Latest Highlights

An automated Design-Build-Test-Learn pipeline for microbial production of fine chemicals. 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.  Communications Biology, 1: 66. (2018). This paper highlights the SYNBIOCHEM D/B/T/L pipeline.

Enzyme discovery: enzyme selection and pathway design. Carbonell P, Koch M, Duigou T, Faulon JL. (2018). Methods Enzymol. 608: 3-27.

SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli. Jervis AJ, Carbonell P, Taylor S, Sung R, Dunstan MS, Robinson CJ, Breitling R, Takano E, Scrutton NS. ACS Synth Biol. 2019 Mar 18. doi: 10.1021/acssynbio.8b00399. Paper

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli. Jervis AJ, Carbonell P, Vinaixa M, Dunstan MS, Hollywood KA, Robinson CJ, Rattray NJW, Yan C, Swainston N, Currin A, Sung R, Toogood H, Taylor S, Faulon JL, Breitling R, Takano E, Scrutton NS. ACS Synth Biol. 2019 Jan 18;8(1):127-136. doi: 10.1021/acssynbio.8b00398. Epub 2019 Jan 7. Paper

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Swainston N, Dunstan M, Jervis AJ, Robinson CJ, Carbonell P, Williams AR, Faulon JL, Scrutton NS, Kell DB. Bioinformatics. 2018 Jul 1;34(13):2327-2329. doi: 10.1093/bioinformatics/bty105. Paper

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters. Del Carratore F, Zych K, Cummings M, Takano E, Medema MH, Breitling R. Commun Biol. 2019 Feb 28;2:83. doi: 10.1038/s42003-019-0333-6. eCollection 2019. Paper

A vitamin K-dependent carboxylase orthologue is involved in antibiotic biosynthesis. Law B, Zhuo Y, Winn M, Francis D, Samborskyy M, Murphy A, Ren L, Leadlay P F and Micklefield J. Nature Catalysis (2018) Web link    This latest Micklefield Lab paper out in describes discovery of a new biosynthetic pathway with a highly unusual carboxylase enzyme (MloH) producing a structurally unique antibiotic malonomycin.              

The Values of Synthetic Biology: Researcher Views of Their Field and Participation in Public Engagement. Rose KM, Howell EL, Scheufele DA, Brossard D, Xenos MA, Shapira P, Youtie J, Kwon S.  BioScience, 68, 10, 782–791.

Point of View: A transatlantic perspective on 20 emerging issues in biological engineering. Wintle B, Boehm C, Rhodes C,  Molloy J, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans N, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman B, Matthewman C, Napier J, Oheigeartaigh S, Patron N, Perello E, Shapira P, Tait J, Takano E, Sutherland W. elifesciences, DOI: Web link

Multifragment DNA Assembly of Biochemical Pathways via Automated Ligase Cycling Reaction. Robinson CJ, Dunstan MS, Swainston N, Titchmarsh J, Takano E, Scrutton NS, Jervis AJ. Methods Enzymol. 2018;608:369-392. doi: 10.1016/bs.mie.2018.04.011. Paper

Engaging the Senses, Understanding Publics: Research Methods, Science Engagement, and Synthetic Biology. Meckin R, Balmer A. Trends Biotechnol. 2017 Nov;35(11):1015-1017. Web link

Retooling microorganisms for the fermentative production of alcohols. Toogood HS, Scrutton NS.
Curr Opin Biotechnol. 2017 Sep 6;50:1-10. doi: 10.1016/j.copbio.2017.08.010. Review Web link

Enzymes make light work of hydrocarbon production. Scrutton NS. Science. 2017 Sep 1;357(6354):872-873. doi: 10.1126/science.aao4399. Web link

Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis. Gahloth D, Dunstan MS, Quaglia D, Klumbys E, Lockhart-Cairns MP, Hill AM, Derrington SR, ScruttonNS, Turner NJ, Leys D. Nat Chem Biol. 2017 Sep;13(9):975-981. doi: 10.1038/nchembio.2434. Web link

Detection and Quantification of Butyrolactones from Streptomyces. Biarnes-Carrera M, Breitling R, Takano E. Methods Mol Biol. 2018;1673:117-128. doi: 10.1007/978-1-4939-7309-5_10. Web link

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets. Del Carratore F, Jankevics A, Eisinga R, Heskes T, Hong F, Breitling R.Bioinformatics. 2017 Sep 1;33(17):2774-2775. doi: 10.1093/bioinformatics/btx292. Web link

Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes. Weise NJ1, Ahmed ST1, Parmeggiani F, Galman JL, Dunstan MS, Charnock SJ, Leys D, Turner NJ. Sci Rep. 2017 Oct 20;7(1):13691. doi: 10.1038/s41598-017-13990-0. Web link

From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy. Fisk H, Xu Y, Westley C, Turner NJ, Micklefield J, Goodacre R. Anal Chem. 2017 Nov 8. doi: 10.1021/acs.analchem.7b03742. Web link

Design and chemical synthesis of eukaryotic chromosomes. 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. Chem Soc Rev. 2017 Nov 2. doi: 10.1039/c7cs00208d. Web link

Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis. Zhao H, Yao Z, Chen X, Wang X, Chen GQ. Microb Biotechnol. 2017 Nov;10(6):1400-1411. doi: 10.1111/1751-7915.12820. Web link

Mapping the substrate scope of monoamine oxidase (MAO-N) as a synthetic tool for the enantioselective synthesis of chiral amines. Herter S, Medina F, Wagschal S, Benhaïm C, Leipold F, Turner NJ. Bioorg Med Chem. 2017 Jul 13. pii: S0968-0896(17)30391-7. doi: 10.1016/j.bmc.2017.07.023. Web link

Cloning and upscale production of monoamine oxidase N (MAO-N D5) by Pichia pastoris. Markošová K, Camattari A, Rosenberg M, Glieder A, Turner NJ, Rebroš M. Biotechnol Lett. 2017 Oct 10. doi: 10.1007/s10529-017-2450-y. Web link

Co-production of microbial polyhydroxyalkanoates with other chemicals. Li T, Elhadi D, Chen GQ. Metab Eng. 2017 Sep;43(Pt A):29-36. doi: 10.1016/j.ymben.2017.07.007. Epub 2017 Aug 3. Review. Web link

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ní Cheallaigh A, Bennett NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS. ACS Catal. 2017 Sep 1;7(9):6268-6282. doi: 10.1021/acscatal.7b01924. Epub 2017 Aug 9. Web link

Adenylation Activity of Carboxylic Acid Reductases Enables the Synthesis of Amides. Wood AJL, Weise NJ, Frampton JD, Dunstan MS, Hollas MA, Derrington SR, Lloyd RC, Quaglia D, Parmeggiani F, Leys D, Turner NJ, Flitsch SL. Angew Chem Int Ed Engl. 2017 Nov 13;56(46):14498-14501. doi: 10.1002/anie.201707918. Web link

biochem4j: Integrated and extensible biochemical knowledge through graph databases. 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. PLoS One. 2017 Jul 14;12(7):e0179130. doi: 10.1371/journal.pone.0179130. Web link

RadH: A Versatile Halogenase for Integration into Synthetic Pathways. Menon BRK, Brandenburger E, Sharif HH, Klemstein U, Shepherd SA, Greaney MF, Micklefield J.Angew Chem Int Ed Engl. 2017 Sep 18;56(39):11841-11845. doi: 10.1002/anie.201706342. Web link

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae. Parker S, Fraczek MG, Wu J, Shamsah S, Manousaki A, Dungrattanalert K, de Almeida RA, Estrada-Rivadeneyra D, Omara W, Delneri D, O’Keefe RT. RNA. 2017 Aug;23(8):1166-1171. doi: 10.1261/rna.061564.117. Web link

Development of Halogenase Enzymes for Use in Synthesis. Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Chem Rev. 2017 May 3. doi: 10.1021/acs.chemrev.7b00032. Web link

Effect of DMSO on Protein Structure and Interactions Assessed by Collision-Induced Dissociation and Unfolding. Chan DS, Kavanagh ME, McLean KJ, Munro AW, Matak-Vinković D, Coyne AG, Abell C. Anal Chem. 2017 Sep 19;89(18):9976-9983. doi: 10.1021/acs.analchem.7b02329. Epub 2017 Aug 25. Web link

A reductive aminase from Aspergillus oryza Aleku G, France S, Man H, Mangas-Sanchez J, Montgomery S, Sharma M, Leipold F, Hussain S, Grogan G & Turner NJ (2017). Nature Chemistry doi:10.1038/nchem.2782 Web link

Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA Currin A, Korovin K, Ababi M, Roper K, Kell DB, Day PJ, King RD. J. Roy Soc Interface DOI: 10.1098/rsif.2016.0990 Web link


2017 Publications

  1. Barran, P. (2017) From Microsolvation to Cell Permeation: Novel Separation Science for Drug Discovery, ACS central science 3, 158-160.
  2. Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Suarez Duran, H. G., de Los Santos, E. L. C., Kim, H. U., Nave, M., Dickschat, J. S., Mitchell, D. A., Shelest, E., Breitling, R., Takano, E., Lee, S. Y., Weber, T., and Medema, M. H. (2017) antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification, Nucleic acids research.
  3. Brandariz-de-Pedro, G., Heyes, D. J., Hardman, S. J., Shanmugam, M., Jones, A. R., Weber, S., Nohr, D., Scrutton, N. S., and Fielding, A. J. (2017) Direct Evidence of an Excited-State Triplet Species upon Photoactivation of the Chlorophyll Precursor Protochlorophyllide, The journal of physical chemistry letters 8, 1219-1223.
  4. Carbonell, P., Lopez, O., Amberg, A., Pastor, M., and Sanz, F. (2017) Hepatotoxicity prediction by systems biology modeling of disturbed metabolic pathways using gene expression data, Altex 34, 219-234.
  5. Currin, A., Korovin, K., Ababi, M., Roper, K., Kell, D. B., Day, P. J., and King, R. D. (2017) Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA, Journal of the Royal Society, Interface 14.
  6. Currin, A., Swainston, N., Day, P. J., and Kell, D. B. (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.
  7. Czarnota, S., Baxter, N. J., Cliff, M. J., Waltho, J. P., Scrutton, N. S., and 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.
  8. Goodacre, R., and Kell, D. B. (2017) Commentary on “Rapid identification of Streptococcus and Enterococcus species using diffuse reflectance-absorbance Fourier transform infrared spectroscopy and artificial neural networks”, FEMS microbiology letters 364.
  9. Hedison, T. M., Hay, S., and Scrutton, N. S. (2017) A perspective on conformational control of electron transfer in nitric oxide synthases, Nitric oxide : biology and chemistry 63, 61-67.
  10. Heyes, D. J., Hardman, S. J., Mansell, D., Ni Cheallaigh, A., Gardiner, J. M., Johannissen, L. O., Greetham, G. M., Towrie, M., and Scrutton, N. S. (2017) Excited-State Properties of Protochlorophyllide Analogues and Implications for Light-Driven Synthesis of Chlorophyll, The journal of physical chemistry. B 121, 1312-1320.
  11. Johannissen, L. O., Leys, D., and Hay, S. (2017) A common mechanism for coenzyme cobalamin-dependent reductive dehalogenases, Physical chemistry chemical physics : PCCP 19, 6090-6094.
  12. Kavanagh, M. E., Chenge, J., Zoufir, A., McLean, K. J., Coyne, A. G., Bender, A., Munro, A. W., and Abell, C. (2017) Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1, Biochemistry 56, 1559-1572.
  13. Kutta, R. J., Archipowa, N., Johannissen, L. O., Jones, A. R., and Scrutton, N. S. (2017) Vertebrate Cryptochromes are Vestigial Flavoproteins, Scientific reports 7, 44906.
  14. Liu, K. C., Hughes, J. M. X., Hay, S., and Scrutton, N. S. (2017) Liver microsomal lipid enhances the activity and redox coupling of colocalized cytochrome P450 reductase-cytochrome P450 3A4 in nanodiscs, The FEBS journal.
  15. Matthews, S., Tee, K. L., Rattray, N. J., McLean, K. J., Leys, D., Parker, D. A., Blankley, R. T., and Munro, A. W. (2017) Production of alkenes and novel secondary products by P450 OleTJE using novel H2 O2 -generating fusion protein systems, FEBS letters 591, 737-750.
  16. McMurry, J. A., Juty, N., Blomberg, N., Burdett, T., Conlin, T., Conte, N., Courtot, M., Deck, J., Dumontier, M., Fellows, D. K., Gonzalez-Beltran, A., Gormanns, P., Grethe, J., Hastings, J., Heriche, J. K., Hermjakob, H., Ison, J. C., Jimenez, R. C., Jupp, S., Kunze, J., Laibe, C., Le Novere, N., Malone, J., Martin, M. J., McEntyre, J. R., Morris, C., Muilu, J., Muller, W., Rocca-Serra, P., Sansone, S. A., Sariyar, M., Snoep, J. L., Soiland-Reyes, S., Stanford, N. J., Swainston, N., Washington, N., Williams, A. R., Wimalaratne, S. M., Winfree, L. M., Wolstencroft, K., Goble, C., Mungall, C. J., Haendel, M. A., and 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, e2001414.
  17. O’Hagan, S., and Kell, D. B. (2017) Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures, Journal of cheminformatics 9, 18.
  18. Scrutton, N. S. (2017) Speeding up enzyme engineering computationally, IUCrJ 4, 5-6.
  19. Shapira, P., Kwon, S. & Youtie, J. Scientometrics (2017). Tracking the emergence of synthetic biology doi:10.1007/s11192-017-2452-5.
  20. Tsigkinopoulou, A., Baker, S. M., and Breitling, R. (2017) Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology, Trends in biotechnology 35, 518-529.
  21. Waller, J., Toogood, H. S., Karuppiah, V., Rattray, N. J. W., Mansell, D. J., Leys, D., Gardiner, J. M., Fryszkowska, A., Ahmed, S. T., Bandichhor, R., Reddy, G. P., and Scrutton, N. S. (2017) Structural insights into the ene-reductase synthesis of profens, Organic & biomolecular chemistry 15, 4440-4448.
  22. Yan, C., Parmeggiani, F., Jones, E. A., Claude, E., Hussain, S. A., Turner, N. J., Flitsch, S. L., and Barran, P. E. (2017) Real-Time Screening of Biocatalysts in Live Bacterial Colonies, Journal of the American Chemical Society 139, 1408-1411.

2016 Publications

    1. Aslan, A. S., Birmingham, W. R., Karaguler, N. G., Turner, N. J. & Binay, B. Semi-Rational Design of Geobacillus stearothermophilus L-Lactate Dehydrogenase to Access Various Chiral alpha-Hydroxy Acids. Applied biochemistry and biotechnology 179, 474-484, doi:10.1007/s12010-016-2007-x (2016).
    1. Bajhaiya, A. K. et al. High-throughput metabolic screening of microalgae genetic variation in response to nutrient limitation. Metabolomics: Official journal of the Metabolomic Society 12, 9, doi:10.1007/s11306-015-0878-4 (2016).
    1. Balmer, A. The secretive ‘second world’ of human synthetic biology. News Article in the Guardian   (2016).
    1. Beveridge, R. et al. Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nature communications 7, 12163, doi:10.1038/ncomms12163 (2016).
    1. Biarnes-Carrera, M., Breitling, R. & Takano, E. Butyrolactone signalling circuits for synthetic biology. Current opinion in chemical biology 28, 91-98, doi:10.1016/j.cbpa.2015.06.024 (2015).
    1. Birt, J. et al. Lack of evidence for the efficacy of enhanced surveillance compared to other specific interventions to control neonatal healthcare-associated infection outbreaks. Transactions of the Royal Society of Tropical Medicine and Hygiene 110, 98-106, doi:10.1093/trstmh/trv116 (2016).
    1. Both, P. et al. Whole-Cell Biocatalysts for Stereoselective C-H Amination Reactions. Angewandte Chemie 55, 1511-1513, doi:10.1002/anie.201510028 (2016).
    1. Breitling, R. & Takano, E. Synthetic biology advances for pharmaceutical production. Current opinion in biotechnology 35, 46-51, doi:10.1016/j.copbio.2015.02.004 (2015).
    1. Breitling, R. & Takano, E. Synthetic Biology of Natural Products. Cold Spring Harbor perspectives in biology, doi:10.1101/cshperspect.a023994 (2016).
    1. Breitling, R., Takano, E. & Gardner, T. S. Judging synthetic biology risks. Science 347, 107, doi:10.1126/science.aaa5253 (2015).
    1. Carbonell, P. et al. SYNBIOCHEM-a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society transactions 44, 675-677, doi:10.1042/BST20160009 (2016)
    1. Carbonell, P. et al. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Natural product reports 33, 925-932, doi:10.1039/c6np00018e (2016).
    1. Carbonell, P., Gok, A., Shapira, P. & Faulon, J. L. Mapping the patent landscape of synthetic biology for fine chemical production pathways. Microbial biotechnology, doi:10.1111/1751-7915.12401 (2016).
    1. Ceroni, F., Carbonell, P., Francois, J. M. & Haynes, K. A. Editorial – Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities. Frontiers in bioengineering and biotechnology 3, 120, doi:10.3389/fbioe.2015.00120 (2015).
    1. Chenge, J. et al. Structural characterization of CYP144A1 – a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis. Scientific reports 6, 26628, doi:10.1038/srep26628 (2016).
    1. Delepine, B., Libis, V., Carbonell, P. & Faulon, J. L. SensiPath: computer-aided design of sensing-enabling metabolic pathways. Nucleic acids research 44, W226-231, doi:10.1093/nar/gkw305 (2016).
    1. Eichler, A. et al. Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling. Chembiochem : a European journal of chemical biology 17, 426-432, doi:10.1002/cbic.201500536 (2016).
    1. Feher, T., Libis, V., Carbonell, P. & Faulon, J. L. A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli. Frontiers in bioengineering and biotechnology 3, 46, doi:10.3389/fbioe.2015.00046 (2015).
    1. Formisano, N. et al. Inexpensive and fast pathogenic bacteria screening using field-effect transistors. Biosensors & bioelectronics 85, 103-109, doi:10.1016/j.bios.2016.04.063 (2016).
    1. Girvan, H. M. & Munro, A. W. Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology. Current opinion in chemical biology 31, 136-145, doi:10.1016/j.cbpa.2016.02.018 (2016).
    1. Gray, C. J. et al. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochimica et biophysica acta 1860, 1688-1709, doi:10.1016/j.bbagen.2016.02.003 (2016).
    1. Grogan, G. & Turner, N. J. InspIRED by Nature: NADPH-Dependent Imine Reductases (IREDs) as Catalysts for the Preparation of Chiral Amines. Chemistry 22, 1900-1907, doi:10.1002/chem.201503954 (2016).
    1. Hastings, J. et al. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic acids research 44, D1214-1219, doi:10.1093/nar/gkv1031 (2016).
    1. Heath, R. S., Pontini, M., Hussain, S. & Turner, N. J. Combined Imine Reductase and Amine Oxidase Catalyzed Deracemization of Nitrogen Heterocycles. Chemcatchem 8, 117-120, doi:10.1002/cctc.201500822 (2016).
    1. Hoeven, R., Hardman, S. J., Heyes, D. J. & Scrutton, N. S. 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, 903-913, doi:10.1021/acs.biochem.5b01355 (2016).
    1. Hugentobler, K. G., Sharif, H., Rasparini, M., Heath, R. S. & Turner, N. J. Biocatalytic approaches to a key building block for the anti-thrombotic agent ticagrelor. Organic & biomolecular chemistry, doi:10.1039/c6ob01382a (2016).
    1. Johannissen, L. O., Hay, S. & Scrutton, N. S. Nuclear quantum tunnelling in enzymatic reactions–an enzymologist’s perspective. Physical chemistry chemical physics : PCCP 17, 30775-30782, doi:10.1039/c5cp00614g (2015).
    1. Kavanagh, M. E. et al. Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Journal of medicinal chemistry 59, 3272-3302, doi:10.1021/acs.jmedchem.6b00007 (2016).
    1. Kavanagh, M. E. et al. Substrate Fragmentation for the Design of M. tuberculosis CYP121 Inhibitors. ChemMedChem, doi:10.1002/cmdc.201600248 (2016).
    1. Kell, D. B. Implications of endogenous roles of transporters for drug discovery: hitchhiking and metabolite-likeness. Nature reviews. Drug discovery 15, 143, doi:10.1038/nrd.2015.44 (2016).
    1. Kell, D. B., Swainston, N., Pir, P. & Oliver, S. G. Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends in biotechnology 33, 237-246, doi:10.1016/j.tibtech.2015.02.001 (2015).
    1. Kent, A. et al. Schedules for Pneumococcal Vaccination of Preterm Infants: An RCT. Pediatrics, doi:10.1542/peds.2015-3945 (2016).
    1. Kent, A. et al. Lymphocyte subpopulations in premature infants: an observational study. Archives of disease in childhood. Fetal and neonatal edition, doi:10.1136/archdischild-2015-309246 (2016).
    1. Knaus, T. et al. Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes. Journal of the American Chemical Society 138, 1033-1039, doi:10.1021/jacs.5b12252 (2016).
    1. Kutta, R. J. et al. The photochemical mechanism of a B12-dependent photoreceptor protein. Nature communications 6, 7907, doi:10.1038/ncomms8907 (2015).
    1. Latham, J. et al. Integrated catalysis opens new arylation pathways via regiodivergent enzymatic C-H activation. Nature communications 7, 11873, doi:10.1038/ncomms11873 (2016).
    1. Law, B. J. et al. Effects of Active-Site Modification and Quaternary Structure on the Regioselectivity of Catechol-O-Methyltransferase. Angewandte Chemie 55, 2683-2687, doi:10.1002/anie.201508287 (2016).
    1. Leys, D. & Scrutton, N. S. 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, doi:10.1016/ (2016).
    1. Libis, V., Delepine, B. & Faulon, J. L. Sensing new chemicals with bacterial transcription factors. Current opinion in microbiology 33, 105-112, doi:10.1016/j.mib.2016.07.006 (2016).
    1. Libis, V., Delepine, B. & Faulon, J. L. Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways. ACS synthetic biology, doi:10.1021/acssynbio.5b00225 (2016).
    1. Longbotham, J. E. et al. Structure and Mechanism of a Viral Collagen Prolyl Hydroxylase. Biochemistry 54, 6093-6105, doi:10.1021/acs.biochem.5b00789 (2015).
    1. Lygidakis, A. et al. Pinpointing a Mechanistic Switch Between Ketoreduction and “Ene” Reduction in Short-Chain Dehydrogenases/Reductases. Angewandte Chemie 55, 9596-9600, doi:10.1002/anie.201603785 (2016).
    1. Mellor, J., Grigoras, I., Carbonell, P. & Faulon, J. L. Semisupervised Gaussian Process for Automated Enzyme Search. ACS synthetic biology 5, 518-528, doi:10.1021/acssynbio.5b00294 (2016).
    1. Mendes, P., Oliver, S. G. & Kell, D. B. Response to ‘The Need for Speed’, by Matsson et al. Trends in pharmacological sciences 37, 245-246, doi:10.1016/ (2016).
    1. Menon, B. R., Hardman, S. J., Scrutton, N. S. & Heyes, D. J. 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, 236-243, doi:10.1016/j.jphotobiol.2016.05.029 (2016).
    1. Morra, R. et al. Dual transcriptional-translational cascade permits cellular level tuneable expression control. Nucleic acids research 44, e21, doi:10.1093/nar/gkv912 (2016).
    1. Muhamadali, H. et al. Metabolomic analysis of riboswitch containing E. coli recombinant expression system. Molecular bioSystems 12, 350-361, doi:10.1039/c5mb00624d (2016).
    1. Peers, M. K. et al. Light-driven biocatalytic reduction of alpha,beta-unsaturated compounds by ene reductases employing transition metal complexes as photosensitizers. Catal Sci Technol 6, 169-177, doi:10.1039/c5cy01642h (2016).
    1. Randles, S. & Laasch, O. Theorising the Normative Business Model. Organ Environ 29, 53-73, doi:10.1177/1086026615592934 (2016).
    1. Rattray, N. J. Analytical medicine: Citizen scientists can aid diagnostics. Nature 528, 193, doi:10.1038/528193c (2015).
    1. Robinson, C. J., Medina-Stacey, D., Wu, M. C., Vincent, H. A. & Micklefield, J. Rewiring Riboswitches to Create New Genetic Circuits in Bacteria. Methods in enzymology 575, 319-348, doi:10.1016/bs.mie.2016.02.022 (2016).
    1. Ruscoe, R. E., Fazakerley, N. J., Huang, H. M., Flitsch, S. & Procter, D. J. Copper-Catalyzed Double Additions and Radical Cyclization Cascades in the Re-Engineering of the Antibacterial Pleuromutilin. Chem-Eur J 22, 116-119, doi:10.1002/chem.201504343 (2016).
    1. S, O. H., Swainston, N., Handl, J. & Kell, D. B. A ‘rule of 0.5’ for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics : Official journal of the Metabolomic Society 11, 323-339, doi:10.1007/s11306-014-0733-z (2015).
    1. Shepherd, S. A. et al. A Structure-Guided Switch in the Regioselectivity of a Tryptophan Halogenase. Chembiochem : a European journal of chemical biology 17, 821-824, doi:10.1002/cbic.201600051 (2016).
    1. Simpson, J. E. et al. Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer-type pathology. Neuropathology and applied neurobiology 42, 167-179, doi:10.1111/nan.12252 (2016).
    1. Staniland, S. et al. Biocatalytic Dynamic Kinetic Resolution for the Synthesis of Atropisomeric Biaryl N-Oxide Lewis Base Catalysts. Angewandte Chemie, doi:10.1002/anie.201605486 (2016).
    1. Struck, A. W. et al. An Enzyme Cascade for Selective Modification of Tyrosine Residues in Structurally Diverse Peptides and Proteins. Journal of the American Chemical Society 138, 3038-3045, doi:10.1021/jacs.5b10928 (2016).
    1. Surman, A. J. et al. Sizing and Discovery of Nanosized Polyoxometalate Clusters by Mass Spectrometry. Journal of the American Chemical Society 138, 3824-3830, doi:10.1021/jacs.6b00070 (2016).
    1. Swainston, N. et al. libChEBI: an API for accessing the ChEBI database. Journal of cheminformatics 8, 11, doi:10.1186/s13321-016-0123-9 (2016).
    1. Swainston, N. et al. Recon 2.2: from reconstruction to model of human metabolism. Metabolomics : Official journal of the Metabolomic Society 12, 109, doi:10.1007/s11306-016-1051-4 (2016).
    1. Toogood, H. S. et al. Natural Product Biosynthesis in Escherichia coli: Mentha Monoterpenoids. Methods in enzymology 575, 247-270, doi:10.1016/bs.mie.2016.02.020 (2016).
    1. van Oosterwijk, N. et al. Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-Selective omega-Transaminases. Biochemistry 55, 4422-4431, doi:10.1021/acs.biochem.6b00370 (2016).
    1. Weissenborn, M. J. et al. Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s. Chemical communications 52, 6158-6161, doi:10.1039/c6cc01749e (2016).
    1. Westley, C., Xu, Y., Carnell, A. J., Turner, N. J. & Goodacre, R. Label-Free Surface Enhanced Raman Scattering Approach for High-Throughput Screening of Biocatalysts. Analytical chemistry 88, 5898-5903, doi:10.1021/acs.analchem.6b00813 (2016).
    1. Willies, S. C., Galman, J. L., Slabu, I. & Turner, N. J. A stereospecific solid-phase screening assay for colonies expressing both (R)- and (S)-selective omega-aminotransferases. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 374, doi:10.1098/rsta.2015.0084 (2016).
    1. Yan, C. et al. Rapid and sensitive monitoring of biocatalytic reactions using ion mobility mass spectrometry. The Analyst 141, 2351-2355, doi:10.1039/c6an00617e (2016).
  1. Zebec, Z. et al. Towards synthesis of monoterpenes and derivatives using synthetic biology. Current opinion in chemical biology 34, 37-43, doi:10.1016/j.cbpa.2016.06.002 (2016).

Publications from SYNBIOCHEM Year 1

    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.
    1. 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).
    1. Barran P, and Ruotolo B. (2015). Ion Mobility Mass Spectrometry. Analyst, 14(20): 6772-6774.
    1. Barran P, Cooper H, and Eyers C. (2015). Protein Structure. Proteomics, 15(16): p. 2731-2732.
    1. 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.
    1. 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.
    1. Biarnes-Carrera M, Breitling R, Takano E, Micklefield J. (2015). Butyrolactone signalling circuits for synthetic biology. Curr. Opin. Chem. Biol. 28: 91-98.
    1. Breitling R, Takano E, Gardner TS. (2015). Judging synthetic biology risks. Science, 347: 107.
    1. Breitling R, Takano E. (2015). Synthetic biology advances for pharmaceutical production. Curr. Opin. Biotechnol. 35: 46-51.
    1. Ceroni F, Carbonell P, François JM, Haynes KA. (2015). Editorial – Synthetic Biology: engineering complexity and refactoring cell capabilities. Frontiers in Synthetic Biology. 3: 120.
    1. Chessher A, Breitling R, Takano E. (2015). Bacterial microcompartments: biomaterials for synthetic biology-based compartmentalization strategies. ACS Biomater. Sci. Eng. 1: 463-616.
    1. 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.
    1. 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.
    1. 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.
    1. Cummings M, Breitling R, Takano E. (2014). Steps towards the synthetic biology of polyketide biosynthesis FEMS Microbiol. Lett. 351: 116-125.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. Kell DB, Lurie-Luke E. (2015). The virtue of innovation: innovation through the lenses of biological evolution. J. R. Soc. Interface, 12: 20141183.
    1. 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.
    1. 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.
    1. Kell DB, Swainston N, Pir P, Oliver SG. (2015). Membrane transporter engineering in industrial biotechnology and whole-cell biocatalysis. Trends Biotechnol. 33: 237-246.
    1. 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,
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. Lewin R, Thompson M and Micklefield J. (2014). Enzymatic Carboxylation and Decarboxylation. Science of Synthesis: Biocatalysis in Organic Synthesis. 2: 133-157.
    1. Libis V, Delepine B, Faulon JL. (2015). Computer-assisted design of metabolic pathways for biosensing – BioSynSys conference, Paris, 7-10, September 2015.
    1. 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.
    1. 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.
    1. 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].
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. Mutti, FG, Knauss, T, Scrutton NS, Breuer, M & Turner, NJT. (2015). Conversion of alcohols to enantiopure amines through dual–enzyme hydrogen-borrowing cascades. Science, 349 (6255): 1525-1529. (Patent application associated with this work).
    1. 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.
    1. 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.
    1. O’Hagan S, Kell DB. (2015). Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites. Front Pharmacol. 6: 105.
    1. O’Reilly E, and Turner NJ. (2015). Enzymatic Cascades for the Regio-and Stereoselective Synthesis of Chiral Amines. Perspectives in Science, 4: 55-61.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. Swainston N, Currin A, Day PJ and Kell DB. (2014). GeneGenie: optimised oligomer design for directed evolution. Nucleic Acids Res 42 (W1): W395-W400.
    1. 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.
    1. 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).
    1. Trosset JY, Carbonell P. (2015). Synthetic biology for pharmaceutical drug discovery. Drug Des. Devel. Ther. 9: 6285-6302.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
    1. 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.
  1. 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