Source: http://www.synbio.ed.ac.uk/publications-0
Timestamp: 2019-04-20 14:52:31+00:00

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Our research is currently being published in high-impact journals and we share a range of tools and platforms with the wider community.
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, 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.
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 17th 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.
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.
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.
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.
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.
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.
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.
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.
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.
Stevenson K, McVey AF, Clark IB, Swain PS, Pilizota T. (2016) ‘General calibration of microbial growth in microplate readers’. Sci Rep. 6:38828.
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.
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.
Waites W, Cavaliere M, Cachat E, Danos V, Davies JA (2018) ‘An information-theoretic measure for patterning in epithelial tissues.’ Under review.
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.

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