Article

Yuan, Y and Liu, J and Murray, RM and Goncalves, J (2012) Decentralised minimal-time dynamic consensus. Proceedings of the American Control Conference. pp. 800-805. ISSN 0743-1619

Herrero, E and Kolmos, E and Bujdoso, N and Yuan, Y and Wang, M and Berns, MC and Uhlworm, H and Coupland, G and Saini, R and Jaskolski, M and Webb, A and Gonçalves, J and Davis, SJ (2012) EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. Plant Cell, 24. pp. 428-443. ISSN 1040-4651

Hamadeh, A and Stan, G-B and Sepulchre, R and Gonçalves, J (2012) Global state synchronization in networks of cyclic feedback systems. IEEE Transactions on Automatic Control, 57. pp. 478-483. ISSN 0018-9286

Yuan, Y and Stan, GB and Warnick, S and Goncalves, J (2011) Robust dynamical network structure reconstruction. AUTOMATICA, 47. pp. 1230-1235. ISSN 0005-1098

Dalchau, N and Baek, SJ and Briggs, HM and Robertson, FC and Dodd, AN and Gardner, MJ and Stancombe, MA and Haydon, MJ and Stan, GB and Gonçalves, JM and Webb, AA (2011) The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proc Natl Acad Sci U S A, 108. pp. 5104-5109.

Yuan, Y and Stan, G-B and Barahona, M and Shi, L and Goncalves, J (2011) Decentralised minimal-time consensus. Proceedings of the IEEE Conference on Decision and Control. pp. 4282-4289. ISSN 0191-2216

Yeung, E and Gonçalves, J and Sandberg, H and Warnick, S (2011) Mathematical relationships between representations of structure in linear interconnected dynamical systems. Proceedings of the American Control Conference. pp. 4348-4353. ISSN 0743-1619

Dalchau, N and Hubbard, KE and Robertson, FC and Hotta, CT and Briggs, HM and Stan, GB and Gonçalves, JM and Webb, AA (2010) Correct biological timing in Arabidopsis requires multiple light-signaling pathways. Proc Natl Acad Sci U S A, 107. pp. 13171-13176.

Jones, CN and Goncalves, J (2010) A cost-effective atomic force microscope for undergraduate control laboratories. IEEE Transactions on Education, 53. pp. 328-334. ISSN 0018-9359

Martins, NC and Goncalves, JM (2009) A Linear Programming Approach to Parameter Fitting for the Master Equation. IEEE T AUTOMAT CONTR, 54. pp. 2451-2455. ISSN 0018-9286

Yeung, E and Gonçalves, J and Sandberg, H and Warnick, S (2009) Network structure preserving model reduction with weak a priori structural information. Proceedings of the IEEE Conference on Decision and Control. pp. 3256-3263. ISSN 0191-2216

May, T and Eccleston, LJ and Markusic, D and Seppen, J and Herrmann, S and Hauser, H and Gonçalves, JM and Wirth, D (2008) Bimodal and hysteretic expression in mammalian cells from a synthetic gene circuit. Public Library of Science ONE, 3. ISSN 1932-6203

Gonçalves, JM and Warnick, S (2008) Necessary and sufficient conditions for dynamical structure reconstruction of LTI networks. IEEE Transactions on Automatic Control, 53. pp. 1670-1674. ISSN 0018-9286

Hamadeh, AO and Gonçalves, JM (2008) Reachability analysis of continuous-time piecewise affine systems. Automatica, 44. pp. 3189-3194. ISSN 0005-1098

Dodd, A and Gardner, M and Hotta, C and Hubbard, K and Dalchau, N and Love, J and Assie, JM and Robertson, F and Jakobsen, M and Goncalves, JM and Sanders, D and Webb, A (2007) The Arabidopsis circadian clock incorporates a cADPR-based feedback loop. Science, 318. pp. 1789-1792. ISSN 0036-8075

Dodd, AN and Gardner, MJ and Hotta, CT and Hubbard, KE and Dalchau, N and Love, J and Assie, JM and Robertson, FC and Jakobsen, MK and Goncalves, J and Sanders, D and Webb, AAR (2007) The Arabidopsis circadian clock incorporates a cADPR-based feedback loop. SCIENCE, 318. pp. 1789-1792. ISSN 0036-8075

Rodrigues, S and Goncalves, JM and Terry, J (2007) Existence and stability of limit cycles in a macroscopic neuronal population model. Physica D: Nonlinear Phenomena, 233. pp. 39-65. ISSN 0167-2789

Bernhardt, K and Carter, EJ and Chand, NS and Lee, J and Xu, Y and Zhu, X and Ajioka, JW and Goncalves, JM and Haseloff, J and Micklem, G and Rowe, D (2007) New tools for self-organised pattern formation. IET Synthetic Biology, 1. pp. 29-31. ISSN 1752-1394

Goncalves, JM (2005) Regions of stability for limit cycle oscillations in piecewise linear systems. IEEE Transactions on Automatic Control, 50. pp. 1877-1882. ISSN 0018-9286

Gonçalves, JM and Megretski, A and Dahleh, M (2003) Global analysis of piecewise linear systems using impact maps and quadratic surface Lyapunov functions. IEEE Transactions on Automatic Control, 48. pp. 2089-2106. ISSN 0018-9286

Gonçalves, JM and Megretski, A and Dahleh, MA (2003) Global analysis of piecewise linear systems using impact maps and surface Lyapunov functions. IEEE Transactions on Automatic Control, 48. pp. 2089-2106. ISSN 0018-9286

Gonçalves, JM (2002) L2-gain of double integrators with saturation nonlinearity. IEEE Transactions on Automatic Control, 47. pp. 2063-2068. ISSN 0018-9286

Gonçalves, JM and Megretski, A and Dahleh, MA (2001) Global stability of relay feedback systems. IEEE Transactions on Automatic Control, 46. pp. 550-562. ISSN 0018-9286

Gonçalves, JM and Dahleh, MA (1998) Necessary conditions for robust stability of a class of nonlinear systems. Automatica, 34. pp. 705-714. ISSN 0005-1098

Book Section

Goncalves, JM and Warnick, S, (2009) Control theory and systems biology. In: Control theory and systems biology. The MIT Press, pp. 265-296. ISBN 0262013347,9780262013345

Conference or Workshop Item

Yuan, Y and Stan, GBV and Shi, L and Barahona, M and Goncalves, JM (2010) Minimal-time uncertain output final value of unknown DT-LTI systems with application to the decentralised network consensus problem. In: 19th International Syposium on Mathematical Theory of Networks and Systems, MTNS 2010, 5-7-2010 to 9-7-2010, Budapest, Hungary.

Yuan, Y and Stan, GBV and Warnick, S and Goncalves, JM (2010) Robust dynamical network reconstruction. In: 19th International Syposium on Mathematical Theory of Networks and Systems, MTNS 2010, 5-7-2010 to 9-7-2010, Budapest, Hungary.

Tonita, RJ and Lestas, IC and Goncalves, JM and Vinnicombe, G (2010) Fluctuations and limitations of a multi-sector economic model with delays. In: American Control Conference 2010, 30-6-2010 to 2-7-2010, Baltimore, USA.

Hamadeh, A and Stan, GB and Goncalves, J (2010) Constructive Synchronization of Networked Feedback Systems. In: UNSPECIFIED pp. 6710-6715..

Tonita, R and Lestas, I and Goncalves, J and Vinnicombe, G (2010) Fluctuations and Limitations of a Multi-Sector Economic Model with Delays. In: UNSPECIFIED pp. 6904-6909..

Yuan, Y and Goncalves, J (2010) Minimal-time network reconstruction for DTLTI systems. In: UNSPECIFIED pp. 2676-2681..

Yuan, Y and Stan, GB and Warnick, S and Goncalves, J (2010) Robust dynamical network reconstruction. In: UNSPECIFIED pp. 810-815..

Yuan, Y and Stan, GBV and Shi, L and Goncalves, JM (2009) Decentralized final value theorem for discrete-time LTI systems with application to minimal time distributed consensus. In: 48th IEEE Conference on Decision and Control, IEEE-CDC 2009, 16-12-2009 to 18-12-2009, Shanghai, China pp. 2664-2669..

Yuan, Y and Stan, GBV and Warnick, S and Goncalves, JM (2009) Minimal dynamical structure realisations with application to network reconstruction from data. In: 48th IEEE Conference on Decision and Control, IEEE-CDC 2009, 16-12-2009 to 18-12-2009, Shanghai, China pp. 4808-4813..

Yuan, Y and Stan, GBV and Goncalves, JM (2009) Biological network reconstruction from data (for biologists). In: Imperial College Institute of Systems and Synthetic Biology Autumn Symposium 2009, 11-11-2009 to 12-11-2009, London, UK.

Yuan, Y and Stan, GBV and Goncalves, JM (2009) Biological network reconstruction from data (for engineers). In: The Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, 14-10-2009 to 16-10-2009, Hinxton, Cambridge UK.

Gonçalves, JM and Martins, N (2008) Batch control of the master equation: a linear programming approach. In: Mathematical Theory of Networks and Systems 2008, 28-7-2008 to 1-8-2008, Blacksburg, VA, USA.

Salinas Varela, AA and Stan, GBV and Gonçalves, JM (2008) Global asymptotic stability of the limit cycle in piecewise linear versions of the Goodwin oscillator. In: 17th IFAC World Congress, 6-7-2008 to 11-7-2008, Seoul, Korea.

Dalchau, N and Goncalves, J and Webb, A (2008) Modelling and simulation of a Ca2+-based feedback loop in the circadian clock of Arabidopsis. In: UNSPECIFIED S45-S45..

Tonita, RJ and Gonçalves, JM and Lestas, IC and Vinnicombe, G (2008) Control theory methods for macro models with stochastic micro foundations. In: 15th World Congress of the International Economic Association, 25-6-2008 to 29-6-2008, Istanbul, Turkey.

Tonita, RJ and Gonçalves, JM and Vinnicombe, G (2008) Heterogeneous agent models in economics: a study of heterogeneous productivity of sectors. In: American Control Conference, ACC' 08, 11-6-2008 to 13-6-2008, Seattle, Washington, USA pp. 336-341..

Han, Y and Hengrung, N and Liew, Y and May, S and Miao, Y and Milde, S and Soh, X and Soirez, L and Wyatt, D and Zhao, Z and Ajioka, J and Brown, J and Gonçalves, JM and Haseloff, J and Micklem, G and Southall, T and Malyshev, D and Crowe, L and Wernisch, L (2008) Bacteria online - University of Cambridge iGEM 2007 project. In: The IET Conference on Synthetic Biology, Systems Biology and Bioinformatics, BioSysBio2008, 20-4-2008 to 22-4-2008, Imperial College, London.

Howes, R and Eccleston, LJ and Gonçalves, JM and Stan, GBV and Warnick, S (2008) Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks. In: 47th IEEE Conference on Decision and Control, 9-12-2008 to 11-12-2008, Cancun, Mexico pp. 173-178..

Hamadeh, AO and Gonçalves, JM and Stan, GBV (2008) Robust synchronization in networks of cyclic feedback systems. In: 47th IEEE Conference on Decision and Control, 9-12-2008 to 11-12-2008, Cancun, Mexico pp. 5268-5273..

Neil, D and Jorge, G and Alex, W (2007) Mathematical models for Ca2+-based circadian signalling in plants. In: 2nd Foundations of Systems Biology in Engineering Conference (FOSBE 2007), 9-9-2007 to 12-9-2007, Stuttgart, Germany.

Guy-Bart, S and Abdullah, H and Rodolphe, S and Jorge, G (2007) Output synchronisation in networks of cyclic biochemical oscillators. In: 2007 American Control Conference (ACC 2007), 9-7-2007 to 13-7-2007, New York, US pp. 3973-3978..

Goncalves, J and Howes, R and Warnick, S (2007) Dynamical structure functions for the reverse engineering of LTI networks. In: 46th IEEE Conference on Decision and Control, 12-12-2007 to 14-12-2007, New Orleans, LA, US pp. 1516-1522..

Neil, D and Jorge M, G and Alex A R, W (2007) Mathematical models of circadian Ca2+ oscillations. In: 8th International Conference on Systems Biology (ICSB 2007), 1-10-2007 to 6-10-2007, Long Beach, CA, US.

Russell, H and Jorge, G and Neil, D and Sean, W (2007) Reconstruction of biological networks through gene silencing and overexpression. In: 8th International Conference on Systems Biology (ICSB 2007), 1-10-2007 to 6-10-2007, Long Beach, CA, US.

Goncalves, J and Howes, R and Warnick, S (2007) Dynamical structure functions for the reverse engineering of LTI networks. In: UNSPECIFIED pp. 2442-2448..

Stan, GB and Hamadeh, A and Sepulchre, R and Goncalves, J (2007) Output synchronization in networks of cyclic biochemical oscillators. In: UNSPECIFIED pp. 3212-3217..

Gardner, M and Hotta, C and Hubbard, K and Dalchau, N and Goncalves, J and Dodd, A and Webb, AAR (2006) Rhythmic regulation of Ca2+ signalling networks. In: Plant Biology 2006, 5-8-2006 to 9-8-2006, Boston, MA, US.

Salinas, A and Papachristodoulou, A and Goncalves, J (2006) On L2 error bounds between systems. In: 17th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2006), 24-7-2006 to 28-7-2006, Kyoto, Japan.

Daniel, E and Guy-Bart, S and Jorge, G and Louis, W (2006) Clinical data based optimal STI strategies for HIV: a reinforcement learning approach. In: 45th IEEE Conference on Decision and Control, 2006, 13-12-2006 to 15-12-2006, San Diego, CA, US pp. 667-672..

Yi, T and Fazel, M and Liu, X and Otitoju, T and Goncalves, J and Papchristodoulou, A and Prajna, S and Doyle, J (2005) Application of robust model validation using SOSTOOLS to the study of G-Protein signalling in yeast. In: Foundations of Systems Biology in Engineering (FOSBE) 2005, 7-8-2005 to 10-8-2005, Santa Barbara, CA, US.

Goncalves, J and Yi, T and Doyle, J (2005) Tradeoffs in networks with positive and negative feedback. In: Foundations of Systems Biology in Engineering (FOSBE) 2005, 7-8-2005 to 10-8-2005, Santa Barbara, CA, US.

Hamadeh, AO and Gonçalves, JM (2005) Reachability analysis of continuous time piecewise linear systems. In: The 44th IEEE Conference on Decision and Control and European Control Conference, -12-2005 to --, Seville, Spain pp. 4169-4174..

J M, G and Yi, T-M (2004) Drosophila circadian rhythms: stability robustness analysis and model reduction. In: 16th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2004), 5-7-2004 to 7-7-2004, Leuven, Belgium 256-..

Spanos, D and Gonçalves, JM (2004) High--order--polynomial surface Lyapunov functions for global stability analysis of limit cycle oscillations in piecewise linear systems. In: The American Control Conference, -- to --.

Gonçalves, JM (2003) Global asymptotic stability of oscillations with sliding modes. In: The 15th IFAC World Congress: Sliding control, nonlinear discrete and stochastic systems, -7-2002 to --, Barcelona, Spain pp. 173-178..

Gonçalves, JM (2003) Regions of stability for limit cycles of piecewise linear systems. In: The 42th IEEE Conference on Decision and Control, -- to -- pp. 651-656..

Gonçalves, JM (2002) Quadratic surface Lyapunov functions in the analysis of feedback systems with double integrators and saturations. In: 10th IEEE Mediterranean Conference on Control and Automation, 9-7-2002 to 12-7-2002, Lisbon, Portugal p. 206-..

Gonçalves, JM (2002) L2-gain of double integrators with saturation nonlinearity. In: The 15th IFAC World Congress, 5, -7-2002 to --, Barcelona, Spain pp. 121-126..

Gonçalves, JM and Megretski, A and Dahleh, MA (2001) Global analysis of piecewise linear systems using impact maps and quadratic surface Lyapunov functions. In: The European Control Conference (ECC) 2001, 4-9-2001 to 7-9-2001, Porto, Portugal pp. 1357-1362..

Gonçalves, JM (2001) Quadratic surface Lyapunov functions in global stability analysis of saturation systems. In: The American Control Conference, 6, -6-2001 to --, Arlington, VA, US pp. 4183-4188..

Gonçalves, JM (2000) Global stability analysis of on/off systems. In: 39th IEEE Conference on Decision and Control, -6-2000 to --, Chicago, IL, US pp. 220-224..

Gonçalves, JM and Megretski, A and Dahleh, MA (2000) Global stability of relay feedback systems. In: The IEEE American Control Conference (2000 ACC), -6-2000 to -- pp. 220-224..

Goncalves, JM (2000) Global stability analysis of on/off systems. In: UNSPECIFIED pp. 1382-1387..

Gonçalves, JM and Megretski, A and Dahleh, MA (1998) Semi-global analysis of relay feedback systems. In: The 37th IEEE Conference on Decision and Control, -12-1998 to --, Tampa, FL, US pp. 1967-1972..

Gonçalves, JM and Dahleh, MA (1995) Necessary and sufficient conditions for robust stability of a class of nonlinear systems. In: The 34th IEEE Conference on Decision and Control, 1, -12-1995 to --, New Orleans, LA, US pp. 401-406..

Monograph

Gonçalves, JM and Megretski, A and Dahleh, MA (2002) Global analysis of piecewise linear systems using impact maps and quadratic surface Lyapunov functions: general theory. Technical Report. California Institute of Technology (Caltech).

Gonçalves, JM (2001) L2-gain of double integrators with saturation nonlinearity. Technical Report. California Institute of Technology (Caltech).

Gonçalves, JM (2000) Quadratic surface Lyapunov functions in global stability analysis of saturation systems. Technical Report. Massachusetts Institute of Technology (MIT).

Gonçalves, JM and Megretski, A and Dahleh, MA (1999) Global stability analysis of relay feedback systems. Technical Report. Massachusetts Institute of Technology (MIT).

Thesis

Gonçalves, JM (2000) Constructive global analysis of hybrid systems. PhD thesis, UNSPECIFIED.