Publications, etc.

Maths papers

•  M. Banaji, Inheritance of oscillation in chemical reaction networks [preprint on arXiv].
•  M. Banaji and C. Pantea, The inheritance of nondegenerate multistationarity in chemical reaction networks [preprint on arXiv].
•  M. Banaji and C. Pantea, Some results on injectivity and multistationarity in chemical reaction networks, SIAM J Appl Dyn Syst 15(2) (2016) 807-869 [preprint on arXiv].
•  M. Banaji and C. Rutherford, Some results on the structure and spectra of matrix-products, Linear Algebra Appl 474 (2015) 192-212 [preprint on arXiv].
•  D. Angeli, M. Banaji and C. Pantea, Combinatorial approaches to Hopf bifurcations in systems of interacting elements, Commun Math Sci 12(6) (2014) 1101-1133 [preprint on arXiv].
•  P. Donnell and M. Banaji, Local and global stability of equilibria for a class of chemical reaction networks, SIAM J Appl Dyn Syst 12(2) (2013) 899-920 [preprint on arXiv].
•  M. Banaji and A. Burbanks, A graph-theoretic condition for irreducibility of a set of cone preserving matrices, Linear Algebra Appl 438 (2013) 4103-4113 [preprint on arXiv].
•  M. Banaji and J. Mierczyński, Global convergence in systems of differential equations arising from chemical reaction networks, J Diff Eq 254(3) (2013) 1357-1374 [preprint on arXiv].
•  M. Banaji, Cycle structure in SR and DSR graphs: implications for multiple equilibria and stable oscillation in chemical reaction networks, in K. Jensen, S. Donatelli and J. Kleijn (eds): Transactions On Petri Nets and Other models of Concurrency (ToPNoC), volume V, series: LNCS, volume 6900 (2012)
•  M. Banaji and C. Rutherford, P-matrices and signed digraphs, Discrete Math 311 (4) (2011) 289-294 [preprint on arXiv].
•  M. Banaji, Graph-theoretic conditions for injectivity of functions on rectangular domains, J Math Anal Appl 370 (2010) 302-311 [preprint on arXiv].
•  M. Banaji, P0-matrix products of matrices, Algebraic and Numeric Biology 2010, series: LNCS, volume 6479, K. Horimoto, M. Nakatsui, and N. Popov (eds.)
•  M. Banaji and D. Angeli, Convergence in strongly monotone systems with an increasing first integral, SIAM J Math Anal 42(1) (2010) 334-353 [preprint on arXiv].
•  M. Banaji and D. Angeli, Addendum to "Convergence in strongly monotone systems with an increasing first integral", SIAM J Math Anal 44(1) (2012) 536-537
•  M. Banaji and G. Craciun, Graph-theoretic criteria for injectivity and unique equilibria in general chemical reaction systems, Adv Appl Math 44 (2010) 168-184 [preprint on arXiv].
•  M. Banaji and G. Craciun, Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements, Comm Math Sci 7(4) (2009) 867-900 [preprint on arXiv].
•  M. Banaji, Monotonicity in chemical reaction systems, Dynamical Systems 24(1) (2009) 1-30 [preprint].
•  M. Banaji, P. Donnell and S. Baigent, P matrix properties, injectivity and stability in chemical reaction systems, SIAM J Appl Math 67(6) (2007) 1523-1547 [preprint].
•  M. Banaji, Strongly asymmetric clustering in systems of phase oscillators, Phys Rev E, 71 (2005) 016212
•  M. Banaji, Clustering in globally coupled oscillators, Dynamical Systems, 17(3) (2002), 263-285
•  M. Banaji and P. Glendinning, Towards a Quasi-periodic Mean Field Theory for Globally Coupled Oscillators, Phys Lett A 251 (1999) 297-302

Mathematical biology/chemistry

•  M. Banaji, Counting chemical reaction networks with NAUTY [preprint on arXiv].
•  P. Donnell, M. Banaji, A. Marginean and C. Pantea, CoNtRol: an open source framework for the analysis of chemical reaction networks, Bioinformatics 30(11) (2014) 1633-1634 [full text]
•  [book chapter] M. Banaji, From structure to dynamics in biological networks, H. Koeppl et al (Eds.), Design and Analysis of Bio-Molecular Circuits, Springer (2010)
•  N. Radde, N. S. Bar and M. Banaji, Graphical methods for analysing feedback in biological networks: a survey, Int J Sys Sci 41(1) (2010) 35-46.
•  P. Donnell, S. Baigent and M. Banaji, Monotone dynamics of two cells dynamically coupled by a voltage-dependent gap junction, J Theor Biol 261(1) (2009) 120-125.
•  P. Donnell, M.Banaji and S. Baigent, Stability in generic mitochondrial models, J Math Chem 46(2) (2009) [preprint on arXiv].
•  M. Banaji and S. Baigent, Electron transfer networks, J Math Chem (2007) DOI:10.1007/s10910-007-9257-3 [preprint]
•  M. Banaji, A generic model of electron transport in mitochondria, J Theor Biol, 243(4) (2006) 501-516. [preprint]

Systems biology/modelling

•  T. Moroz, M. Banaji, N. J. Robertson, C. E. Cooper and I. Tachtsidis, Computational modelling of the piglet brain to simulate near-infrared spectroscopy and magnetic resonance spectroscopy data collected during oxygen deprivation, J Roy Soc Interface doi:10.1098/rsif.2011.0766 (2012)
•  B. Jelfs, M. Banaji, I. Tachtsidis, C. E. Cooper and C. E. Elwell, Modelling noninvasively measured cerebral signals during a hypoxemia challenge: Steps towards individualised modelling, PLoS One 7(6): e38297.
•  M. D. Papademetriou, I. Tachtsidis, M. Banaji, M. J. Elliott, A. Hoskote and C. E. Elwell Regional cerebral oxygenation measured by optical topography in an infant supported on veno-arterial Extra-Corporeal Membrane Oxygenation, J Thorac Cardiovasc Surg 141(5) (2011) e31-e33.
•  M. Banaji, I. Tachtsidis, D. Delpy and S. Baigent, A physiological model of cerebral blood flow control, Math Biosci 194(2) (2005) 125-173.
•  M. Banaji, A. Mallet, C. Elwell, P. Nicholls and C. Cooper, A model of brain circulation and metabolism: NIRS signal changes during physiological challenges, PLoS Comput Biol (2008) [paper free on PLoS].
•  V. Stadlbauer, G. Wright, M.Banaji, A. Mukhopadhayay, K. Moore and R. Jalan, Relationship between activation of the sympathetic nervous system and renal blood flow autoregulation in cirrhosis, Gastroenterology 134(1) (2008) 111-119.
•  [book chapter] M. Banaji and S. Baigent, A flexible, iterative, approach to physiological modelling, in: R. Paton, L.A. McNamara (Eds.), Multidisciplinary approaches to theory in medicine, Elsevier (2005)

Refereed conference papers, software

•  M. Banaji, P. Donnell, C. Pantea and A. Marginean, CoNtRol: an open source framework for the analysis of chemical reaction networks.
•  T. Moroz, M. Banaji, M. Tisdall, C. E. Cooper, C. E. Elwell and I. Tachtsidis, Development of a model to aid NIRS data interpretation: Results from a hypercapnia study in healthy adults, Adv Exp Med Bio, 737 (2012) 293-300.
•  M. Banaji, Cycle structure in SR and DSR graphs: implications for multiple equilibria and stable oscillation in chemical reaction networks, Proceedings of the International Workshop on Biological Processes & Petri Nets, Braga (2010)
•  M. Banaji, A. Mallet, C.E. Elwell, P.Nicholls, I. Tachtsidis, M. Smith and C.E. Cooper, Modelling of mitochondrial oxygen consumption and NIRS detection of cytochrome oxidase redox state, Adv Exp Med Bio 662 (2010) 285-292.
•  M. Banaji, BRAINCIRC modelling environment, sourceforge page. (2004-2008).


Talks, etc.

•  Some combinatorial and algebraic problems arising from the study of chemical reaction networks in Dynamics in Networks with Special Properties MBI, Ohio (Jan 2016).
•  Some results on nonexpansive dynamical systems with applications to chemical reaction networks (Applied Maths seminar). Leicester (May 2015).
•  Nonexpansivity in chemical reaction networks. Applied and Computational Mathematics seminar. Madison, Wisconsin (April 2015).
•  Matrices, exterior algebra and combinatorics LSBU maths study group London (March 2015).
•  Some mathematical problems arising in the study of chemical reaction networks, TIFR, Bombay (August 2013).
•  Some combinatorial problems arising in the study of bio/chemical networks, 24th British Combinatorial Conference (Royal Holloway, London, July 2013).
•  Matrix stability from bipartite graphs, Queen Mary Combinatorics Study Group (Feb. 2013).
•  Identifying monotone and strongly monotone dynamical systems, Kent Mathematics Colloquium (Jan. 2013)
•  Equilibria of monotone semiflows with increasing integrals, at POSTA 2012, (Maynooth, Ireland, September 2012).
•  Some Results on Chemical Reaction Networks without the Assumption of Mass Action, at SIAM Life Sciences, (San Diego, August 2012).
•  Some results on reaction networks without assuming mass-action, at Theorems on Biological Circuits IV, (Harvard, July 2011).
•  (presented by C. Rutherford) On the structure and density of sign-P-matrices and their associated graphs, at 23rd British Combinatorial Conference, (Exeter, July 2011)
•  Monotone dynamics in chemical reaction networks, at SMB/ECMTB, (Krakow, June 2011).
•  Injectivity and multistationarity: graph-theoretic approaches, University of Warwick, Network Seminar (March 2010)
•  Convergence in strongly monotone systems with an increasing first integral, UCL, London Dynamical Systems Group meeting, (Feb. 2010)
•  Combinatorial approaches to injectivity of functions, London South Bank University, maths study group meeting (Nov 2009)
•  Combinatorial approaches to injectivity of functions with applications to multiple equilibria in dynamical systems, Queen Mary, University of London, Dynamical systems and statistical physics seminar (Oct 2009)
•  Graph theoretic approaches to injectivity in general dynamical systems, Rutgers, DIMACS (May 2009)
•  Predicting the behaviour of interaction networks from their structure, Manchester, CICADA (April 2009)
•  Making predictions about interaction networks from their structure, Institute for Systems Theory and Automatic Control (Stuttgart, Jan. 2009)
•  Using a model to extract useful information from brain NIRS data (Essex, Nov. 2008)
•  (with P. Donnell, S. Baigent and G. Craciun), Injectivity and monotonicity in chemical reaction networks, (invited by minisymposium organiser), SIAM Conference on Life Sciences (Montreal, Aug. 2008)
•  (with P. Donnell, S. Baigent and G. Craciun), Chemistry without kinetics: Predicting reaction network behaviour from network topology, European Conference on Mathematical and Theoretical Biology (ECMTB) (Edinburgh, July 2008)
•  Interpreting brain NIRS signals (Essex, June 2008)
•  Multiple equilibria in chemical reaction networks: making predictions from network structure, invited presentation at LMS-supported workshop Nonlinear dynamics of chemical and biochemical reaction networks (UCL, May 2008)
•  Making predictions about reaction networks from their structure (Essex, Sept 2007)
•  Modelling circulatory systems, presentation at workshop on "Vital Organ Modelling" (Oxford, March 2007)
•  Modelling the regulation of cerebral blood flow, poster and short talk at workshop on "Blood Flow in the Microcirculation: Function, Regulation, and Adaptation" (Ohio, Jan 2007) Abstract.
•  Chemistry without kinetics: How reaction network topology constrains system behaiour, Applied Maths Seminar presented in UCL Dept of Mathematics (UCL, Jan 2007).
•  Qualitative predictions from biological models, at "Systems Biology 2006 - the challenge of crossing scales" (UCL, December 2006)
•  (with P. Donnell and S. Baigent), Parameter sensitivity analysis of generic models, in Proceedings of the MIAS IRC (2006)
•  (with P. Donnell and S. Baigent), Stability in models of mitochondrial electron transport, in Proceedings of the MIAS IRC (2006)
•  (with I. Tachtsidis, M. Tisdall, M. Smith, S. Baigent, C.E. Elwell and D.T. Delpy), The application of the BRAINCIRC model of human brain circulation to head trauma patients: implications when modelling pathology, in Proceedings of the MIAS IRC (2006)
•  (with P. Donnell), Computational modelling of the cererbal circulation, poster presented at European Conference on Mathematical and Theoretical Biology (Dresden, 2005)
•  (with P. Donnell), Graph Theoretic modelling of the cerebral circulation, poster presented at European Conference on Mathematical and Theoretical Biology (Dresden, 2005)
•  Modelling large biological systems: key theoretical issues (Essex, May 2005)
•  (with S. Baigent), Qualitative models of mitochondrial metabolism, in Proceedings of the MIAS IRC (2005). Abstract.
•  (with P. Donnell), Qualitative Approaches to modelling the cerebral circulation, in Proceedings of the MIAS IRC (2005) Abstract. (2005)
•  (with M. M. Tisdall, I. Tachtsidis, D. T. Delpy, C. E. Elwell and M. M. Smith), Multimodal modelling simulation of hypercapnoeic challenge in acutely brain injured adult patient, in Proceedings of the MIAS IRC (2005) Abstract.
•  (with I. Tachtsidis, D. T. Delpy and S. Baigent), Model parameter setting during a CO2 challenge in healthy volunteers, in Proceedings of the MIAS IRC (2005) Abstract.
•  Modelling the human brain circulation, presentation at Society for Mathematical Biology Annual meeting (Michigan, 2004)
•  (with P. Donnell), Pathways of control in the cerebral vasculature, in Proceedings of the MIAS IRC (2004) Abstract.
•  (with I. Tachtsidis, D.T. Delpy and S. Baigent), A computational model of the cerebral circulation: model predictions with experimental data during a CO2 challenge, in Proceedings of the MIAS IRC (2004) Abstract.
•  (with I. Tachtsidis, D.T. Delpy and S. Baigent), A physiological model of the human brain circulation, in Proceedings of the IPEM on modelling of blood flow in cardiovascular disease, York (2003)