Publications

A list of publications:

Balmer, A, Calvert, J, Marris, C, Molyneux-Hodgson, S, Frow, E, Kearnes, M, Bulpin, K, Schyfter, P, Mackenzie, A, 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): 3-25.

Balmer, A, Calvert, J, Marris, C, Molyneux-Hodgson, S, Frow, E, Kearnes, M, Bulpin, K, Schyfter, P, Mackenzie, A,  Martin, P. (2016)  ‘Five Rules of Thumb for Post-ELSI Interdisciplinary Collaborations’ Journal of Responsible Innovation 3 (1): 73-80.

Bates, M., Lachoff, J., Meech, D., Zulkower, V., Moisy, A., Luo, Y., et al. (2017). ‘Genetic Constructor: An Online DNA Design Platform’. ACS Synthetic Biology, acssynbio.7b00236.

Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. (2016) ‘Genome Enginering. The Genome Project-Write.’ Science. 353(6295):126-7.

Bowyer J, Jia Zhao, Rosser S, Colloms S, Bates D. (2015) ‘Development and experimental validation of a mechanistic model of in vitro recombination’ IEEE Eng Med Biol. 2015:945-8.

Bowyer J, Zhao J, Subsoontorn P, Wong W, Rosser S, Bates D. (2016) ‘Mechanistic Modeling of a Rewritable Recombinase Addressable Data Module.’ IEEE Trans Biomed Circuits Syst. 10(6):1161-1170.

Bressan RB, Dewari PS, Kalantzaki M, Gangoso E, Matjusaitis M, Garcia-Diaz C, Blin C, Grant V, Bulstrode H, Gogolok S, Skarnes WC & Pollard SM (2017) ‘Efficient CRISPR/Cas9-assisted gene targeting enables rapid and precise genetic manipulation of mammalian neural stem cells.’ Development 144, 635–648.

Bulstrode H, Johnstone E, Marqués-Torrejón MÁ, Ferguson KM, Bressan RB, Blin C, Grant V, Gogolok S, Gangoso E, Gagrica S, Ender C, Fotaki V, Sproul D, Bertone P & Pollard SM (2017) ‘Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators.’ Genes & development 31, 757–773.

Cachat E, Liu W, Davies JA (2017) .Synthetic self-patterning and morphogenesis in mammalian cells: a proof-of-concept step towards the goal of synthetic tissue development.. IET Engineering Biology doi: 10.1049/enb.2017.0013

Cachat E, Liu W, Martin KC, Yuan X, Yin H, Hohenstein P, Davies JA (2016) .2- and 3-dimensional synthetic de novo large-scale patterning by mammalian cells through phase separation.. Scientific Reports 6:20664. doi: 10.1038/srep20664.

Calvert, J and Schyfter, P (2017) ‘What can Science and Technology Studies learn from art and design? Reflections on Synthetic Aesthetics’ Social Studies of Science 47(2): 195-215.

Calvert, J (2014) ‘Governing in the context of uncertainty’ commentary in the special edition ‘Synthetic future: can we create what we want out of synthetic biology?’ Hastings Center Report 44(6): S31-S33

Cavaliere, M, Yang, G, Danos, V, & Dakos, V. (2016) ‘Detecting the Collapse of Cooperation in Evolving Networks’. Nature Scientific Reports, 6.

Cavaliere, M. and Sanchez, A. ‘The Evolutionary Resilience of Distributed Cellular Computing.’ Proceedings of the 17^th Int. Conference on Membrane Computing, CMC17, Lecture Notes in Computer Science, LNCS, Springer, to appear.

Craig, T., Holland, R., D'Amore, R., Johnson, J. R., McCue, H. V., West, A., et al. (2017). ‘Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.’ ACS Synthetic Biology, acssynbio.7b00212.

Davies JA and Cachat E. (2016) ‘Synthetic biology meets tissue engineering.’ Biochem Soc Trans. 2016 Jun 15;44(3):696-701.

Davies J. A. (2017) ‘Using synthetic biology to explore principles of development’. Review for Development. 144: 1146-1158

Davies JA (2017) ‘The inter-dependence of basic and applied biomedical sciences: lessons from kidney development and tissue-engineering.’ Porto Biomed J. 2: 136-139

Ellis T, Cai Y. ‘Synthetic Biology in Europe.’ (2016) ACS Synth Biol. Oct 21;5(10):1033.

Erliandri, I., F. Haiqing, M. Nakano, J.-H. Kim, K.H. Miga, M. Liskovykh, W.C. Earnshaw, H. Masumoto, N. Kouprina, M.I. Aladjem, Vladimir Larionov. (2015). ‘Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome’. Nucleic Acids Res. 42:11502-11516. 

Fletcher, L, Rosser, S, Elfick, A. (2016) ‘Exploring Synthetic and Systems Biology at the University of Edinburgh.’Biochem Soc Trans. Jun 15;44(3):692-5.

Fletcher, E and Rosser S. ‘Synthetic Biology – Engineering Tomorrow’s Medicines’ in Engineering Health, Royal Society of Chemistry 2017 ISBN 978-1-78262-084-6

Fogg PC, Colloms S, Rosser SJ, Stark M, Smith MC. (2014) ‘New applications for phage integrases.’ J Mol Biol.  Jul 29;426(15):2703-16

Gogolok, S., Garcia-Diaz, C. & Pollard, S. M. (2016) ‘STAR: a simple TAL effector assembly reaction using isothermal assembly’.  Sci. Rep. 1–9 (DOI:10.1038/srep33209)

Kanigowska P, Shen Y, Zheng Y, Rosser S, Cai Y. (2016) ‘Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology.’ J Lab Autom Feb;21(1):49-56.

Kim J.H., H.S. Lee, N.C. Lee, N.V. Goncharov, V. Kumeiko, H. Masumoto, W.C. Earnshaw, N. Kouprina, V. Larionov (2016). ‘Development of a novel HAC-based "gain of signal" quantitative assay for measuring chromosome instability (CIN) in cancer cells.’  Oncotarget 7:14841-14856. 

Kleinjan DA, Wardrope C, Nga Sou S, Rosser SJ. (2017) ‘Drug-tunable multidimensional synthetic gene control using inducible degron-tagged dCas9 effectors.’ Nat Commun. Oct 30;8(1):1191

Kononenko, A.V., R. Bansal  N.C.O Lee, B.R. Grimes, H. Masumoto, W.C. Earnshaw, V. Larionov, N. Kouprina. (2014). ‘A portable BRCA1-HAC module for analysis of BRCA1 tumor suppressor function’. Nucleic Acids Res. Vol. 42, No. 21, e164, 01.12.2014.

Kononenko, A., N.C.O. Lee, M. Liskovykh, H. Masumoto, W.C. Earnshaw, V. Larionov, N. Kouprina, (2014) ‘Generation of a conditionally self-eliminating HAC gene delivery vector through incorporation of a tTAVP64 expression cassette’.  Nucleic Acids Res. 43: e57

Lee N.C.O, J.H. Kim, N. Petrov, H.S. Lee, H. Masumoto, W.C. Earnshaw, V. Larionov and N. Kouprina (2017). ‘Method to assemble genomic DNA fragments or genes on Human Artificial Chromosome with regulated kinetochore using a multi-integrase system.’ ACS Synth Biol. 7:63-74.

Markakis K, De la Heras A, Elfick A (2017) ‘An analytical approach for the calculation of promoter activities based on fluorescent protein expression data.’ IET Engineering Biology 1(2), 77-85

Martella A, Pollard SM, Dai J, Cai Y. Mammalian (2016) ‘Synthetic Biology: Time for Big MACs.’ ACS Synth Biol. Oct 21;5(10):1040-1049.

Martella, A., Matjusaitis, M., Auxillos, J., Pollard, S.M., Cai, Y. (2017) ‘EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.’ ACS Synthetic Biology, 6(7) pp. 1380 - 1392

Martin, K.C., Yuan, X., Stimac, G., Bannerman, K., Anderson, J., Roy, C., Glykofrydis, F., Yin, H., Davies, J.A. (2017) ‘Symmetry-breaking in branching epithelia: Cells on micro-patterns under flow challenge the hypothesis of positive feedback by a secreted autocrine inhibitor of motility.’ Journal of Anatomy Article in Press

Martins, N.M.C., J. Bergmann, N. Shono, H. Kimura, V.Larionov, H. Masumoto and W.C. Earnshaw. (2015). ‘Epigenetic engineering shows that a human centromere resists silencing mediated by H3K27me3/K9me3.’ Mol. Biol. Cell. 27:177-196.

Merrick CA, Zhao J, Rosser SJ. (2018) ‘Serine Integrases: Advancing Synthetic Biology.’ ACS Synth Biol 7(2):299-310

Mittra, J., Mastroeni, M. and Tait, J. (2014) Engaging with Uncertainty and Risk in Agricultural Biotechnology Regulation: Delivering Safety and Innovation. Report from ESRC Knowledge Exchange Project with Syngenta, Jan. 2014. http://innogen.ac.uk/reports/883

Molina, O., N. Kouprina, H. Masumoto, V. Larionov and W.C. Earnshaw (2017) ‘Using human artificial chromosomes to study centromere assembly and function.’ Chromosoma 126:559-575. 

Molina O., M. Carmena, I.E. Maudlin & William C. Earnshaw. (2016). ‘PREditOR: a synthetic biology approach to removing heterochromatin from cells.’ Chromosome Res. 24:495-509. 

Molina O., G. Vargiu, M.A. Abad1, A. Zhiteneva, J. Arulanandam, H. Masumoto, N. Kouprina, V. Larionov and William C Earnshaw. (2016) ‘Epigenetic engineering reveals a balance between histone modifications and transcription in kinetochore maintenance.’ Nature Commun. 7:13334. 

Ohzeki J., N.Shono, K. Otake, N.M.C. Martins, K. Kugou, H. Kimura, T. Nagase, V. Larionov, W.C. Earnshaw and H. Masumoto. (2016). ‘KAT7/HBO1/MYST2 regulates CENP-A chromatin assembly by antagonizing Suv39h1-mediated centromere inactivation.’ Dev. Cell. 37:413-27.

Ohzeki J, Larionov V, Earnshaw WC, Masumoto H. (2015). ‘Genetic and epigenetic regulation of centromeres: a look at HAC formation.’ Chromosome Res. 23:87-103. 

Olorunniji FJ, McPherson AL, Rosser SJ, Smith MCM, Colloms SD, Stark WM. (2017) ‘Control of serine integrase recombination directionality by fusion with the directionality factor.’ Nucleic Acids Res. Jun 28.

Olorunniji FJ, Merrick C, Rosser SJ, Smith MCM, Stark WM, Colloms SD. (2017) ‘Multipart DNA Assembly Using Site-Specific Recombinases from the Large Serine Integrase Family.’ Methods Mol Biol 1642:303-323

Olorunniji FJ, Rosser SJ, Marshall Stark W. (2017) ‘Purification and In Vitro Characterization of Zinc Finger Recombinases’. Methods Mol Biol.;1642:229-245

Olorunniji FJ, Rosser SJ, Stark WM. (2016) ‘Site-specific recombinases: molecular machines for the Genetic Revolution.’ Biochem J. 15;473(6):673-84

Pesenti E., N. Kouprina, M. Liskovykh, J. Aurich-Costa, V. Larionov, H. Masumoto, W.C. Earnshaw and O. Molina. (2018). ‘Generation of a synthetic human chromosome with two centromeric domains for advanced epigenetic engineering studies.’ ACS Synthetic Biology, in press. 

Quinn JY, et al.(2015) ‘SBOL Visual: A Graphical Language for Genetic Designs.’ PLoS Biol. Dec 3;13(12):e1002310.

Schyfter, P and Calvert, J (2015) ‘Intentions, expectations and institutions: engineering the future of synthetic biology in the US and the UK.’ Science as Culture 24 (4): 359–383

Shono, N., J. Ohzeki, K. Otake, N.M.C Martins, T. Nagase, H. Kimura, V. Larionov, W.C. Earnshaw, and H. Masumoto (2015). ‘CENP-C and CENP-I are key connecting factors for kinetochore and CENP-A assembly.’ J. Cell Sci. 128: 4572-4587

Swain PS, Stevenson K, Leary A, Montano-Gutierrez LF, Clark IB, Vogel J, Pilizota T. (2016) ‘Inferring time derivatives including cell growth rates using Gaussian processes.’ Nat Commun. 7:13766

Stevenson K, McVey AF, Clark IB, Swain PS, Pilizota T. (2016) ‘General calibration of microbial growth in microplate readers’. Sci Rep. 6:38828.

Tabriz, A.G., Mills, C.G., Mullins, J.J., Davies, J.A. Shu, W. (2017) ‘Rapid fabrication of cell-laden alginate hydrogel 3D structures by micro dip-coating’. Frontiers in Bioengineering and Biotechnology. 5:13

Tait, J. (2016) ‘Environmental Regulation of Advanced Innovative Biotechnologies: Anticipating future regulatory oversight.’ Report to ShARE Group of Environment Agencies of the UK and Republic of Ireland. (http://www.sepa.org.uk/media/219333/environmental-regulation-of-advanced-innovative-biotechnologies-anticipating-future-regulatory-oversight.pdf) 

Tait, J., (2014) ‘Bringing it all Together’. In Annual Report of the Government Chief Scientific Adviser, 2014. Innovation: Managing Risk not Avoiding It. Evidence and Case Studies, pp 129-136  (https://www.gov.uk/government/publications/innovation-managing-risk-not-avoiding-it)

Tait, J., Banda, G., Watkins, A. (2017) ‘Proportionate and adaptive governance of innovative technologies (PAGIT): A framework to guide policy and regulatory decision making’ Innogen Institiute: https://www.innogen.ac.uk/reports/1222

Tait, J et al Committee on Gene Drive Research in Non-human Organisms: Recommendations for Responsible Conduct (2016). Gene Drives on the Horizon: Advancing Science, Navigating Uncertainty and Aligning Research with Public Values. Washington DC, the National Academies Press.

Tait, J. and Banda, G. (2016) Proportionate and Adaptive Governance of Innovative Technologies: the role of regulations, guidelines and standards. Full Report to British Standards Institution. (http://www.bsigroup.com/research-pagit-uk)

Tillotson, R., J. Selfridge, M. V. Koerner, K. K. E. Gadalla, J. Guy, D. De Sousa, R. D. Hector, S. R. Cobb and A. Bird (2017). ‘Radically truncated MeCP2 rescues Rett syndrome-like neurological defects.’ Nature 550(7676): 398-401.

Trubitsyna M, Michlewski G, Finnegan DJ, Elfick A, Rosser SJ, Richardson JM, French CE. (2017) ‘Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection.’ Nucleic Acids Res. doi: 10.1093/nar/gkx113.

Tsikritsis D, Shi H, Wang Y, Velugotla S, Srsen V, Elfick APD, Downes AR (2016) ‘Label-Free biomarkers of human embryonic stem cell differentiation’. Cytometry: Part A 89 (6) 575-584

Waites W, Cavaliere M, Cachat E, Danos V, Davies JA (2018) ‘Organoid and tissue patterning through phase separation: Use of a vertex model to relate dynamics of patterning to underlying biophysical parameters.’ bioRxiv 136366, 2017. Pending publication

Waites W, Cavaliere M, Cachat E, Danos V, Davies JA (2018) ‘An information-theoretic measure for patterning in epithelial tissues.’ Under review.

Wintle et al. (2017) ‘A transatlantic perspective on 20 emerging issues in biological engineering.’ eLife, 6:e30247

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. Chem Soc Rev. Nov 27;46(23):7191-7207

 

Other tools for the Community include:

SynPharm: A freely accessible database of ligand-responsive protein sequences, derived from interactions from the Guide to PHARMACOLOGY and using data from the Protein Data Bank.

More information can be found here

Research Development Management Systems. More information about data management systems can be found here