Imperial College London

Dr Guy-Bart Stan

Faculty of EngineeringDepartment of Bioengineering

Reader in Engineering Design for Synthetic Biology
 
 
 
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Contact

 

+44 (0)20 7594 6375g.stan Website

 
 
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Location

 

B703Royal School of MinesSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

111 results found

Boo A, Ellis T, Stan G-B, 2019, Host-aware synthetic biology, Current Opinion in Systems Biology, Vol: 14, Pages: 66-72, ISSN: 2452-3100

JOURNAL ARTICLE

Kylilis N, Riangrungroj P, Lai H-E, Salema V, Fernández LÁ, Stan G-BV, Freemont PS, Polizzi KMet al., 2019, Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications., ACS Sens, Vol: 4, Pages: 370-378

Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design to detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straightforward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanobodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites, as well as routine medical testing and personalized medicine.

JOURNAL ARTICLE

Kylilis N, Riangrungroj P, Lai H-E, Salema V, Fernandez LA, Stan G-B, Freemont P, Polizzi Ket al., 2019, A low-cost biological agglutination assay for medical diagnostic applications, ACS Sensors, ISSN: 2379-3694

Affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing are key in addressing challenges in the diagnosis of medical conditions and for improving global health in general. Ideally, POC diagnostic tests should be highly selective for the biomarker, user-friendly, have a flexible design architecture and a low cost of production. Here we developed a novel agglutination assay based on whole E. coli cells surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design as a new diagnostic platform by the detection of a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations supported using straight-forward design rules and a mathematical model. Finally, we re-engineer E. coli cells for the detection of a medically relevant biomarker by the display of two different antibodies against the human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for both field-testing in the developing world, emergency or disaster relief sites as well as routine medical testing and personalized medicine.

JOURNAL ARTICLE

Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2019, The Exit Time Finite State Projection Scheme: Bounding Exit Distributions and Occupation Measures of Continuous-Time Markov Chains, SIAM Journal on Scientific Computing, Vol: 41, Pages: A748-A769, ISSN: 1064-8275

JOURNAL ARTICLE

Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2018, Approximation schemes for countably-infinite linear programs with moment bounds

We introduce approximation schemes for a type ofcountably-infinite-dimensional linear programs (CILPs) whose feasible pointsare unsigned measures and whose optimal values are bounds on the averages ofthese measures. In particular, we explain how to approximate the program'soptimal value, optimal points, and minimal point (should one exist) by solvingfinite-dimensional linear programs. We show that the approximations converge tothe CILP's optimal value, optimal points, and minimal point as the size of thefinite-dimensional program approaches that of the CILP. Inbuilt in our schemesis a degree of error control: they yield lower and upper bounds on the optimalvalues and we give a simple bound on the approximation error of the minimalpoint. To motivate our work, we discuss applications of our schemes taken fromthe Markov chain literature: stationary distributions, occupation measures, andexit distributions.

JOURNAL ARTICLE

Kylilis N, Tuza ZA, Stan G-B, Polizzi KMet al., 2018, Tools for engineering coordinated system behaviour in synthetic microbial consortia, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723

JOURNAL ARTICLE

Pan W, Yuan Y, Ljung L, Goncalves J, Stan G-Bet al., 2018, Identification of Nonlinear State-Space Systems From Heterogeneous Datasets, IEEE TRANSACTIONS ON CONTROL OF NETWORK SYSTEMS, Vol: 5, Pages: 737-747, ISSN: 2325-5870

JOURNAL ARTICLE

Ceroni F, Boo A, Furini S, Gorochowski TE, Borkowski O, Ladak YN, Awan AR, Gilbert C, Stan G-B, Ellis Tet al., 2018, Burden-driven feedback control of gene expression, NATURE METHODS, Vol: 15, Pages: 387-+, ISSN: 1548-7091

JOURNAL ARTICLE

Avalos JL, Toettcher JE, Lalanne J-B, Li G-W, Gomes ALC, Johns NI, Wang HH, Ellis T, Stan G-B, Mure LS, Panda S, Cooper HM, Fernandez-Martinez J, Rout MP, Akey CW, Kim SJ, Sali A, Bastarache L, Denny JCet al., 2018, Principles of Systems Biology, No. 28, CELL SYSTEMS, Vol: 6, Pages: 397-399, ISSN: 2405-4712

JOURNAL ARTICLE

Tomazou M, Barahona M, Polizzi KM, Stan G-Bet al., 2018, Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation, CELL SYSTEMS, Vol: 6, Pages: 508-+, ISSN: 2405-4712

JOURNAL ARTICLE

Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan G-B, Ellis Tet al., 2018, Cell-free prediction of protein expression costs for growing cells, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723

JOURNAL ARTICLE

Tomazou M, Stan G-B, 2018, Portable gene expression guaranteed, NATURE BIOTECHNOLOGY, Vol: 36, Pages: 313-314, ISSN: 1087-0156

JOURNAL ARTICLE

Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grunberg R, Luna A, Le Novere N, Pocock M, Sauro H, Sexton JT, Stan G-B, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat Aet al., 2018, Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0, JOURNAL OF INTEGRATIVE BIOINFORMATICS, Vol: 15, ISSN: 1613-4516

JOURNAL ARTICLE

Tuza ZA, Stan G-B, 2018, Characterization of Biologically Relevant Network Structures form Time-series Data, Publisher: IEEE

WORKING PAPER

O'Clery N, Yuan Y, Stan G-B, Barahona Met al., 2018, Global Network Prediction from Local Node Dynamics., CoRR, Vol: abs/1809.00409

JOURNAL ARTICLE

Kylilis N, Stan G-B, Polizzi K, 2017, Tools for engineering coordinated system behaviour in synthetic microbial consortia, Publisher: bioRxiv

Advancing synthetic biology to the multicellular level requires the development of multiple orthogonal cell-to-cell communication channels to propagate information with minimal signal interference. The development of quorum sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on reducing signal leakage between systems of cognate AHL/transcription factor pairs. However, the use of non-cognate signals as a design feature has received limited attention so far. Here, we demonstrate the largest library of AHL-receiver devices constructed to date with all cognate and non-cognate chemical signal interactions quantified and we develop a software tool that allows automated selection of orthogonal chemical channels. We use this approach to identify up to four orthogonal channels in silico and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels will facilitate the design of synthetic microbial consortia for novel applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation, and spatial organisation.

WORKING PAPER

Hancock EJ, Ang J, Papachristodoulou A, Stan G-Bet al., 2017, The Interplay between Feedback and Buffering in Cellular Homeostasis, CELL SYSTEMS, Vol: 5, Pages: 498-+, ISSN: 2405-4712

JOURNAL ARTICLE

Ceroni F, Furini S, Gorochowski T, Boo A, Borkowski O, Ladak Y, Awan A, Gilbert C, Stan G-B, Ellis Tet al., 2017, Burden-driven feedback control of gene expression

Cells use feedback regulation to ensure robust growth despite fluctuating demands on resources and different environmental conditions. Yet the expression of foreign proteins from engineered constructs is an unnatural burden on resources that cells are not adapted for. Here we combined multiplex RNAseq with an in vivo assay to reveal the major transcriptional changes in two E. coli strains when a set of inducible synthetic constructs are expressed. We identified that native promoters related to the heat-shock response activate expression rapidly in response to synthetic expression, regardless of the construct. Using these promoters, we built a CRISPR/dCas9-based feedback regulation system that automatically adjusts synthetic construct expression in response to burden. Cells equipped with this general-use controller maintain capacity for native gene expression to ensure robust growth and as such outperform unregulated cells at protein yields in batch production. This engineered feedback is the first example of a universal, burden-based biomolecular control system and is modular, tuneable and portable.

WORKING PAPER

Borkowski O, Bricio Garberi C, Murgiano M, Stan G-B, Ellis Tet al., 2017, Cell-free prediction of protein expression costs for growing cells

Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any gene is a major challenge, as multiple processes and factors determine translation efficiency. Here, to enable prediction of the cost of gene expression in bacteria, we describe a standard cell-free lysate assay that determines the relationship between in vivo and cell-free measurements and γ, a relative measure of the resource consumption when a given protein is expressed. When combined with a computational model of translation, this enables prediction of the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.

WORKING PAPER

Mısırlı G, Madsen C, de Murieta IS, Bultelle M, Flanagan K, Pocock M, Hallinan J, McLaughlin JA, Clark-Casey J, Lyne M, Micklem G, Stan G-B, Kitney R, Wipat Aet al., 2017, Constructing synthetic biology workflows in the cloud, Engineering Biology, Vol: 1, Pages: 61-65

JOURNAL ARTICLE

Walker BJ, Stan G-BV, Polizzi KM, 2017, Intracellular delivery of biologic therapeutics by bacterial secretion systems, EXPERT REVIEWS IN MOLECULAR MEDICINE, Vol: 19, ISSN: 1462-3994

JOURNAL ARTICLE

Kuntz J, Thomas P, Stan G-B, Barahona Met al., 2017, Rigorous bounds on the stationary distributions of the chemical master equation via mathematical programming

The stochastic dynamics of biochemical networks are usually modelled with thechemical master equation (CME). The stationary distributions of CMEs are seldomsolvable analytically, and numerical methods typically produce estimates withuncontrolled errors. Here, we introduce mathematical programming approachesthat yield approximations of these distributions with computable error boundswhich enable the verification of their accuracy. First, we use semidefiniteprogramming to compute increasingly tighter upper and lower bounds on themoments of the stationary distributions for networks with rationalpropensities. Second, we use these moment bounds to formulate linear programsthat yield convergent upper and lower bounds on the stationary distributionsthemselves, their marginals and stationary averages. The bounds obtained alsoprovide a computational test for the uniqueness of the distribution. In theunique case, the bounds form an approximation of the stationary distributionwith a computable bound on its error. In the non-unique case, our approachyields converging approximations of the ergodic distributions. We illustrateour methodology through several biochemical examples taken from the literature:Schl\"ogl's model for a chemical bifurcation, a two-dimensional toggle switch,and a model for bursty gene expression.

JOURNAL ARTICLE

Foo M, Sawlekar R, Kim J, Bates DG, Stan G-B, Kulkarni Vet al., 2017, Biomolecular implementation of nonlinear system theoretic operators, European Control Conference (ECC), Publisher: IEEE, Pages: 1824-1831

Synthesis of biomolecular circuits for controlling molecular-scale processes is an important goal of synthetic biology with a wide range of in vitro and in vivo applications, including biomass maximization, nanoscale drug delivery, and many others. In this paper, we present new results on how abstract chemical reactions can be used to implement commonly used system theoretic operators such as the polynomial functions, rational functions and Hill-type nonlinearity. We first describe how idealised versions of multi-molecular reactions, catalysis, annihilation, and degradation can be combined to implement these operators. We then show how such chemical reactions can be implemented using enzyme-free, entropy-driven DNA reactions. Our results are illustrated through three applications: (1) implementation of a Stan-Sepulchre oscillator, (2) the computation of the ratio of two signals, and (3) a PI+antiwindup controller for regulating the output of a static nonlinear plant.

CONFERENCE PAPER

Tomazou M, Stan GB, 2017, Engineering autoregulation in enzymatic degradation based systems for robust dynamics and improved host capacity, Pages: 161-162

CONFERENCE PAPER

Borkowski O, Ceroni F, Stan G-B, Ellis Tet al., 2016, Overloaded and stressed: whole-cell considerations for bacterial synthetic biology, CURRENT OPINION IN MICROBIOLOGY, Vol: 33, Pages: 123-130, ISSN: 1369-5274

JOURNAL ARTICLE

Pan W, Menolascina F, Stan G-B, 2016, Online Model Selection for Synthetic Gene Networks, 55th IEEE Conference on Decision and Control (CDC), Publisher: IEEE, Pages: 776-782, ISSN: 0743-1546

CONFERENCE PAPER

Kuntz J, Ottobre M, Stan G-B, Barahona Met al., 2016, BOUNDING STATIONARY AVERAGES OF POLYNOMIAL DIFFUSIONS VIA SEMIDEFINITE PROGRAMMING, SIAM JOURNAL ON SCIENTIFIC COMPUTING, Vol: 38, Pages: A3891-A3920, ISSN: 1064-8275

JOURNAL ARTICLE

Sootla A, Oyarzun D, Angeli D, Stan G-Bet al., 2016, Shaping pulses to control bistable systems: Analysis, computation and counterexamples, AUTOMATICA, Vol: 63, Pages: 254-264, ISSN: 0005-1098

JOURNAL ARTICLE

Pan W, Yuan Y, Goncalves J, Stan G-Bet al., 2016, A Sparse Bayesian Approach to the Identification of Nonlinear State-Space Systems, IEEE TRANSACTIONS ON AUTOMATIC CONTROL, Vol: 61, Pages: 182-187, ISSN: 0018-9286

JOURNAL ARTICLE

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