Guy-Bart STAN's research webpage
Selected Publications
- Computational Re-Design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation, M. Tomazou, M. Barahona, K. Polizzi G.-B. Stan, Cell Systems, Volume 6 (2018), n°4, pp. 508-520, doi:10.1016/j.cels.2018.03.013.
- Burden-driven feedback control of gene expression, F. Ceroni, A. Boo, S. Furini, T. E. Gorochowski, O. Borkowski, Y. N. Ladak, A. R. Awan, C. Gilbert, G.-B. Stan, T. Ellis, Nature Methods, Volume 15 (2018), pp. 387-393, doi:10.1038/nmeth.4635.
- Cell-free prediction of protein expression costs for growing cells, O. Borkowski, C. Bricio, M. Murgiano, B. Rothschild-Mancinelli, G.-B. Stan, T. Ellis, Nature Communications, Volume 9 (2018), doi:10.1038/s41467-018-03970-x.
- The Interplay Between Feedback and Buffering in Homeostasis, E. Hancock, J. Ang, A. Papachristodoulou, G.-B. Stan, Cell Systems, Volume 5 (2017), n°5, doi:10.1016/j.cels.2017.09.013.
- Identification of Nonlinear State-Space Systems from Heterogeneous Datasets, W. Pan, Y. Yuan, L. Ljung, J. Goncalves, G.-B. Stan, IEEE Transactions on Network Control Systems , 2017, doi:10.1109/TCNS.2017.2758966.
- Quantifying cellular capacity identifies gene expression designs with reduced burden, F. Ceroni, R. Algar, G.-B. Stan, T. Ellis, Nature Methods, Volume 12 (2015), n°5, doi:10.1038/nmeth.3339. Preprint available here. The paper made the cover of the May 2015 issue of Nature Methods.
- Simplified Mechanistic Models of Gene Regulation for Analysis and Design, E. Hancock, G.-B. Stan, J. Arpino, A. Papachristodoulou, Journal of the Royal Society Interface, Volume 12 (2015), n°108, doi:10.1098/rsif.2015.0312. A preprint is available here, while the supplementary information is available here.
- Noise propagation in synthetic gene circuits for metabolic control, D. Oyarzun, J.-B. Lugagne, G.-B. Stan, ACS Synthetic Biology (2014), doi:10.1021/sb400126a.
- Synthetic gene circuits for metabolic control: design trade-offs and constraints, D. Oyarzun, G.-B. Stan, Journal of the Royal Society Interface, Volume 10 (2013), n°78, doi:10.1098/rsif.2012.0671.
- The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology, M. Galdzicki, K. Clancy, E. Oberortner, M. Pocock, J. Quinn, C. Rodriguez, N. Roehner, M. Wilson, L. Adam, J. C. Anderson, B. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Gruenberg, J. Hallinan, N. Hillson, J. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. Plahar, E. Sirin, G.-B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. Myers, H. Sauro, Nature Biotechnology, Volume 32 (2014), n°6, pp. 545–550, doi:10.1038/nbt.2891.
- Engineering and ethical perspectives in synthetic biology, J. Anderson, N. Strelkowa, G.-B. Stan, T. Douglas, J. Savulescu, M. Barahona, and A. Papachristodoulou, EMBO reports, Volume 13 (2012), n°7, pp. 584-590, doi:10.1038/embor.2012.81.
- Essential information for synthetic DNA sequences, J. Peccoud, J. C. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. W. Lux, C. A. Rodriguez, G.-B. Stan, H. M. Sauro, Nature Biotechnology, Volume 22 (Jan 2011), n°1, p. 22, doi:10.1038/nbt.1753.
Research interests
I am passionate about developing new concepts and methods and applying the produced results to real-life problems. Currently, my main research interests are: Nonlinear Dynamical Systems Analysis and Control, Synthetic Biology, Systems Biology.
I am currently interested in the modelling, analysis, design, control, and implementation of cellular systems (in particular biomolecular feedback systems and gene regulatory networks); and in applications of systems and control engineering methods to the problem of robustly and optimally controlling natural or synthetic biology systems, e.g., robust control of gene regulation networks or optimal drug cocktails scheduling for chronic-like diseases treatments (e.g. cancer and HIV).
Curriculum Vitae
You can download a pdf version of my CV here.
For a visual timeline of my career you can follow this link on Vizualize.me.
For a citations report of my published papers you can follow this link on Google Scholar Citations or this link on ResearchGate.
Openings
General information about us
Interested in working with us in design and control of synthetic biology systems at the Department of Bioengineering of Imperial College London? There are always positions available for outstanding prospective PhD students and postdoctoral staff.
Hereafter, you will find links which provide you with information about openings and how to apply. Please email us if you wish to join the Stan Group.
Joining as a PostDoctoral Research Associate
List of PostDoctoral Fellowships
If you are a highly motivated and dynamic postdoctoral researcher with experience in synthetic biology, biomathematics, biophysics, or modelling and control of biological systems and you are looking to join us, please email us with your CV. Information about competitive PostDoctoral Fellowships is available hereafter.
If you would like to apply for a PostDoctoral Fellowship to work in my group, this list of PostDoctoral Fellowships might be useful. In particular, if you want to conduct your own research, which is aligned with the core research work in my group, I can sponsor you for an Imperial College Research Fellowship for 4 years. Imperial College's prestigious Research Fellowships financially supports the brightest and very best early career researchers from across the world, providing a level of commitment and support that is rare from a UK university. We are also welcoming and supporting outstanding postdocs applying for a Marie Sklodowska-Curie Individual Fellowship. Please contact me if you are interested.
Also, Dr Nick Jones has compiled a list of fellowships that you might also want to consider.
Another list of independent PostDoc funding (in Biology) has been compiled by Dr Dieter Lucas.
Joining as a PhD student
Competitive PhD Scholarship
Information about the Imperial College PhD Scholarship scheme is available here. Additionally, information about all Scholarship Schemes (including a scholarships search tool) is available here. Furthermore, Ph.D. studentships in the Department of Bioengineering are advertised here.
Information about the PhD programme in the Department of Bioengineering and how to apply can be found here. For general information on the tuition fees and cost of living in London, please read this link. For other sources of funding you can also look at here and here (BioEngineering funding) and here (fees and funding).
Finally, there are also other PhD scholarship schemes such as for example the Crick PhD Programme.
Please check the College entry requirements carefully before applying.
For support of research-related travel expenses you can check this link.
Group members
The current list of group members is available at the people section of our group website.
For more information about the various students I have supervised see the Supervisory Experience section of my CV.
Books
Synthetic Biology: a Primer (Revised Edition), G. Baldwin, T. Bayer, R. Dickinson, T. Ellis, P. Freemont, R. Kitney, K. Polizzi, N. Rose, G.-B. Stan, Imperial College Press, Oct. 2015, ISBN-10: 1783268794, ISBN-13: 978-1783268795.
A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, Eds.: V. Kulkarni, G.-B. Stan, K. Raman, Springer, July 2014, ISBN: 978-94-017-9040-6 (Print), 978-94-017-9041-3 (Online). Click here for amazon.co.uk link.
A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, Eds.: V. Kulkarni, G.-B. Stan, K. Raman, Springer, July 2014, ISBN: 978-94-017-9046-8 (Print), 978-94-017-9047-5 (Online). Click here for amazon.co.uk link.
Full list of Publications
2018
- Computational Re-Design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation, M. Tomazou, M. Barahona, K. Polizzi G.-B. Stan, Cell Systems, Volume 6 (2018), n°4, pp. 508-520, doi:10.1016/j.cels.2018.03.013.
- Burden-driven feedback control of gene expression, F. Ceroni, A. Boo, S. Furini, T. E. Gorochowski, O. Borkowski, Y. N. Ladak, A. R. Awan, C. Gilbert, G.-B. Stan, T. Ellis, Nature Methods, Volume 15 (2018), pp. 387-393, doi:10.1038/nmeth.4635.
- Cell-free prediction of protein expression costs for growing cells, O. Borkowski, C. Bricio, M. Murgiano, B. Rothschild-Mancinelli, G.-B. Stan, T. Ellis, Nature Communications, Volume 9 (2018), doi:10.1038/s41467-018-03970-x.
- Portable gene expression guaranteed, M. Tomazou, G.-B. Stan, Nature Biotechnology News and Views, Volume 36 (2018), n°4, pp. 313-314, doi:10.1038/nbt.4119
- Investigating the consequences of asymmetric endoplasmic reticulum inheritance in Saccharomyces cerevisiae under stress using a combination of single cell measurements and mathematical modelling, F. Jonas, K. Royle, R. Aw, G.-B. Stan, K. Polizzi, Systems and Synthetic Biology, Volume 3 (2018), n°1, pp. 64-75, doi:10.1016/j.synbio.2018.01.001.
- Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0, R. S. Cox, C. Madsen, J. McLaughlin, T. Nguyen, N. Roehner, A. Wipat, B. Bartley, J. Beal, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Grunberg, A. Luna, C. Myers, N. Le Novere, M. Pocock, H. Sauro, J. T. Sexton, G.-B. Stan, J. J. Tabor, C. Voigt, Z. Zundel, K. Polizzi, Journal of Integrative Bioinformatics, Volume 15 (2018), n°1, doi:10.1515/jib-2017-0074.
2017
- The Interplay Between Feedback and Buffering in Homeostasis, E. Hancock, J. Ang, A. Papachristodoulou, G.-B. Stan, Cell Systems, Volume 5 (2017), n°5, doi:10.1016/j.cels.2017.09.013.
- Identification of Nonlinear State-Space Systems from Heterogeneous Datasets, W. Pan, Y. Yuan, L. Ljung, J. Goncalves, G.-B. Stan, IEEE Transactions on Network Control Systems, 2017, doi:10.1109/TCNS.2017.2758966.
- Constructing Synthetic Biology Workflows in the Cloud, G. Misirli, C. Madsen, I. Sainz de Murieta, M. Bultelle, K. Flanagan, M. Pocock, J. Hallinan, J. A. Mclaughlin, J. Clark-Casey, M. Lyne, G. Micklem G.-B. Stan, R. Kitney, A. Wipat, IET Engineering Biology, Volume 1 (2017), n°1, pp. 61-65, doi:10.1049/enb.2017.0001.
- Intracellular delivery of biologic therapeutics by bacterial secretion systems, B. Walker, G.-B. Stan, K. Polizzi, Expert Reviews in Molecular Medicine, Volume 19 (2017), e6, doi:10.1017/erm.2017.7.
2016
- Bounding stationary averages of polynomial diffusions via semidefinite programming, J. Kuntz, M. Ottobre, G.-B. Stan, M. Barahona, SIAM Journal on Scientific Computing, Volume 38 (2016), n°6, pp. A3891–A3920, doi:10.1137/16M107801X.
- Overloaded and stressed: whole-cell considerations for bacterial synthetic biology, O. Borkowski, F. Ceroni, G.-B. Stan, T. Ellis, Current Opinion in Microbiology, Volume 33 (2016), pp. 123-130, doi:10.1016/j.mib.2016.07.009.
- A Sparse Bayesian Approach to the Identification of Nonlinear State-Space Systems, W. Pan, Y. Yuan, J. Gonçalves, G.-B. Stan, IEEE Transacations on Automatic Control, Volume 61 (2016), n°1, pp. 182-187, doi:10.1109/TAC.2015.2426291.
- Shaping Pulses to Control Bistable Systems: Analysis, Computation and Counterexamples, A. Sootla, D. Oyarzun, D. Angeli, G.-B. Stan, Automatica, Volume 63 (2016), pp. 254-264, doi:10.1016/j.automatica.2015.10.037.
- Biomolecular implementation of nonlinear system theoretic operators, M. Foo, R. Sawlekar, J. Kim, D. Bates, G.-B. Stan, V. Kulkarni, Proceedings of the 15th European Control Conference (ECC 2016), Aalborg, Denmark, June 29 - July 1, 2016.
- Online Model Selection for Synthetic Gene Networks, W. Pan, F. Menolascina G.-B. Stan, Proceedings of the 55th IEEE Conference on Decision and Control (CDC 2016), Las Vegas, NV, USA, 12-14 December, 2016.
2015
- SBOL Visual: A Graphical Language for Genetic Designs, J. Y. Quinn, R. S. Cox III, A. Adler, J. Beal, S. Bhatia, Y. Cai, J. Chen, K. Clancy, M. Galdzicki, N. J. Hilson, N. Le Novere, A. J. Maheshwari, J. A. McLaughlin, C. J. Myers, U. P, M. Pocock, C. Rodriguez, L. Soldatova, G.-B. Stan, N. Swainston, A. Wipat, H. M. Sauro, PLoS Biology, 2015, doi:10.1371/journal.pbio.1002310.
- A minimal realization technique for the dynamical structure function of a class of LTI systems, Y. Yuan, A. Rai, E. Yeung, G.-B. Stan, S. Warnick, J. Gonçalves, IEEE Transactions on Control of Network Systems, Volume 4 (2015), n°2, doi:10.1109/TCNS.2015.2498468.
- Simplified Mechanistic Models of Gene Regulation for Analysis and Design, E. Hancock, G.-B. Stan, J. Arpino, A. Papachristodoulou, Journal of the Royal Society Interface, Volume 12 (2015), n°108, doi:10.1098/rsif.2015.0312. A preprint is available here, while the supplementary information is available here.
- Quantifying cellular capacity identifies gene expression designs with reduced burden, F. Ceroni, R. Algar, G.-B. Stan, T. Ellis, Nature Methods, Volume 12 (2015), n°5, doi:10.1038/nmeth.3339. Preprint available here. The paper made the cover of the May 2015 issue of Nature Methods.
- Online fault diagnosis for nonlinear power systems, W. Pan, Y. Yuan, H. Sandberg, J. Gonçalves, G.-B. Stan, Automatica, Volume 55 (2015), pp. 27-36, doi:10.1016/j.automatica.2015.02.032.
- A forward-design approach to increase the production of poly-3-hydroxybutyrate in genetically engineered Escherichia coli, R. Kelwick, M. Kopniczky, I. Bower, W. Chi, M. H. W. Chin, S. Fan, J. Pilcher, J. Strutt, A. J. Webb, K. Jensen, G.-B. Stan, R. Kitney, P. Freemont, PLoS ONE, Volume 10, (2015), n°2, doi:10.1371/journal.pone.0117202.
- The Moveable Feast of Predictive Reward Discounting in Humans, B. Schoenhense, L. Dickens, B. Caldas, G.-B. Stan, A. Faisal, Proceedings of the 2nd Multidisciplinary Conference on Reinforcement Learning and Decision Making (RDLM 2015), The University of Alberta, Edmonton, Alberta, Canada, 7-10 June, 2015.
- Shaping Pulses to Control Bistable Biological Systems, A. Sootla, D. Oyarzun, D. Angeli, G.-B. Stan, Proceedings of the 2015 American Control Conference (ACC 2015), Palmer House Hilton, Chicago, IL, 1-3 July, 2015.
- Identifying Biochemical Reaction Networks From Heterogeneous Datasets, W. Pan, Y. Yuan, L. Ljung, J. Gonçalves, G.-B. Stan, Proceedings of the 54th IEEE Conference on Decision and Control (CDC 2015), Osaka International Convention Center, Osaka, Japan, 15-18 December, 2015.
2014
- Model Reduction of Genetic-Metabolic Networks via Time Scale Separation, J. Kuntz, D. Oyarzun, G.-B. Stan, A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, Eds.: V. Kulkarni, G.-B. Stan, K. Raman, Springer, July 2014, pp. 181-210, doi:10.1007/978-94-017-9041-3_7.
- Analysis of Synchronizing Biochemical Networks via Incremental Dissipativity, A. Hamadeh, J. Gonçalves, G.-B. Stan, A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, Eds.: V. Kulkarni, G.-B. Stan, K. Raman, Springer, July 2014, pp. 117-139, doi:10.1007/978-94-017-9047-5_5.
- Noise propagation in synthetic gene circuits for metabolic control, D. Oyarzun, J.-B. Lugagne, G.-B. Stan, ACS Synthetic Biology (2014), doi:10.1021/sb400126a.
- GeneGuard: a Modular Plasmid System Designed for Biosafety, O. Wright, M. Dalmans, G.-B. Stan, T. Ellis, ACS Synthetic Biology (2014), doi:10.1021/sb500234s.
- The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology, M. Galdzicki, K. Clancy, E. Oberortner, M. Pocock, J. Quinn, C. Rodriguez, N. Roehner, M. Wilson, L. Adam, J. C. Anderson, B. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Gruenberg, J. Hallinan, N. Hillson, J. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. Plahar, E. Sirin, G.-B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. Myers, H. Sauro, Nature Biotechnology, Volume 32 (2014), pp. 545–550, doi:10.1038/nbt.2891.
- Mathematical modeling of HIV dynamics after antiretroviral therapy initiation: A clinical research study, P. S. Rivadeneira, C. H. Moog, G.-B. Stan, C. Brunet, F. Raffi, V. Ferre, V. Costanza, M.-J. Mhawej, F. Biafore, D. A. Ouattara, D. Ernst, R. Fonteneau, X. Xia, AIDS Research and Human Retroviruses, Volume 30 (2014), n°9, pp. 831-834, doi:10.1089/AID.2013.0286.
- Mathematical modeling of HIV dynamics after antiretroviral therapy initiation: A Review, P. S. Rivadeneira, C. H. Moog, G.-B. Stan, C. Brunet, F. Raffi, V. Ferre, V. Costanza, M.-J. Mhawej, F. Biafore, D. A. Ouattara, D. Ernst, R. Fonteneau, X. Xia, BioResearch Open Access, Volume 3 (2014), n°5, pp. 233-241, doi:10.1089/biores.2014.0024.
- Modelling essential interactions between synthetic genes and their chassis cell, R. Algar, T. Ellis, G.-B. Stan, Proceedings of the 53rd IEEE Conference on Decision and Control (CDC 2014), J.W. Marriott Hotel, Los Angeles, CA, USA, 15-17 December, 2014.
- Inference of Switched Biochemical Reaction Networks Using Sparse Bayesian Learning, W. Pan, Y. Yuan, A. Sootla, G.-B. Stan, Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2014), Nancy, France, 15-19 September, 2014.
- Distributed Reconstruction of Nonlinear Networks: An ADMM Approach, W. Pan, A. Sootla, G.-B. Stan, Proceedings of the 19th IFAC World Congress (IFAC 2014), Cape Town, South Africa, 24-29 August, 2014.
- Toggling a Genetic Switch Using Reinforcement Learning, A. Sootla, N. Strelkowa, D. Ernst, M. Barahona, G.-B. Stan, Proceedings of the 9th French Meeting on Planning, Decision Making and Learning (JFPDA 2014), Liege, Belgium, 12-13 May, 2014.
2013
- Observability and coarse-graining of consensus dynamics through the External Equitable Partition, N. O'Clery, Y. Yuan, G.-B. Stan, M. Barahona, Physical Review E, Volume 88 (2013), n°4, doi:10.1103/PhysRevE.88.042805.
- Tuning the Dials of Synthetic Biology: A Review, J. Arpino, E. Hancock, J. Anderson, M. Barahona, G.-B. Stan, A. Papachristodoulou, K. Polizzi, Microbiology, Special Issue on Synthetic Biology, Volume 159 (2013), pp. 1236-1253 doi:10.1099/mic.0.067975-0.
- Building-in Biosafety for Synthetic Biology, O. Wright, G.-B. Stan, T. Ellis, Microbiology, Special Issue on Synthetic Biology, Volume 159 (2013), pp. 1221-1235, doi:10.1099/mic.0.066308-0.
- Synthetic gene circuits for metabolic control: design trade-offs and constraints, D. Oyarzun, G.-B. Stan, Journal of the Royal Society Interface, Volume 10 (2013), n°78, doi:10.1098/rsif.2012.0671.
- Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study, K. Papadimitriou, G.-B. Stan, M. Drakakis, PLoS ONE, Volume 8 (2013), n°2, doi:10.1371/journal.pone.0053591.
- Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0, J. Quinn, J. Beal, S. Bhatia, P. Cai, J. Chen, K. Clancy, N. Hillson, M. Galdzicki, A. Maheshwari, U. P, M. Pocock, C. Rodriguez, G.-B. Stan, D. Endy, BBF RFC #93, 2013, doi:1721.1/78249
- Decentralised Minimal-time Consensus, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Automatica, Volume 49 (2013), n°5, pp. 1227-1235, doi:10.1016/j.automatica.2013.02.015
- Nonlinear Heat Transfer Processes in a Two-Phase Thermofluidic Oscillator, C. Markides, O. Adebayo, R. Solanki, G.-B. Stan, Applied Energy, Volume 104 (2013), pp. 958-977, doi:10.1016/j.apenergy.2012.11.056.
- Real-time Fault Diagnosis for Large-Scale Nonlinear Power Networks, W. Pan, Y. Yuan, H. Sandberg, J. Gonçalves, G.-B. Stan, Proceedings of the 52nd IEEE Conference on Decision and Control (CDC 2013), Palazzo dei Congressi, Florence, Italy, 10-13 December, 2013.
- On Periodic Reference Tracking Using Batch-Mode Reinforcement Learning with Application to Gene Regulatory Network Control, A. Sootla, N. Strelkowa, D. Ernst, M. Barahona, G.-B. Stan, Proceedings of the 52nd IEEE Conference on Decision and Control (CDC 2013), Palazzo dei Congressi, Florence, Italy, 10-13 December, 2013.
- Control of protein concentrations in heterogeneous cell populations, A. Vignoni, D. Oyarzun, J. Pico, G.-B. Stan, Proceedings of the 12th European Control Conference (ECC 2013), ETH Zurich, Switzerland, 17-19 July, 2013.
- Stochastic simulation of enzymatic reactions under transcriptional feedback regulation, J.-B. Lugagne, D. Oyarzun, G.-B. Stan, Proceedings of the 12th European Control Conference (ECC 2013), ETH Zurich, Switzerland, 17-19 July, 2013.
2012
- Engineering and ethical perspectives in synthetic biology, J. Anderson, N. Strelkowa, G.-B. Stan, T. Douglas, J. Savulescu, M. Barahona, and A. Papachristodoulou, EMBO reports, Volume 13 (2012), n°7, pp. 584-590, doi:10.1038/embor.2012.81.
- Global State Synchronization in Networks of Cyclic Feedback Systems, A. O. Hamadeh, G.-B. Stan, R. Sepulchre, and J. M. Gonçalves, IEEE Transacations on Automatic Control, Volume 57 (2012), n°2, pp. 478-483, doi:10.1109/TAC.2011.2164015.
- Arterial Reservoir-Excess Pressure and Ventricular Work, K. H. Parker, J. Alastruey, G.-B. Stan, Medical & Biological Engineering & Computing Journal, Volume 50 (2012), n°4, pp. 419-424, doi:10.1007/s11517-012-0872-1, Supplementary material.
- Synthetic Biology Open Language (SBOL) Version 1.1.0, M. Galdzicki, M. L. Wilson, C. A. Rodriguez, M. R. Pocock, E. Oberortner, L. Adam, A. Adler, J. C. Anderson, J. Beal, C. Yizhi, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grunberg, T. S. Ham, J. N. Hillson, J. D. Johnson, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T. F. Smith, G.-B. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, BBF RFC 87, 2012, doi:1721.1/73909
- Design constraints in an operon circuit for engineered control of metabolic networks, D. Oyarzun, G.-B. Stan, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012.
- Reconstruction of Arbitrary Biochemical Reaction Networks: A Compressive Sensing Approach, W. Pan, Y. Yuan, J. Gonçalves, G.-B. Stan, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012.
- Dynamical Structure Function Identifiability Conditions Enabling Signal Structure Reconstruction, J. Adebayo, T. Southwick, V. Chetty, E. Yeung, Y. Yuan, J. Gonçalves, J. Grose, J. Prince, G.-B. Stan, S. Warnick, Proceedings of the 51st IEEE Conference on Decision and Control (CDC 2012), Maui, Hawaii, USA, 10-13 December, 2012.
- Design tradeoffs in a synthetic gene control circuit for metabolic networks, D. Oyarzun, G.-B. Stan, Proceedings of the 2012 American Control Conference (ACC 2012), Montreal, Canada, 27-29 June, 2012.
2011
- The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose, N. Dalchau, S. J. Baek, H. M. Briggs, F. C. Robertson, A. N. Dodd, M. J. Gardner, M. A. Stancombe, M. J. Haydon, G.-B. Stan, J. M. Gonçalves, A. A. R. Webb, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Volume 108 (2011), n°12, pp. 5104-5109, doi:10.1073/pnas.1015452108, Supplementary material.
- Essential information for synthetic DNA sequences, J. Peccoud, J. C. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. W. Lux, C. A. Rodriguez, G.-B. Stan, H. M. Sauro, Nature Biotechnology, Volume 22 (Jan 2011), n°1, p. 22, doi:10.1038/nbt.1753.
- Computational design approaches and tools for synthetic biology, J. MacDonald, C. Barnes, R. Kitney, P. Freemont, G.-B. Stan, Integrative Biology, Special Issue on Synthetic Biology, Volume 3 (2011), n°2, pp. 97-108, doi:10.1039/c0ib00077a. Top ten most accessed Integrative Biology articles in February, March, May, June, July, and August 2011. Second most highly 2013 cited Integrative Biology submission from the U.K.
- Fast consensus via predictive pinning control, H.-T. Zhang, M. Z. Q. Chen, G.-B. Stan, IEEE Transaction on Circuits and Systems I, Volume 58 (2011), n°9, pp. 2247-2258, doi:10.1109/TCSI.2011.2123450.
- Robust dynamical network structure reconstruction, Y. Yuan, G.-B. Stan, S. Warnick, J. M. Gonçalves, Automatica, Special Issue on Systems Biology, Volume 47 (2011), n°6, pp. 1230-1235, doi:10.1016/j.automatica.2011.03.008.
- Synthetic Biology Open Language (SBOL) Version 1.0.0, M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, J. C. Anderson, J. Beal, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Grunberg, T. S. Ham, A. Kuchinsky, M. W. Lux, C. Madsen, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. F. Smith, G.-B. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, BBF RFC 84, 2011, doi:1721.1/66172
- Network of passive oscillators, V. Kulkarni, M. Riedel, G.-B. Stan, Proceedings of the 49th Annual Allerton Conference on Communication, Control, and Computing, University of Illinois at Urbana-Champaign, Allerton Retreat Center, Monticello, Illinois, USA, 28-30 September, 2011.
- Decentralised Minimal-time Consensus, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Proceedings of the 50th IEEE Conference on Decision and Control (CDC 2011), Orlando, Florida, USA, 12-15 December, 2011.
2010
- Correct biological timing in Arabidopsis requires multiple light signaling pathways, N. Dalchau, K. E. Hubbard, C. T. Hotta, F. C. Robertson, H. M. Briggs, G.-B. Stan, J. M. Gonçalves, A. A. R. Webb, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Volume 107 (2010), n° 29, pp. 13171-13176, doi:10.1073/pnas.1001429107, Supplementary material.
- Constructive Synchronization of Networked Feedback Systems, A. O. Hamadeh, G.-B. Stan, J. Gonçalves, Proceedings of the 49th IEEE Conference on Decision and Control (CDC 2010), Atlanta, Georgia, USA, 15-17 December, 2010.
- Robust Dynamical Network Reconstruction, Y. Yuan, G.-B. Stan, S. Warnick, J. Gonçalves, Proceedings of the 49th IEEE Conference on Decision and Control (CDC 2010), Atlanta, Georgia, USA, 15-17 December, 2010.
- Minimal-time output final value of unknown DT-LTI systems with application to the decentralised network consensus problem, Y. Yuan, G.-B. Stan, L. Shi, M. Barahona, J. Gonçalves, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2010), University Congress Center, Budapest, Hungary, 5-9 July, 2010.
- Robust dynamical network structure reconstruction with application to systems biology, Y. Yuan, G.-B. Stan, S. Warnick, J. Gonçalves, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2010), University Congress Center, Budapest, Hungary, 5-9 July, 2010.
2009
- Apoptosis characterizes immunological failure of HIV infected patients, M.-J. Mhawej, C. Brunet-François, R. Fonteneau, D. Ernst, V. Ferré, G.-B. Stan, F. Raffi, C. H. Moog, IFAC Control Engineering Practice, Volume 17 (2009), pp. 798-804, doi:10.1016/j.conengprac.2009.01.001
- Decentralized final value theorem for discrete-time LTI systems with application to minimal-time distributed consensus, Y. Yuan, G.-B. Stan, L. Shi, J. Gonçalves, Proceedings of the 48th IEEE Conference on Decision and Control (CDC 2009), Shangai, China, 16-18 December, 2009.
- Minimal dynamical structure realisations with application to network reconstruction from data, Y. Yuan, G.-B. Stan, Sean Warnick, J. Gonçalves, Proceedings of the 48th IEEE Conference on Decision and Control (CDC 2009), Shangai, China, 16-18 December, 2009.
2008
- Collective behavior coordination with predictive mechanisms, H.-T. Zhang, M. Z. Chen, G.-B. Stan, T. Zhou and J. M. Maciejowski, IEEE Circuits and Systems Magazine, Volume 8 (2008), n° 3, pp. 67-85 doi:10.1109/MCAS.2008.928446
- Ultrafast Consensus via Predictive Mechanisms, H.-T. Zhang, M. Z. Chen, T. Zhou, and G.-B. Stan, Europhysics Letters, Volume 83 (2008), n° 4, doi:10.1209/0295-5075/83/40003
- Modelling the influence of activation-induced apoptosis of CD4+ and CD8+ T-cells on the immune system response of a HIV infected patient, G.-B. Stan, F. Belmudes, R. Fonteneau, F. Zeggwagh, M.-A. Lefebvre, C. Michelet, and D. Ernst, IET Systems Biology, Volume 2 (2008), n° 2, pp. 94-102, doi:10.1049/iet-syb:20070029
- Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks, R. Howes, L. Eccleston, J. Gonçalves, G.-B. Stan, S. Warnick, Proceedings of the 47th IEEE Conference on Decision and Control (CDC 2008), Cancun, Mexico, 9-11 December, 2008.
- Robust Synchronization in Networks of Cyclic Feedback Systems, A. O. Hamadeh, G.-B. Stan, J. Gonçalves, Proceedings of the 47th IEEE Conference on Decision and Control (CDC 2008), Cancun, Mexico, 9-11 December, 2008.
- Global Asymptotic Stability of the Limit Cycle in Piecewise Linear versions of the Goodwin Oscillator, A. Salinas-Varela, G.-B. Stan, J. Gonçalves, Proceedings of the 17th IFAC World Congress (IFAC 2008), Seoul, Korea, 6-11 July, 2008.
2007
- Analysis of interconnected oscillators by dissipativity theory, G.-B. Stan, R. Sepulchre, IEEE Transactions on Automatic Control, Volume 52 (2007), n° 2, pp. 256-270, doi:10.1109/TAC.2006.890471
- The cross-entropy method for power system combinatorial optimization problems, D. Ernst, M. Glavic, G.-B. Stan, S. Mannor, L. Wehenkel, Proceedings of the 7th IEEE Power Engineering Society (PowerTech 2007), Lausanne, Switzerland, 1-5 July, 2007.
- Output synchronization in networks of cyclic biochemical oscillators, G.-B. Stan, A. O. Hamadeh, J. Gonçalves, R. Sepulchre, Proceedings of the 26th American Control Conference (ACC 2007), Times Square, New York City, USA, July 11-13, 2007.
2006
- Clinical data based optimal STI strategies for HIV: a reinforcement learning approach, D. Ernst, G.-B. Stan, J. Gonçalves, L. Wehenkel, Proceedings of the 45th IEEE Conference on Decision and Control (CDC 2006), San Diego, CA, USA, December 13-15, 2006.
- Clinical data based optimal STI strategies for HIV: a reinforcement learning approach, D. Ernst, G.-B. Stan, J. Gonçalves, L. Wehenkel, Proceedings of the 15th annual machine learning conference of Belgium and The Netherlands (BENELEARN 2006), Ghent, Belgium, May 11-12, 2006.
2005
- Feedback Mechanisms for Global Oscillations in Lure Systems, R. Sepulchre, G.-B. Stan, Systems & Control Letters, Volume 54 (2005), n° 8 , pp. 809-818, doi:10.1016/j.sysconle.2004.12.004
- Global analysis and synthesis of oscillations: a dissipativity approach, G.-B. Stan, Ph.D. thesis, University of Liege, Belgium, March, 2005.
2004
- Global Analysis of Limit Cycles in Networks of Oscillators, G.-B. Stan, R. Sepulchre, Proceedings of the 6th IFAC International Symposium on Nonlinear Control Systems (NOLCOS 2004), Stuttgart, Germany, September 1-3, 2004, pp. 1433-1438.
- Dissipativity and Global Analysis of Limit Cycles in Networks of Oscillators, G.-B. Stan, R. Sepulchre, Proceedings of the 16th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2004), Leuven, Belgium, July 5-9, 2004.
2003
2002
2001
Internal Reports
- Comparison of Algorithms for Biological Network Reconstruction from Data, Openwetware webpage of Nuri Purswani as part of her MSc project with me in 2010.
- Global Analysis of Limit Cycles in the Chua System, Internal report, Cambridge University, UK, April 2006, available upon request.
- Dissipativity and Global Analysis of Limit Cycles, Internal Report, Montefiore, Ulg, 2004, available upon request.
Lecture Notes
- The lecture notes and exercises for the course Modelling in Biology in the Department of Bioengineering at Imperial Collge can be found here:
- The lecture notes and exercises for the Matlab practicals of the MRes course in Systems and Synthetic Biology at Imperial College can be found in the following zip file. Also, you can download here some advice for starting MRes students.
- The lecture notes of the course "Robust Multivariable Control: Design of Multivariable Systems (Dynamic Programming, H-2 and H-infinity optimal control)" that I have lectured during the lent terms of 2008 and 2009 at the Department of Engineering of the University of Cambridge are accessible on the following webpage. A summary of the course that I have been involved with is given hereafter:
- Analysis of multivariable systems (6L, Dr J.M Gonçalves)
- Performance measures for multi-input/multi-output systems.
- Stabilisation: stability conditions, all stabilising controllers, small gain theorem.
- Models for uncertain systems.
- Robust stability and performance. Loop shaping design.
- Design of multivariable systems (6L, Dr Guy-Bart Stan)
- Optimal control with full information (dynamic programming).
- The Kalman filter and "LQG" control.
- Optimal control with an "H-infinity" criterion.
- State-space tools for robustness analysis.
Handounts for the second part of the course (design of multivariable systems): part 1, part 2, part 3. Example papers, solutions.
- Slides of the lecture Convergence d'une série de Fourier (in French), May 14, 2009.
- Corresponding lecture notes: Convergence d'une série de Fourier (in French), May 14, 2009. A java applet showing the usefulness and applications of Fourier series is availabe on the Falstad website . This applet should be used in parallel with these lecture notes to illustrate the introduced concepts.
Ph.D. Thesis
The title of my Ph. D. thesis is Global analysis and synthesis of oscillations: a dissipativity approach.
Abstract:
The main theme of this research concerns the global (as opposed to local) analysis and synthesis of stable limit cycle oscillations in dynamical systems. The global analysis of oscillations in systems and networks of interconnected systems is a longstanding problem. Dynamical systems that exhibit robust nonlinear oscillations are called oscillators. Oscillators are ubiquitous in physical, biological, biochemical, and electromechanical systems. Detailed models of oscillators abound in the literature, most frequently in the form of a set of nonlinear differential equations whose solutions robustly converge to a limit cycle oscillation. Local stability analysis is possible by means of Floquet theory but global stability analysis is usually restricted to simple (second order) models. For these simple models, global analysis is performed by using specific low dimensional tools (phase plane methods, Poincaré-Bendixson theorem, etc.) which do not generalise easily to complex (high dimensional) models. As a consequence, global analysis of complex models is quite difficult since there currently exists no general analysis method. This lack of general analysis methods typically forces complex models of oscillators to be studied only through numerical simulation methods. Although numerical simulations of these models may give a first insight into their behaviour, a more in-depth understanding is generally impeded by the complexity of the models and the challenge of rigorous global stability analysis. Moreover, even in the case of simple models, the low dimensional methods used for their analysis do not generalise to the analysis of a network of interconnected oscillators. These considerations show the need for developing general methods that allow the global analysis of oscillators, either isolated or in interconnection. This thesis constitutes the first step towards the development of such a unified oscillators theory. In this aim, this thesis considers an extension of the dissipativity theory introduced by Willems. Nowadays, dissipativity is considered as one of the most general nonlinear (global) stability analysis method for equilibrium points in dynamical systems and networks of interconnected dynamical systems. In this thesis, we show that dissipativity theory can be extended to allow (global) stability analysis of limit cycles in many Lure-type models of oscillators and networks of oscillators. These Lure-type models of oscillators have been named passive oscillators. As the main contributions of this research, we show the implications of this extended dissipativity theory for
- the global stability analysis of isolated passive oscillators
- the global stability analysis of networks of passive oscillators
- the global stability analysis of synchronised oscillations in networks of identical passive oscillators
Furthermore, based on these results, we also propose a limit cycle oscillations synthesis method based on the design of a nonlinear parametric proportional-integral controller aimed at the generation of limit cycle oscillations with large basins of attraction in stabilisable nonlinear systems.
You can download here a summary of my (Ph.D.) F.N.R.S. research project Research.pdf (in french).
Masters Thesis
The translated title of my master thesis is Creation of an autonomous impulse response measurement system for rooms and transducers with different methods - "Réalisation d'une chaine de mesure autonome de la réponse impulsionnelle de salle selon différentes méthodes" (the manuscript is in french).
Abstract:
In this thesis, we compare four of the most used impulse response measurement techniques: Maximum Length Sequence (MLS), Inverse Repeated Sequence (IRS), Time Stretched Pulses, and Logarithmic Sinesweep. These methods are generally used for the measurement of the impulse response of acoustical systems such as transducers, rooms, and binaural impulse responses. The choice of one of these methods depending on the measurement conditions is critical. Therefore an extensive comparison has been realised. This comparison has been done through the implementation and realisation of a complete, fast, reliable, and cheap measurement system. In particular, these different methods have been compared with respect to best achievable signal-to-noise ratio, ease of use, harmonic distortion rejection/measurement, and robustness to measurement conditions (temperature change, impulsive and white noise, etc.). It is shown that in the presence of non white noise, the MLS and IRS techniques are more appropriate. On the contrary, in quiet environments the Logarithmic Sinesweep method is the most accurate: it allows for a direct improvement of the signal-to-noise ratio of up to 30 dB over the other methods, which can be critical for audio virtual reality systems such as auralization systems. Indeed, capturing binaural room impulse responses for high-quality auralization purposes requires a signal-to-noise ratio of more than 90 dB which is unattainable with other measurement techniques due to inherent nonlinearities in the measurement system (especially the loudspeaker), but fairly easy to reach with logarithmic sinesweeps due to the possibility of completely rejecting (and measuring) harmonic distortions. As a consequence, the sinesweep method opens the way for the development of high-quality auralization and sound spatialisation systems, which constitute the basis for advanced audio virtual reality systems.