Publications

2017

Organisation of feed-forward loop motifs reveals architectural principles in natural and engineered networks

Gorochowski T.E., Grierson C.S., di Bernardo M.
bioRxiv 188821, 10.1101/188821, 2017.

Burden-driven feedback control of gene expression

Ceroni F., Furini S., Gorochowski T.E., Boo A., Borkowski O., Ladak Y.N., Awan A.R., Gilbert C., Stan G.B., Ellis T.
bioRxiv 177030, 10.1101/177030, 2017.

Automated visualization of genetic designs using DNAplotlib

Bartoli V., Dixon D.O.R., Gorochowski T.E.
Methods in Molecular Biology, Synthetic Biology. (submitted)

How behaviour and the environment influence transmission in mobile groups

Gorochowski T.E., Richardson T.O.
Temporal Network Epidemiology, 2017. (in press)

A standard-enabled workflow for synthetic biology

Myers C.J., Beal J., Gorochowski T.E., Kuwahara H., Madsen C., McLaughlin J.A., Mısırlı G., Nguyen T., Oberortner E., Samineni M., Wipat A., Zhang M., Zundel Z.
Biochemical Society Transactions 45, 793-803, 2017.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

Woodruff L., Gorochowski T.E., Roehner N., Mikkelsen T., Densmore D., Gordon D.B., Nicol R., Voigt C.A.
Nucleic Acids Research 45, 1553-1565, 2017.

2016

Agent-based modelling in synthetic biology

Gorochowski T.E.
Essays in Biochemistry 60, 325-336, 2016.

DNAplotlib: programmable visualization of genetic designs and associated data

Der B.S., Glassey E., Bartley B.A., Enghuus C., Goodman D.B., Gordon D.B., Voigt C.A., Gorochowski T.E.
ACS Synthetic Biology, 2016. (online)

A minimal model of ribosome allocation dynamics captures trade-offs in expression between endogenous and synthetic genes

Gorochowski T.E., Avcilar-Kucukgoze I., Bovenberg R.A.L., Roubos J.A., Ignatova Z.
ACS Synthetic Biology 5, 710-720, 2016.

2015

Memory and combinatorial logic based on DNA inversions: dynamics and evolutionary stability

Fernandez-Rodriguez J., Yang L., Gorochowski T.E., Gordon D.B., Voigt C.A.
ACS Synthetic Biology 4, 1361-1372, 2015.

Beyond close-proximity interactions: the role of spatial coincidence in transmission networks

Richardson T.O., Gorochowski T.E.
Journal of the Royal Society Interface 12, 111, 2015.

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Gorochowski T.E., Ignatova Z., Bovenberg R.A.L., Roubos J.A.
Nucleic Acids Research 43, 2993-3011, 2015.

2014

Computational modelling and analysis of hippocampal-prefrontal information coding during a spatial decision-making task

Jahans-Price T., Gorochowski T.E., Wilson M., Jones M.W., Bogacz R.
Frontiers in Behavioral Neuroscience 8, 62, 2014.

Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli

Gorochowski T.E., van den Berg E., Kerkman R., Roubos J.A., Bovenberg R.A.L.
ACS Synthetic Biology 3, 129-139, 2014.

2013

Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability

Wohlgemuth S.E., Gorochowski T.E., Roubos J.A.
Nucleic Acids Research 41, 8021-8033, 2013.

2012

BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology

Gorochowski T.E., Matyjaszkiewicz A., Todd T., Oak N., Kowalska K., Reid S., Tsaneva-Atanasova K.T., Savery N.J., Grierson C.S., di Bernardo M.
PLoS ONE 7, e42790, 2012.

Using aging to visually uncover evolutionary processes on networks

Gorochowski T.E., di Bernardo M., Grierson C.S.
IEEE Transactions on Visualization and Computer Graphics 18, 1343-1352, 2012.

Evolving dynamical networks: a formalism for describing complex systems

Gorochowski T.E., di Bernardo M., Grierson C.S.
Complexity 17, 18-25, 2012.

2010

Synchronization and control of complex networks via contraction, adaptation and evolution

DeLellis P., di Bernardo M., Gorochowski T.E., Russo G.
IEEE Circuits and Systems Magazine: Special Issue on Complex Networks 10, 64-82, 2010.

A dynamical approach to the evolution of complex networks

Gorochowski T.E., di Bernardo M., Grierson C.S.
Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems , 1083-1087, 2010.

Evolving enhanced topologies for the synchronization of dynamical complex networks

Gorochowski T.E., di Bernardo M., Grierson C.S.
Physical Review E 81, 23690, 2010.