Publications

Selected works

Bartoli et al. Nature Communications 2020.

Developing tunable genetic parts for engineering self-adaptive biosystems.

Gorochowski et al. Science Advances 2018.

Learning how to build complex networks from simple regulatory motifs.

Gorochowski et al. Molecular Systems Biology 15, e8719, 2019.

Sequencing methods to characterise genetic parts and circuits in absolute units.

Boo et al. Nature Methods 15, 387-393, 2018.

Burden-driven feedback control of gene expression for robust biosystems.

Gorochowski et al. Molecular Systems Biology 2017.

Debugging complex genetic circuitry with RNA sequencing.

Pre-prints

An engineering theory of evolution
Castle S.D., Grierson C.S., Gorochowski T.E.
Preprints, 2020080574, 2020.

Harnessing the central dogma for stringent multi-level control of gene expression
Greco F.V., Grierson C.S., Gorochowski T.E.
bioRxiv, 2020.07.04.187500, 2020.

Cheetah: a computational toolkit for cybergenetic control
Pedone E., de Cesare I., Zamora C., Haener D., Postiglione L., Shannon B., Savery N., Grierson C.S., di Bernardo M., Gorochowski T.E., Marucci L.
bioRxiv, 2020.06.25.171751, 2020.

All published works

2020

Precision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads
Park Y., Borujeni A.E., Gorochowski T.E., Shin J., Voigt C.A.
Molecular Systems Biology 16, e9584, 2020.

Advances in engineering CRISPR-Cas9 as a molecular Swiss Army knife
Meaker G.A., Hair E.J., Gorochowski T.E.
Synthetic Biology , , 2020.

Characterizing genetic parts and devices using RNA sequencing
Vipin D., Ignatova Z., Gorochowski T.E.
In: Menolascina F. (eds) Synthetic Gene Circuits: Methods and Protocols, Methods in Molecular Biology, Springer, 2020. (in press)

Self-adaptive biosystems through tunable genetic parts and circuits
Bartoli V., di Bernardo M., Gorochowski T.E.
Current Opinion in Systems Biology 24, 78-85, 2020.

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
McLaughlin J.A., Beal J., Misirli G., Grünberg R., Bartley B.A., Scott-Brown J., Vaidyanathan P., Fontanarrosa P., Oberortner E., Wipat A., Gorochowski T.E., Myers C.J.
Frontiers in Bioengineering and Biotechnology 8, 1009, 2020.

Sequencing enabling design and learning in synthetic biology
Gilliot P.A., Gorochowski T.E.
Current Opinion in Chemical Biology 58, 54-62, 2020.

Towards engineering biosystems with emergent collective functions
Gorochowski T.E., Hauert S., Kreft J.-U., Marucci L., Stillman N.R., Tang T.-Y.D., Bandiera L., Bartoli V., Dixon D.O.R., Fedorec A.J.H., Fellermann H., Fletcher A.G., Foster T., Giuggioli L., Matyjaszkiewicz A., McCormick S., Montes Olivas S., Naylor J., Rubio Denniss A., Ward D.
Frontiers in Bioengineering and Biotechnology 8, 705, 2020.

Tunable genetic devices through simultaneous control of transcription and translation
Bartoli V., Meaker G.A., di Bernardo M., Gorochowski T.E.
Nature Communications 11, 2095, 2020.

  • 'Behind the Paper' at the Nature Biotechnology Community (link).

SBOL Visual 2 Ontology
Misirli G., Beal J., Gorochowski T.E., Stan G.-B., Wipat A., Chris Myers
ACS Synthetic Biology 9, 972-977, 2020.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2020
Schreiber F., Sommer B., Czauderna T., Golebiewski M., Gorochowski T.E., Hucka M., König M., Myers C., Nickerson D., Waltemath D.
Journal of Integrative Bioinformatics 17, , 2020.

Synthetic Biology Open Language (SBOL) Version 3.0
Baig H., Fontanarossa P., Kulkarni V., McLaughlin J., Vaidyanathan P., Bartley B., Grunberg R., Crowther M., Scott-Brown J., Bissell M., Clancy K., Gorochowski T.E., Misirli G., Oberortner E., Sauro H., Wipat A., Beal J., Myers C.
Journal of Integrative Bioinformatics 17, 17, 2020.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.2
Baig H., Fontanarossa P., Kulkarni V., McLaughlin J., Vaidyanathan P., Bartley B., Bhatia S., Bhakta S., Bissell M., Clancy K., Cox S.R., Goñi-Moreno A., Gorochowski T.E., Grunberg R., Luna A., Madsen C., Misirli G., Nguyen T., Le Novere N., Palchick Z., Pocock M., Roehner N., Sauro H., Scott-Brown J., Sexton J.T., Stan G.-B., Tabor J.J., Vilar M.V., Voigt C.A., Wipat A., Zong D., Zundel Z., Beal J., Myers C.
Journal of Integrative Bioinformatics 17, 14, 2020.

2019

Pathways to cellular supremacy in biocomputing
Grozinger L., Amos M., Gorochowski T.E., Carbonell P., Oyarzún D.A., Stoof R., Fellermann H., Zuliani P., Tas H., Goñi-Moreno A.
Nature Communications 10, 5250, 2019.

Communicating Structure and Function in Synthetic Biology Diagrams
Beal J., Nguyen T., Gorochowski T.E., Goñi-Moreno A., Scott-Brown J., McLaughlin J.A., Madsen C., Aleritsch B., Bartley B., Bhatia S., Bissell M., Castillo-Hair S., Clancy K., Luna A., Le Novére N., Palchick Z., Pocock M., Sauro H., Sexton J.T., Tabor J.J., Voigt C.A., Zundel Z., Myers C., Wipat A.
ACS Synthetic Biology 8, 1818-1825, 2019.

Living computers powered by biochemistry
Greco F.V., Tarnowski M.J., Gorochowski T.E.
The Biochemist 41, 14-18, 2019.

Absolute quantification of translational regulation and burden using combined sequencing approaches
Gorochowski T.E., Chelysheva I., Eriksen M., Nair P., Pedersen S., Ignatova Z.
Molecular Systems Biology 15, e8719, 2019.

CRISPR/Cas12a multiplex genome editing of Saccharomyces cerevisiae and the creation of yeast pixel art
Ciurkot K., Vonk B., Gorochowski T.E., Roubos J.A., Verwaal R.
Journal of Visualized Experiments 147, e59350, 2019.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
Beal J., Nguyen T., Gorochowski T.E., Goñi-Moreno A., Cox R.S., Madsen C., McLaughlin J.A., Roehner N., Aleritsch B., Bartley B., Bhatia S., Bissell M., Clancy K., Grünberg R., Luna A., Le Novére N., Palchick Z., Pocock M., Sauro H., Sexton J.T., Stan G.-B., Tabor J.J., Voigt C.A., Zundel Z., Myers C., Wipat A.
Journal of Integrative Bioinformatics , 20180101, 2019.

Synthetic Biology Open Language (SBOL) Version 2.3
Madsen C., Goñi-Moreno A., Palchick Z., Roehner N., Beal J., Bissell M., Gennari J.H., Sauro H., Clancy K., Misirli G., Myers C., Oberortner E., Macklin C., Tarter Y., Meng J., Grünberg R., Atallah C., McLaughlin J., Cox R.S., Bartley B., Pocock M., Gorochowski T.E., Scott-Brown J., Nguyen T., Samineni M., Zhang M., Zundel Z., Choi K., Zhang Z., Densmore D., Missier P., Quinn J., Stan G.-B., Wipat A.
Journal of Integrative Bioinformatics , 20190025, 2019.

Augmented reality for the engineering of collective behaviours in microsystems
Rubio Denniss A., Gorochowski T.E., Hauert S.
International Conference on Manipulation, Automation and Robotics at Small Scales (MARSS) , , 2019.

2018

Designing efficient translation
Gorochowski T.E., Ellis T.
Nature Biotechnology 36, 934-935, 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 15, 387-393, 2018.

  • Featured on the journal cover (link).

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.

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. (eds) Synthetic Biology. Methods in Molecular Biology 1772, Humana Press, New York, NY, 2018.

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.

  • Highlighted in editorial at Molecular Systems Biology (link).

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.

  • Featured on the journal cover (link).

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.

  • Featured on the journal cover (link).

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.