Highlights
Theory to engineer evolution
Tunable parts for adaptive circuits
Painting with yeast cells
Pre-prints
Cas9-based enrichment for targeted long-read metabarcoding
Nikolaeva-Reynolds L., Cammies C., Crichton R., Gorochowski T.E.
bioRxiv, 2024. (DOI: )
Analysis and control of untemplated DNA polymerase activity for guided synthesis of kilobase-scale DNA sequences
Castle S.D., Woolfson A., Linshiz G., Riley B.T., Samuel I.D.W., Holliger P., Oldfield L., Hessel A., Gorochowski T.E.
bioRxiv, 2024. (DOI: 10.1101/2024.08.29.610422)
Combinatorial Design Testing in Genomes with POLAR-seq
Ciurkot K., Lu X., Malyshava A., Soro L., Lees A., Gorochowski T.E., Ellis T.
bioRxiv, 2024. (DOI: 10.1101/2024.06.06.597521)
Scalable design of repeat protein structural dynamics via probabilistic coarse-grained models
Sarvaharman S., Neary T.E., Gorochowski T.E., Parmeggiani F.
bioRxiv, 2024. (DOI: 10.1101/2024.03.13.584748)
Engineering orthogonal ribosomes for real-time monitoring using fluorescence
Csibra E., Klopprogge B., Hau Sørensen G., Gorochowski T.E.
bioRxiv, 2023. (DOI: 10.1101/2023.11.19.567736)
Accelerated design of Escherichia coli genomes with reduced size using a whole-cell model and machine learning surrogate
Gherman I.M., Rees-Garbutt J., Pang W., Abdallah Z., Gorochowski T.E., Grierson C.S., Marucci L.
bioRxiv, 2023. (DOI: 10.1101/2023.10.30.564402)
Constructor algorithms for building unconventional computers able to solve NP-complete problems
McCaffrey T., Gorochowski T.E., Spector L.
arXiv, 2023. (DOI: 10.48550/arXiv.2309.10082)
How biological concepts and evolutionary theories are inspiring advances in machine intelligence
Gutai A.R., Gorochowski T.E.
Preprints, 2021. (DOI: 10.20944/preprints202109.0234.v1)
All publications
2024
Data hazards in synthetic biology
Zelenka N., Di Cara N., Sharma K., Sarvaharman S., Ghataora J., Parmeggiani F., Nivala J., Abdallah Z., Marucci L., Gorochowski T.E.
Synthetic Biology 9, ysae010, 2024.
Transfer learning for cross-context prediction of protein expression from 5'UTR sequence
Gilliot P.A., Gorochowski T.E.
Nucleic Acids Research 52, e58, 2024.
Engineering is evolution: a perspective on design processes to engineer biology
Castle S.D., Stock M., Gorochowski T.E.
Nature Communications 15, 3640, 2024.
Open-endedness in synthetic biology: a route to continual innovation for biological design
Stock M., Gorochowski T.E.
Science Advances 10, eadi3621, 2024.
Accelerating genetic sensor development, scale-up and deployment using synthetic biology
Joshi S.H.-N., Jenkins C., Ulaeto D., Gorochowski T.E.
BioDesign Research 6, 31, 2024.
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024
Golebiewski M., Bader G., Gleeson P., Gorochowski T.E., Keating S.M., König M., Myers C.J., Nickerson D.P., Sommer B., Waltemath D., Schreiber F.
Journal of Integrative Bioinformatics , 20240015, 2024.
Optimization of periodic treatment strategies for bacterial biofilms using an agent-based in silico approach
Blee J.A., Gorochowski T.E., Hauert S.
Journal of the Royal Society Interface 21, 20240078, 2024.
Long-term imaging and spatio-temporal control of living cells using targeted light based on closed-loop feedback
Wijewardhane N., Rubio Denniss A., Uppington M., Hauser H., Gorochowski T.E., Piddini E., Hauert S.
Journal of Micro and Bio Robotics 20, 2, 2024.
Editorial: Biological fabrication beyond tissue engineering.
Dade-Robertson M., Gorochowski T.E., Gobbo P., Nguyen P.Q., Zhang M.
Frontiers in Bioengineering and Biotechnology 12, 1435569, 2024.
2023
Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting
Tarnowski M.J., Varliero G., Scown J., Phelps E., Gorochowski T.E.
Royal Society Open Science 10, 230963, 2023.
Ten simple rules for managing laboratory information
Berezin C.-T., Aguilera L.U., Billerbeck S., Bourne P., Densmore D., Freemont P., Gorochowski T.E., Hernandez S.I., Hillson N.J., King C.R., Köpke M., Ma S., Miller K., Moon T.S., Moore J., Munsky B., Myers C.J., Nicholas D.A., Peccoud S., Zhou W., Peccoud J.
PLOS Computational Biology 19, e1011652, 2023.
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays
Gilliot P.A., Gorochowski T.E.
Bioinformatics 39, btad277, 2023.
Bridging the Gap between Mechanistic Biological Models and Machine Learning Surrogates
Gherman I.M., Marucci L., Abdallah Z., Grierson C.S., Gorochowski T.E., Pang W.
PLOS Computational Biology 19, e1010988, 2023.
Synthetic Biology Open Language (SBOL) Version 3.1.0
Buecherl L., Mitchell T., Scott-Brown J., Vaidyanathan P., Vidal G., Baig H., Bartley B., Beal J., Crowther M., Fontanarrosa P., Gorochowski T.E., Grünberg R., Kulkarni V., McLaughlin J., Mısırlı G., Oberortner E., Wipat A., Myers C.
Journal of Integrative Bioinformatics , 20220058, 2023.
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022
König M., Gleeson P., Golebiewski M., Gorochowski T.E., Hucka M., Keating S.M., Myers C., Nickerson D., Sommer B., Waltemath D., Schreiber F.
Journal of Integrative Bioinformatics 20, 20230004, 2023.
Design and analysis of massively parallel reporter assays using FORECAST
Gilliot P.A., Gorochowski T.E.
In: Selvarajoo K. (eds) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology 2553, 41-56, 2023.
2022
Advanced medical micro-robotics for early diagnosis and therapeutic interventions
Zhang D., Gorochowski T.E., Marucci L., Lee H-.T., Gil B., Li B., Hauert S., Yeatman E.
Frontiers in Robotics and AI 9, , 2022.
Towards the fully automated monitoring of ecological communities
Besson M., Alison J., Bjerge K., Gorochowski T.E., Høye T.T., Jucker T., Mann H.M.R., Clements C.F.
Ecology Letters 25, 2753-2775, 2022.
Long-term imaging and spatio-temporal control of living cells using light
Wijewardhane N.S., Rubio Dennis A., Uppington M., Hauser H., Gorochowski T.E., Piddini E., Hauert S.
Proceedings of the MARSS Conference , , 2022.
Q-learning for real time control of heterogeneous microagent collectives
Rubio Dennis A., Mateu L.F., Gorochowski T.E., Hauert S.
Proceedings of the ALIFE Conference , 19, 2022.
An open platform for high-resolution light-based control of microscopic collectives
Rubio Dennis A., Gorochowski T.E., Hauert S.
Advanced Intelligent Systems , 2200009, 2022.
Improving the robustness of engineered bacteria to nutrient stress using programmed proteolysis
Szydlo K., Ignatova Z., Gorochowski T.E.
ACS Synthetic Biology 11, 1049-1059, 2022.
Massively parallel characterisation of engineered transcript isoforms using direct RNA sequencing
Tarnowski M.J., Gorochowski T.E.
Nature Communications 13, 434, 2022.
Design and assembly of multi-level transcriptional and translational regulators for stringent control of gene expression
Greco F.V., Irvine T., Grierson C.S., Gorochowski T.E.
In: Chappell J., Takahashi M.K. (eds) Riboregulator Design and Analysis. Methods in Molecular Biology 2518, 99–110, 2022.
2021
paraSBOLv: a foundation for standard-compliant genetic design visualization tools
Clark C.C., Scott-Brown J., Gorochowski T.E.
Synthetic Biology 6, ysab022, 2021.
Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a
Ciurkot K., Gorochowski T.E., Roubos J., Verwaal R.
Nucleic Acids Research 49, 7775-7790, 2021.
Towards an engineering theory of evolution
Castle S.D., Grierson C.S., Gorochowski T.E.
Nature Communications 12, 3326, 2021.
Harnessing the central dogma for stringent multi-level control of gene expression
Greco F.V., Pandi A., Erb E.J., Grierson C.S., Gorochowski T.E.
Nature Communications 12, 1738, 2021.
Towards collaborative and automated development of resources for data standards in synthetic biology
Misirli G., Ajibode J.S., Beal J., Scott-Brown J., Gorochowski T.E., Myers C.
Proceedings of the 13th International Workshop on Bio-Design Automation , , 2021.
Synthetic Biology Open Language Visual (SBOL Visual) Version 3.0
Baig H., Fontanarossa P., Scott-Brown J., McLaughlin J., Vaidyanathan P., Gorochowski T.E., Misirli G., Beal J., Myers C.
Journal of Integrative Bioinformatics 18, 20210013, 2021.
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.
ACS Synthetic Biology 10, 979-989, 2021.
Editorial: Computer-Aided Biodesign Across Scales
Gorochowski T.E., Karr J.R., Parmeggiani F., Yordanov B.
Frontiers in Bioengineering and Biotechnology 9, 700418, 2021.
Characterizing genetic parts and devices using RNA sequencing
Vipin D., Ignatova Z., Gorochowski T.E.
In: Menolascina F. (eds) Synthetic Gene Circuits. Methods in Molecular Biology 2229, 175-187, 2021.
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 5, ysaa021, 2020.
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.
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. (online)
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.
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.
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.