2021
Range, J., Halupczok, C., Lohmann, J., Swainston, N., Kettner, C., Bergmann, F. T., . . . Pleiss, J. (2021). EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS JOURNAL. doi:10.1111/febs.16318DOI: 10.1111/febs.16318
Yeoh, J. W., Swainston, N., Vegh, P., Zulkower, V., Carbonell, P., Holowko, M. B., . . . Poh, C. L. (2021). SynBiopython: an open-source software library for <i>Synthetic Biology</i>. SYNTHETIC BIOLOGY, 6. doi:10.1093/synbio/ysab001DOI: 10.1093/synbio/ysab001
2020
Kell, D. B., Samanta, S., & Swainston, N. (2020). Deep learning and generative methods in cheminformatics and chemical biology: navigating small molecule space intelligently. BIOCHEMICAL JOURNAL, 477(23), 4559-4580. doi:10.1042/BCJ20200781DOI: 10.1042/BCJ20200781
Khemchandani, Y., O'Hagan, S., Samanta, S., Swainston, N., Roberts, T. J., Bollegala, D., & Kell, D. B. (2020). DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. Journal of Cheminformatics, 12(1). doi:10.1186/s13321-020-00454-3DOI: 10.1186/s13321-020-00454-3
Keating, S. M., Waltemath, D., Koenig, M., Zhang, F., Draeger, A., Chaouiya, C., . . . Hucka, M. (2020). SBML Level 3: an extensible format for the exchange and reuse of biological models. MOLECULAR SYSTEMS BIOLOGY, 16(8). doi:10.15252/msb.20199110DOI: 10.15252/msb.20199110
Khemchandani, Y., O'Hagan, S., Samanta, S., Swainston, N., Roberts, T., Bollegala, D., & Kell, D. (2020). DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. doi:10.21203/rs.3.rs-32446/v2DOI: 10.21203/rs.3.rs-32446/v2
Samanta, S., O'Hagan, S., Swainston, N., Roberts, T. J., & Kell, D. B. (2020). VAE-Sim: A Novel Molecular Similarity Measure Based on a Variational Autoencoder.. Molecules, 25(15). doi:10.3390/molecules25153446DOI: 10.3390/molecules25153446
Robinson, C. J., Carbonell, P., Jervis, A. J., Yan, C., Hollywood, K. A., Dunstan, M. S., . . . Scrutton, N. S. (2020). Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers. METABOLIC ENGINEERING, 60, 168-182. doi:10.1016/j.ymben.2020.04.008DOI: 10.1016/j.ymben.2020.04.008
The RESOLUTE consortium: unlocking SLC transporters for drug discovery (Journal article)
Superti-Furga, G., Lackner, D., Wiedmer, T., Ingles-Prieto, A., & Steppan, C. M. (2020). The RESOLUTE consortium: unlocking SLC transporters for drug discovery. NATURE REVIEWS DRUG DISCOVERY, 19(7), 429-430. doi:10.1038/d41573-020-00056-6DOI: 10.1038/d41573-020-00056-6
Khemchandani, Y., O'Hagan, S., Samanta, S., Swainston, N., Roberts, T., Bollegala, D., & Kell, D. (2020). DeepGraphMol, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. doi:10.21203/rs.3.rs-32446/v1DOI: 10.21203/rs.3.rs-32446/v1
<i>DNA Scanner</i>: a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors (Journal article)
Doci, G., Fuchs, L., Kharbanda, Y., Schickling, P., Zulkower, V., Hillson, N., . . . Kabisch, J. (2020). <i>DNA Scanner</i>: a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors. SYNTHETIC BIOLOGY, 5(1). doi:10.1093/synbio/ysaa011DOI: 10.1093/synbio/ysaa011
2019
Currin, A., Kwok, J., Sadler, J. C., Bell, E. L., Swainston, N., Ababi, M., . . . Kell, D. B. (2019). GeneORator: An Effective Strategy for Navigating Protein Sequence Space More Efficiently through Boolean OR-Type DNA Libraries. ACS SYNTHETIC BIOLOGY, 8(6), 1371-1378. doi:10.1021/acssynbio.9b00063DOI: 10.1021/acssynbio.9b00063
Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in <i>Escherichia coli</i> (Journal article)
Jervis, A. J., Carbonell, P., Vinaixa, M., Dunstan, M. S., Hollywood, K. A., Robinson, C. J., . . . Scrutton, N. S. (2019). Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in <i>Escherichia coli</i>. ACS SYNTHETIC BIOLOGY, 8(1), 127-136. doi:10.1021/acssynbio.8b00398DOI: 10.1021/acssynbio.8b00398
Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries (Journal article)
Currin, A., Swainston, N., Dunstan, M. S., Jervis, A. J., Mulherin, P., Robinson, C. J., . . . Breitling, R. (2019). Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries. SYNTHETIC BIOLOGY, 4(1). doi:10.1093/synbio/ysz025DOI: 10.1093/synbio/ysz025
2018
Carbonell, P., Jervis, A. J., Robinson, C. J., Yan, C., Dunstan, M., Swainston, N., . . . Scrutton, N. S. (2018). An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. COMMUNICATIONS BIOLOGY, 1. doi:10.1038/s42003-018-0076-9DOI: 10.1038/s42003-018-0076-9
Rationalizing Context-Dependent Performance of Dynamic RNA Regulatory Devices (Journal article)
Kent, R., Halliwell, S., Young, K., Swainston, N., & Dixon, N. (2018). Rationalizing Context-Dependent Performance of Dynamic RNA Regulatory Devices. ACS SYNTHETIC BIOLOGY, 7(7), 1660-1668. doi:10.1021/acssynbio.8b00041DOI: 10.1021/acssynbio.8b00041
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts (Journal article)
Swainston, N., Dunstan, M., Jervis, A. J., Robinson, C. J., Carbonell, P., Williams, A. R., . . . Kell, D. B. (2018). PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. Bioinformatics, 34(13), 2327-2329. doi:10.1093/bioinformatics/bty105DOI: 10.1093/bioinformatics/bty105
Selenzyme: enzyme selection tool for pathway design (Journal article)
Carbonell, P., Wong, J., Swainston, N., Takano, E., Turner, N. J., Scrutton, N. S., . . . Faulon, J. -L. (2018). Selenzyme: enzyme selection tool for pathway design. BIOINFORMATICS, 34(12), 2153-2154. doi:10.1093/bioinformatics/bty065DOI: 10.1093/bioinformatics/bty065
Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase (Journal article)
Currin, A., Dunstan, M. S., Johannissen, L. O., Hollywood, K. A., Vinaixa, M., Jervis, A. J., . . . Scrutton, N. S. (2018). Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase. ACS CATALYSIS, 8(3), 2012-2020. doi:10.1021/acscatal.7b04115DOI: 10.1021/acscatal.7b04115
CodonGenie: optimised ambiguous codon design tools (Journal article)
Swainston, N., Currin, A., Green, L., Breitling, R., Day, P. J., & Kell, D. B. (n.d.). CodonGenie: optimised ambiguous codon design tools. doi:10.7287/peerj.preprints.2797DOI: 10.7287/peerj.preprints.2797
Fast and Flexible Synthesis of Combinatorial Libraries for Directed Evolution (Chapter)
Sadler, J. C., Green, L., Swainston, N., Kell, D. B., & Currin, A. (2018). Fast and Flexible Synthesis of Combinatorial Libraries for Directed Evolution. In ENZYMES IN SYNTHETIC BIOLOGY (Vol. 608, pp. 59-79). doi:10.1016/bs.mie.2018.04.006DOI: 10.1016/bs.mie.2018.04.006
2017
A Metabolic Reaction Balancing Web Service for Computational Systems Biology (Journal article)
Dobson, P., Mendes, P., Kell, D., & Swainston, N. (2017). A Metabolic Reaction Balancing Web Service for Computational Systems Biology. doi:10.1101/187328DOI: 10.1101/187328
Swainston, N., Batista-Navarro, R., Carbonell, P., Dobson, P. D., Dunstan, M., Jervis, A. J., . . . Breitling, R. (n.d.). biochem4j: Integrated and extensible biochemical knowledge through graph databases. PLOS ONE, 12(7). doi:10.1371/journal.pone.0179130DOI: 10.1371/journal.pone.0179130
CodonGenie: optimised ambiguous codon design tools (Journal article)
Swainston, N., Currin, A., Green, L., Breitling, R., Day, P. J., & Kell, D. B. (2017). CodonGenie: optimised ambiguous codon design tools. PEERJ COMPUTER SCIENCE. doi:10.7717/peerj-cs.120DOI: 10.7717/peerj-cs.120
SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution (Chapter)
Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2017). SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution. In SYNTHETIC DNA: METHODS AND PROTOCOLS (Vol. 1472, pp. 63-78). doi:10.1007/978-1-4939-6343-0_5DOI: 10.1007/978-1-4939-6343-0_5
2016
SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production (Journal article)
Le Feuvre, R. A., Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A. J., . . . Turner, N. J. (2016). SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, 1(4), 271-275. doi:10.1016/j.synbio.2016.07.001DOI: 10.1016/j.synbio.2016.07.001
Recon 2.2: from reconstruction to model of human metabolism (Journal article)
Swainston, N., Smallbone, K., Hefzi, H., Dobson, P. D., Brewer, J., Hanscho, M., . . . Mendes, P. (2016). Recon 2.2: from reconstruction to model of human metabolism. METABOLOMICS, 12(7). doi:10.1007/s11306-016-1051-4DOI: 10.1007/s11306-016-1051-4
SYNBIOCHEM - a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals (Journal article)
Carbonell, P., Currin, A., Dunstan, M., Fellows, D., Jervis, A., Rattray, N. J. W., . . . Turner, N. J. (2016). SYNBIOCHEM - a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. BIOCHEMICAL SOCIETY TRANSACTIONS, 44, 675-677. doi:10.1042/BST20160009DOI: 10.1042/BST20160009
libChEBI: an API for accessing the ChEBI database (Journal article)
Swainston, N., Hastings, J., Dekker, A., Muthukrishnan, V., May, J., Steinbeck, C., & Mendes, P. (2016). libChEBI: an API for accessing the ChEBI database. JOURNAL OF CHEMINFORMATICS, 8. doi:10.1186/s13321-016-0123-9DOI: 10.1186/s13321-016-0123-9
2015
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs (vol 11, pg 323, 2015) (Journal article)
O'Hagan, S., Swainston, N., Handl, J., & Kell, D. B. (2015). A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs (vol 11, pg 323, 2015). METABOLOMICS, 11(2), 340. doi:10.1007/s11306-014-0745-8DOI: 10.1007/s11306-014-0745-8
Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis (Journal article)
Kell, D. B., Swainston, N., Pir, P., & Oliver, S. G. (2015). Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. TRENDS IN BIOTECHNOLOGY, 33(4), 237-246. doi:10.1016/j.tibtech.2015.02.001DOI: 10.1016/j.tibtech.2015.02.001
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently (Journal article)
Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2015). Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. CHEMICAL SOCIETY REVIEWS, 44(5), 1172-1239. doi:10.1039/c4cs00351aDOI: 10.1039/c4cs00351a
2014
GeneGenie: optimized oligomer design for directed evolution (Journal article)
Swainston, N., Currin, A., Day, P. J., & Kell, D. B. (2014). GeneGenie: optimized oligomer design for directed evolution. NUCLEIC ACIDS RESEARCH, 42(W1), W395-W400. doi:10.1093/nar/gku336DOI: 10.1093/nar/gku336
SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution (Journal article)
Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2014). SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution. PROTEIN ENGINEERING DESIGN & SELECTION, 27(9), 273-280. doi:10.1093/protein/gzu029DOI: 10.1093/protein/gzu029
2013
Path2Models: large-scale generation of computational models from biochemical pathway maps (Journal article)
Buechel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., . . . Le Novere, N. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC SYSTEMS BIOLOGY, 7. doi:10.1186/1752-0509-7-116DOI: 10.1186/1752-0509-7-116
A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes (Journal article)
Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., . . . Mendes, P. (2013). A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS LETTERS, 587(17), 2832-2841. doi:10.1016/j.febslet.2013.06.043DOI: 10.1016/j.febslet.2013.06.043
An analysis of a 'community-driven' reconstruction of the human metabolic network (Journal article)
Swainston, N., Mendes, P., & Kell, D. B. (2013). An analysis of a 'community-driven' reconstruction of the human metabolic network. METABOLOMICS, 9(4), 757-764. doi:10.1007/s11306-013-0564-3DOI: 10.1007/s11306-013-0564-3
A community-driven global reconstruction of human metabolism (Journal article)
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., . . . Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. NATURE BIOTECHNOLOGY, 31(5), 419-+. doi:10.1038/nbt.2488DOI: 10.1038/nbt.2488
2012
Improving metabolic flux predictions using absolute gene expression data (Journal article)
Lee, D., Smallbone, K., Dunn, W. B., Murabito, E., Winder, C. L., Kell, D. B., . . . Swainston, N. (2012). Improving metabolic flux predictions using absolute gene expression data. BMC SYSTEMS BIOLOGY, 6. doi:10.1186/1752-0509-6-73DOI: 10.1186/1752-0509-6-73
2011
The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. (Journal article)
Swainston, N., Smallbone, K., Mendes, P., Kell, D., & Paton, N. (2011). The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.. Journal of integrative bioinformatics, 8(2), 186. doi:10.2390/biecoll-jib-2011-186DOI: 10.2390/biecoll-jib-2011-186
2010
Systematic integration of experimental data and models in systems biology (Journal article)
Li, P., Dada, J. O., Jameson, D., Spasic, I., Swainston, N., Carroll, K., . . . Paton, N. W. (2010). Systematic integration of experimental data and models in systems biology. BMC BIOINFORMATICS, 11. doi:10.1186/1471-2105-11-582DOI: 10.1186/1471-2105-11-582
Further developments towards a genome-scale metabolic model of yeast (Journal article)
Dobson, P. D., Smallbone, K., Jameson, D., Simeonidis, E., Lanthaler, K., Pir, P., . . . Mendes, P. (2010). Further developments towards a genome-scale metabolic model of yeast. BMC SYSTEMS BIOLOGY, 4. doi:10.1186/1752-0509-4-145DOI: 10.1186/1752-0509-4-145
Enzyme kinetics informatics: from instrument to browser (Journal article)
Swainston, N., Golebiewski, M., Messiha, H. L., Malys, N., Kania, R., Kengne, S., . . . Rojas, I. (2010). Enzyme kinetics informatics: from instrument to browser. FEBS JOURNAL, 277(18), 3769-3779. doi:10.1111/j.1742-4658.2010.07778.xDOI: 10.1111/j.1742-4658.2010.07778.x
2009
Information management for high content live cell imaging (Journal article)
Jameson, D., Turner, D. A., Ankers, J., Kennedy, S., Ryan, S., Swainston, N., . . . Paton, N. W. (2009). Information management for high content live cell imaging. BMC BIOINFORMATICS, 10. doi:10.1186/1471-2105-10-226DOI: 10.1186/1471-2105-10-226
Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics (Journal article)
Brown, M., Dunn, W. B., Dobson, P., Patel, Y., Winder, C. L., Francis-McIntyre, S., . . . Kell, D. B. (2009). Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. ANALYST, 134(7), 1322-1332. doi:10.1039/b901179jDOI: 10.1039/b901179j
2008
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology (Journal article)
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., . . . Kell, D. B. (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. NATURE BIOTECHNOLOGY, 26(10), 1155-1160. doi:10.1038/nbt1492DOI: 10.1038/nbt1492
2007
Capture and analysis of quantitative proteomic data (Journal article)
Lau, K. W., Jones, A. R., Swainston, N., Siepen, J. A., & Hubbard, S. J. (2007). Capture and analysis of quantitative proteomic data. PROTEOMICS, 7(16), 2787-2799. doi:10.1002/pmic.200700127DOI: 10.1002/pmic.200700127
Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., . . . Oliver, S. G. (2007). Growth control of the eukaryote cell: a systems biology study in yeast.. Journal of biology, 6(2), 4. doi:10.1186/jbiol54DOI: 10.1186/jbiol54
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ™ (Journal article)
Siepen, J. A., Swainston, N., Jones, A. R., Hart, S. R., Hermjakob, H., Jones, P., & Hubbard, S. J. (2007). An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ™. PROTEOME SCIENCE, 5. doi:10.1186/1477-5956-5-4DOI: 10.1186/1477-5956-5-4
