Peer-Reviewed Publications

2018

Organisation of feed-forward loop motifs reveals architectural principles in natural and engineered networks
Gorochowski T.E., Grierson C.S., di Bernardo M.
Science Advances 4, eaap9751, 2018.

Burden-driven feedback control of gene expression
Ceroni F., Boo A., Furini S., Gorochowski T.E., Borkowski O., Ladak Y.N., Awan A.R., Gilbert C., Stan G.B., Ellis T.
Nature Methods , , 2018.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0
Cox R.S., Madsen, C., McLaughlin J., Nguyen T., Roehner N., Bartley B., Bhatia S., Bissell M, Clancy K., Gorochowski T.E., Grunberg R., Luna A., Le Novere N., Pocock M., Sauro H., Sexton J.T., Stan G.-B., Tabor J.J., Voigt C.A., Myers C., Beal J., Wipat A.
Journal of Integrative Bioinformatics , 20170074, 2018.

Automated visualization of genetic designs using DNAplotlib
Bartoli V., Dixon D.O.R., Gorochowski T.E.
In: Braman J. (ed.) Synthetic Biology: Methods and Protocols, Methods in Molecular Biology, 2018. (in press)

2017

Genetic circuit characterization and debugging using RNA-seq
Gorochowski T.E., Espah Borujeni A., Park Y., Nielsen A.A.K., Zhang J., Der B.S., Gordon D.B., Voigt C.A.
Molecular Systems Biology 13, 952, 2017.

How behaviour and the environment influence transmission in mobile groups
Gorochowski T.E., Richardson T.O.
In: Masuda N., Holme P. (eds.) Temporal Network Epidemiology. Theoretical Biology. , Springer, Singapore, 2017.

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.

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 6, 1115-1119, 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.

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.

Pre-Prints