120.
  11. Chessher A, Breitling R, Takano E. (2015). Bacterial microcompartments: biomaterials for synthetic biology-based compartmentalization strategies. ACS Biomater. Sci. Eng. 1: 463-616.
  12. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA. (2014). Insights into secondary metabolism from a global analysis of bacterial biosynthetic gene clusters. Cell, 158: 412-21. Highlighted in Nature Chemical Biology, 10: 798-800.
  13. Cole H, Porrini M, Morris R, Smith T, Kalapothakis J, Weidt S, Mackay CL, MacPhee CE and Barran PE. (2015). Early stages of insulin fibrillogenesis examined with ion mobility mass spectrometry and molecular modelling. Analyst, 14(20): 7000-7011.
  14. Creek DJ, Mazet M, Achcar F, Anderson J, Kim DH, Kamour R, Morand P, Millerioux Y, Biran M, Kerkhoven EJ, Chokkathukalam A, Weidt S, Burgess KEV, 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(3):e1004689.
  15. Cummings M, Breitling R, Takano E. (2014). Steps towards the synthetic biology of polyketide biosynthesis FEMS Microbiol. Lett. 351: 116-125.
  16. Currin A, Swainston N, Day PJ, Kell DB. (2014). SpeedyGenes: a novel approach for the efficient production of error-corrected, synthetic gene libraries. Protein Eng. Design Sel. 27: 273-280.
  17. Currin A, Swainston N, Day PJ, Kell DB. (2015). Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem. Soc. Rev. 44: 1172-1239.
  18. de Graaff C, Bensch L, Boersma SJ, Cioc RC, van Lint MJ, Janssen E, Turner NJ, Orru RVA and Ruijter E. (2015). Asymmetric Synthesis of Tetracyclic Pyrroloindolines and Constrained Tryptamines by a Switchable Cascade Reaction. Angew. Chem. Int. Ed. 54: 14133-14136.
  19. Dickinson ER, Jurneczko E, Nicholson J, Hupp TR, Zawacka-Pankau J, Selivanova G, Barran PE. (2015). The use of ion mobility mass spectrometry to probe modulation of the structure of p53 and of MDM2 by small molecule inhibitors. Front Mol Biosci. 2: 39.
  20. Dickinson ER, Jurneczko E, Pacholarz KJ, Clarke DJ, Reeves M, Ball KL, Hupp T, Campopiano D, Nikolova PV, Barran PE. (2015). Insights into the Conformations of Three Structurally Diverse Proteins: Cytochrome c, p53, and MDM2, Provided by Variable-Temperature Ion Mobility Mass Spectrometry. Analytical Chemistry. 87(6): 3231-3238.
  21. Diez V, Loznik M, Taylor S, Winn M, Rattray NJ, Podmore H, Micklefield J, Goodacre R, Medema MH, Müller U, Bovenberg R, Janssen DB, & Takano E. (2015). Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block. ACS Synth. Biol. 4(7): 796-807.
  22. Fehér T, Libis V, Carbonell P, Faulon JL. (2015). A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Front Bioeng. Biotechnol. 3: 46.
  23. Gromski PS, Xu Y, Kotze KL, Correa E, Ellis DI, Armitage EG, Turner ML. & Goodacre R. (2014). Influence of missing values substitutes on multivariate analysis of metabolomics data. Metabolites, 4: 433-452.
  24. Hardman SJ, Hauck AF, Clark IP, Heyes DJ, Scrutton NS. (2014). Comprehensive analysis of the green-to-blue photoconversion of full-length Cyanobacteriochrome Tlr0924. Biophys. J. 107(9): 2195-203.
  25. Harvey SR, et al., Barran PE. (2015). Electron capture dissociation and drift tube ion mobility-mass spectrometry coupled with site directed mutations provide insights into the conformational diversity of a metamorphic protein. Physical Chemistry Chemical Physics. 17(16): 10538-10550.
  26. Herter S, McKenna SM, Frazer AR, Leimkühler S, Carnell AJ, and Turner NJ. (2015). Galactose Oxidase Variants for the Oxidation of Amino Alcohols in Enzyme Cascade Synthesis. Chem. Cat. Chem. 7: 2313-2317.
  27. Hussain S, Leipold F, Man H, Wells E, France SP, Mulholland KR, Grogan G and Turner NJ. (2015). An (R)-Imine Reductase [(R)-IRED biocatalyst] for the Asymmetric Reduction of Cyclic Imines. Chem. Cat. Chem. 7: 579-583.
  28. Jankevics A, Breitling R. (2015). Chapter 6: Advanced LC–MS applications for identification and quantification of the metabolome. In: Advanced LC-MS applications for metabolomics. 84–93. Future Science Group, London, UK.
  29. Jones AR, Rentergent J, Scrutton NS, & Hay S. (2015). Probing reversible chemistry in coenzyme B12‐dependent ethanolamine ammonia lyase with kinetic isotope effects. Chemistry A European Journal, 21: 8826–8831.
  30. Kell DB, Lurie-Luke E. (2015). The virtue of innovation: innovation through the lenses of biological evolution. J. R. Soc. Interface, 12: 20141183.
  31. Kell DB, Potgieter M & Pretorius E. (2015). Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology. F1000 Research 4: 179.
  32. Kell DB, Pretorius E. (2015). On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr. Biol. 7, 1339-1377.DOI: 10.1039/c5ib00158g.
  33. Kell DB, Swainston N, Pir P, Oliver SG. (2015). Membrane transporter engineering in industrial biotechnology and whole-cell biocatalysis. Trends Biotechnol. 33: 237-246.
  34. Kell DB. (2015). The transporter-mediated cellular uptake of pharmaceutical drugs is based on their metabolite-likeness and not on their bulk biophysical properties: Towards a systems pharmacology. Perspectives in Science, http://dx.doi.org/10.1016/j.pisc.2015.06.004.
  35. Kell DB. (2015). What would be the observable consequences if phospholipid bilayer diffusion of drugs into cells is negligible? Trends Pharmacol. Sci. 36: 15-21.
  36. Kelly PP, Eichler A, Herter S, Kranz DC, Turner NJ and Flitsch SL, Beilstein J. (2015). Active Site Diversification of P450cam with Indole Generates Catalysts for Benzylic Oxidation Reactions. Org. Chem. 11: 1713-1720.
  37. 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, 11: 1721–1732.
  38. Knaus T, Mutti FG, Humphreys LD, Turner NJ, and Scrutton NS. (2015). Systematic Methodology for the Development of Biocatalytic Hydrogen-Borrowing Cascades: Application to the Synthesis of Chiral α-Substituted Carboxylic Acids from α-Substituted α, β-Unsaturated Aldehydes. Org. Biomol. Chem. 13: 223-233.
  39. Kutta RJ, Hardman SJ, Johannissen LO, Bellina B, Messiha HL, Ortiz-Guerrero JM, Elías-Arnanz M, Padmanabhan S, Barran P, Scrutton NS, Jones AR. (2015). The photochemical mechanism of a B12-dependent photoreceptor protein. Nat. Commun. 6: 7907.
  40. Law BJC, Struck A-W, Bennett MR, Wilkinson B, and Micklefield J. (2015). Site-specific Bioalkylation of Rapamycin by the RapM 16-O-Methyltransferase. Chemical Science, 6: 2885-2892.
  41. Lewin R, Goodall M, Thompson ML, Leigh J, Breuer M, Baldenius K and Micklefield J. (2015). Enzymatic Enantioselective Decarboxylative Protonation of Heteroaryl Malonates. Chem. Eur. J. 17: 6557-6563.
  42. Lewin R, Thompson M and Micklefield J. (2014). Enzymatic Carboxylation and Decarboxylation. Science of Synthesis: Biocatalysis in Organic Synthesis. 2: 133-157.
  43. Libis V, Delepine B, Faulon JL. (2015). Computer-assisted design of metabolic pathways for biosensing  – BioSynSys conference, Paris, 7-10, September 2015.
  44. Liu W, Sakr E, Schaeffer P, Talbot HM, Donisi J, Härtner T, Kannenberg E, Takano E, Rohmer M. (2014). Ribosylhopane, a novel bacterial hopanoid, as precursor of C35 bacteriohopanepolyols in Streptomyces coelicolor A3(2). Chem. Bio. Chem. 15: 2156–2161.
  45. Man H, Wells E, Hussain S, Leipold F, Hart S,  Turkenburg JP, Turner NJ, and Grogan G. (2015). Structure, Activity and Stereoselectivity of NADPH-Dependent Oxidoreductases Catalysing the S-Selective Reduction of the Imine Substrate 2-Methylpyrroline. Chem. Bio. Chem. 16: 1052-1059.
  46. Martiny V, Carbonell P, Chevillard F, Moroy G, Nicot A, Vayer P, Villoutreix B, Miteva M. (2015). Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6. Bioinformatics, pii: btv486. [Epub ahead of print].
  47. McLean KJ, Hans M, Meijrink B, van Scheppingen WB, Vollebregt A, Tee KL, van der Laan JM, Leys D, Munro AW, van den Berg MA. (2015). Single-step fermentative production of the cholesterol-lowering drug pravastatin via reprogramming of Penicillium chrysogenum. Proc. Natl. Acad. Sci. 112(9): 2847-52.
  48. Medema MH, Kottmann R, Yilmaz P, Cummings M, [146 co-authors in alphabetical order], Breitling R, Takano E, Glöckner FO. (2015). The Minimum Information about a Biosynthetic Gene cluster (MIBiG) specification. Nature Chem. Biol. 11(9): 625-31.
  49. Mellor J, Carbonell P, Faulon JL. (2015). Gaussian process-based model for automated enzyme selection in pathway design  – Synthetic Biology UK, London, 1-3, September, 2015.
  50. Mendes P, Oliver SG, Kell DB. (2015). Fitting transporter activities to cellular drug concentrations and fluxes: why the bumblebee can fly. Trends Pharmacol. Sci. 36 (11): 710-723.
  51. Menon N, Pásztor A, Menon BRK, Kallio P, Fisher K, Akhtar MK, Leys D, Jones PR & Scrutton NS. (2015). A microbial platform for renewable propane synthesis based on a fermentative butanol pathway. Biotechnology for Biofuels, 8: 61.
  52. Morra R, Shankar J, Robinson CJ, Halliwell S, Butler L, Upton M, Hay S, Micklefield J, Dixon N. (2015). Dual transcriptional-translational cascade permits cellular level tuneable expression control. Nucleic Acids Research, Pub online Sept, DOI: 10.1093/nar/gkv912. 44: e21.
  53. Muhamadali H, Xu Y, Ellis DI, Allwood JW, Rattray NJ, Correa E, Alrabiah H, Lloyd JR, Goodacre R. (2015). Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up. Appl. Environ. Microbiol. 81(10): 3288-98.
  54. Muhamadali H, Xu Y, Ellis DI, Trivedi D, Rattray N, Bernaerts K. & Goodacre R. (2015). Metabolomics investigation of recombinant mTNFα production in Streptomyces lividans. Microbial Cell Factories, 14: 157. Supplementary Information.
  55. Mutti, FG, Knauss, T, Scrutton NS, Breuer, M & Turner, NJ. (2015). Conversion of alcohols to enantiopure amines through dual–enzyme hydrogen-borrowing cascades. Science, 349 (6255): 1525-1529. (Patent application associated with this work).
  56. O’Hagan S, Kell DB. (2015). Software review: The KNIME workflow environment and its applications in Genetic Programming and machine learning. Genetic Progr. Evol. Mach 16: 387-391.
  57. O’Hagan S, Kell DB. (2015). The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities. Peer J. 3, e1405.
  58. O’Hagan S, Kell DB. (2015). Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites. Front Pharmacol. 6: 105.
  59. O’Reilly E, and Turner NJ. (2015). Enzymatic Cascades for the Regio-and Stereoselective Synthesis of Chiral Amines. Perspectives in Science, 4: 55-61.
  60. Pacholarz KJ and Barran PE. (2015). Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry. Analytical Chemistry, 87(12): 6271-6279.
  61. Parmeggiani, Lovelock SL, Weise NJ, Ahmed ST, and Turner NJ. (2015). Synthesis of D- and L-Phenylalanine Derivatives by Phenylalanine Ammonia Lyases via a Multienzymatic Cascade Process. Angew. Chem. Int. Ed. 54: 4608-4611.
  62. Payne KA, White MD, Fisher K, Khara B, Bailey SS, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Beveridge R, Barran P, Rigby SE, Scrutton NS, Hay S, Leys D. (2015). New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature, 522(7557): 497-501.
  63. Phillips AS, Gomes AF, Kalapothakis JMD, Gillam JE, Gasparavicius J, Gozzo FC, Kunath T, MacPhee C, Barran PE. (2015). Conformational dynamics of alpha-synuclein: insights from mass spectrometry. Analyst, 140(9): 3070-3081.
  64. Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM. (2015). SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biol. 13(12): e1002310. doi: 10.1371/journal.pbio.1002310.
  65. Robinson CJ, Vincent HA, Wu M-C, Lowe PT, Dunstan MS, Leys D, and Micklefield J. (2014). Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species. J. Am. Chem. Soc. 136: 10615-10624.
  66. Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. (2015): TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res. 43: D637–44.
  67. Shapira P, Youtiec J, and Li Y. (2015). Social science contributions compared in synthetic biology and nanotechnology. Journal of Responsible Innovation 2:1, 143-148.
  68. Shepherd SA, Karthikeyan C, Latham J, Struck A-W, Thompson ML, Menon B, Levy C, Leys D, and Micklefield J. (2015). Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes. Chemical Science, 6: 3454-3460.
  69. Swainston N, Currin A, Day PJ and Kell DB. (2014). GeneGenie: optimised oligomer design for directed evolution. Nucleic Acids Res 42 (W1): W395-W400.
  70. Takano E, Breitling R. (2015). Chapter 23: Synthetic biology of antibiotic production. In: Synthetic Biology: Advances in Molecular Biology and Medicine (Meyers RA, ed.) Vol. 2: 699–722. Wiley-VCH.
  71. Toogood HS, Cheallaigh AN, Tait S, Mansell DJ, Jervis A, Lygidakis A, Humphreys L1, Takano E, Gardiner JM, Scrutton NS. (2015). Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli. ACS Synth Biol. 4 (10): 1112–1123. (Patent application associated with this work).
  72. Trosset JY, Carbonell P. (2015). Synthetic biology for pharmaceutical drug discovery. Drug Des. Devel. Ther. 9: 6285-6302.
  73. Vincent HA, Robinson CJ, Wu MC, Dixon N, Micklefield J. (2014). Generation of orthogonally selective bacterial riboswitches by targeted mutagenesis and in vivo screening. Methods Mol. Biol. 1111: 107-29.
  74. Wandy J, Daly R, Breitling R, Rogers S. (2015). Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets. Bioinformatics, 31: 1999–2006.
  75. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. (2015). antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucl. Acids Res. 43(W1): 237-43.
  76. Weise NJ, Parmeggiani F, Ahmed ST, and Turner NJ. (2015). The Bacterial Ammonia Lyase EncP: A Tunable Biocatalyst for the Synthesis of Unnatural Amino Acids. J. Am. Chem. Soc. 137: 12977-12983.
  77. White MD, Payne KA, Fisher K, Marshall SA, Parker D, Rattray NJ, Trivedi DK, Goodacre R, Rigby SE, Scrutton NS, Hay S, Leys D. (2015). UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature, 522(7557): 502-6.
  78. Wu M-C, Lowe PT., Robinson CJ, Vincent HA, Dixon N, Leigh J and Micklefield J. (2015). Rational Re-engineering of the Transcriptional Silencing PreQ1 Riboswitch. J. Am. Chem. Soc. 137: 9015–9021.
  79. Wu M-C, Styles MQ, Nunns L, Law BJC. & Micklefield J. (2015). Engineered Biosynthesis of Enduracidin Lipogyclopeptide Antibiotics using the Ramoplanin Mannosyltransferase Ram29.  Microbiology, 161: 1338-1347.

Blogs and Media

  1. Balmer A, Choosing an iGEM Project Weblink
  2. Balmer A. Public Perceptions, Knowledge Deficit and Expertise in Synthetic Biology. Weblink
  3. Gök A, Shapira P. “Tracking Synthetic Biology.” Blog post, Nesta. January 22, 2015. Weblink
  4. Li Y, and Shapira P. “Synthetic biology in China: An update from the field.” Blog – Rising Powers and Interdependent Futures, July 3, 2015. Weblink
  5. Shapira P. “Why synthetic biology has the potential to reshape our lives,” Blog, Policy@Manchester, October 28, 2015. Weblink
  6. Shapira P, and Gök A. “UK Synthetic Biology Centres tasked with addressing public concerns,” Science Political Science, The Guardian, January 30, 2015. Weblink

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol (2020)

M. S. Dunstan, C. J. Robinson, A. J. Jervis, C. Yan, P. Carbonell, K. A. Hollywood, A. Currin, N. Swainston, R. Le Feuvre, J. Micklefield, J.-L. Faulon, R. Breitling, N. Turner, E. Takano, N. S. Scrutton

Synthetic Biology, In Press, DOI: 10.1093/synbio/ysaa012 Open Access