Publications

You can view some of my academic publications on arXiv, on ResearchGate, or on ORCID.

Pandemic-related writing (popular and technical) is available here (no longer updated).

Mathematical papers and preprints

• [preprint] M. Banaji, Some bounds on positive equilibria in mass action networks (2024), (https://arxiv.org/abs/2409.06877)

• M. Banaji, B. Boros and J. Hofbauer Bifurcations in planar, quadratic mass-action networks with few reactions and low molecularity, Nonlinear Dyn. (2024), (https://doi.org/10.1007/s11071-024-10068-1)

• [preprint] M. Banaji, B. Boros and J. Hofbauer The inheritance of local bifurcations in mass action networks (2023), (http://arxiv.org/abs/2312.12897)

• M. Banaji, B. Boros and J. Hofbauer Oscillations in three-reaction quadratic mass-action systems, Stud Appl Math (2023), (https://doi.org/10.1111/sapm.12639)

• M. Banaji, B. Boros and J. Hofbauer The smallest bimolecular mass-action system with a vertical Andronov–Hopf bifurcation, Appl Math Lett (2023), (https://doi.org/10.1016/j.aml.2023.108671)

• M. Banaji and B. Boros The smallest bimolecular mass action reaction networks admitting Andronov-Hopf bifurcation, Nonlinearity 36(2)(2023) 1398–1433, (https://doi.org/10.1088/1361-6544/acb0a8)

• M. Banaji, Splitting reactions preserves nondegenerate behaviours in chemical reaction networks (2023), SIAM J Appl Math 83(2) 748–769 (preprint: https://arxiv.org/abs/2201.13105)

• M. Banaji, B. Boros and J. Hofbauer, Adding species to chemical reaction networks: preserving rank preserves nondegenerate behaviours, Appl Math Comput 426 (2022) p127109. (Available open access)

• M. Banaji, Building Oscillatory Chemical Reaction Networks by Adding Reversible Reactions, SIAM J Appl Math, 80(4) (2020) 1751–1777. (preprint at https://arxiv.org/abs/1906.09070)

• [preprint] M. Banaji, The determinant of the second additive compound of a square matrix: a formula and applications, (2018) (https://arxiv.org/abs/1806.07162)

• M. Banaji and C. Pantea, The inheritance of nondegenerate multistationarity in chemical reaction networks, SIAM J Appl Math, 78(2) (2018) 1105–1130. (preprint at https://arxiv.org/abs/1608.08400)

• M. Banaji, Inheritance of oscillation in chemical reaction networks, Applied Math Comput, 325 (2018) 191–209. (preprint at https://arxiv.org/abs/1706.00684)

• [preprint] M. Banaji, Counting chemical reactions with NAUTY (2017), (https://arxiv.org/abs/1705.10820)

• 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 at https://arxiv.org/abs/1309.6771)

• M. Banaji and C. Rutherford, Some results on the structure and spectra of matrix-products, Linear Algebra Appl 474, (2015) 192-212. (preprint at https://arxiv.org/abs/1405.7299)

• 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 at https://arxiv.org/abs/1301.7076)

• 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 at https://arxiv.org/abs/1211.2153)

• 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 at http://arxiv.org/abs/1112).

• M. Banaji and J. Mierczyński, Global convergence in systems of differential equations arising from chemical reaction networks, J Differ Equations 254 (3) (2013), 1359-1374. (preprint at https://arxiv.org/abs/1205.1716)

• M. Banaji, Cycle structure in SR and DSR graphs: implications for multiple equilibria and stable oscillation in chemical reaction networks, in Transactions on Petri Nets and other models of Concurrency (ToPNoC), volume V, series: LNCS, volume 6900, K. Jensen, S. Donatelli and J. Kleijn (eds) (2012)

• M. Banaji and C. Rutherford, P-matrices and signed digraphs, Discrete Math 311 (4) (2011) 289-294. (preprint at https://arxiv.org/abs/1006.0152)

• M. Banaji, Graph-theoretic conditions for injectivity of functions on rectangular domains, J Math Anal Appl, 370 (2010) 302-311. (preprint at https://arxiv.org/abs/0911.0843)

• M. Banaji, P0-matrix products of matrices, in Algebraic and Numeric Biology 2010, series: LNCS, volume 6479, K. Horimoto, M. Nakatsui, and N. Popov (eds.) (2010)

• M. Banaji and D. Angeli Convergence in strongly monotone systems with an increasing first integral, SIAM J Math Anal, 42(1) (2010) 334-353; 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 at https://arxiv.org/abs/0809.1308)

• M. Banaji and G. Craciun, Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements, Commun Math Sci, 7(4) (2009) 867-900. (preprint at https://arxiv.org/abs/0903.1190)

• M. Banaji, Monotonicity in chemical reaction systems, Dynamical Systems 24(1) (2009) 1-30

• 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

• 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, computational bio/medical modelling, data analysis

• 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) 1633-4

• 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 Royal Soc Interface 9(72) (2012) 1499-509

• 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) (2012) e38297

• M. D. Papademetriou, I. Tachtsidis, M. Banaji, M. J. Elliott, A. Hoskote and C. E. Elwell, Regional cerebral oxygenation measured by multichannel near-infrared spectroscopy (optical topography) in an infant supported on venoarterial extracorporeal membrane oxygenation, J Thorac Cardiovasc Surg 141(5) (2011) e31-e33

• N. Radde, N. S. Bar and M. Banaji, Graphical methods for analysing feedback in biological networks: a survey, Int J Systems 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 (2009) 120-125

• P. Donnell, M.Banaji and S. Baigent, Stability in generic mitochondrial models, J Math Chem 46(2) (2009) 322-339

• 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 4(11):e1000212 (2008)

• 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

• M. Banaji and S. Baigent, Electron transfer networks, J Math Chem, 43(4) (2008) 1355-1370

• M. Banaji, A generic model of electron transport in mitochondria, J Theor Biol, 243(4) (2006) 501-516

• M. Banaji, I. Tachtsidis, D. Delpy and S. Baigent, A physiological model of cerebral blood flow control, Math Biosci, 194(2) (2005) 125-173

Book chapters, refereed conference papers, and software

• [open source software] P. Donnell, M. Banaji, A. Marginean and C. Pantea, CoNtRol: Chemical Reaction Network analysis tool, (https://control.math.wvu.edu/) (2013–present)

• [Conference paper] D. Highton et al, Modelling Cerebrovascular Reactivity: A Novel Near-Infrared Biomarker of Cerebral Autoregulation? Adv Exp Med Biol 765 (2012) 231-238

• [book chapter] M. Banaji, From structure to dynamics in biological networks, in H. Koeppl et al (Eds.), Design and Analysis of Bio-Molecular Circuits, Springer (2011)

• [book chapter] M. Banaji and S. Baigent, A flexible, iterative, approach to physiological modelling, in: R. Paton and L.A. McNamara (Eds.), Multidisciplinary approaches to theory in medicine, Elsevier (2005)

• [Conference paper] Z. Rong, M. Banaji, T. Moroz and C. E. Cooper, Can mitochondrial cytochrome oxidase mediate hypoxic vasodilation via nitric oxide metabolism?, Adv Exp Med Biol 765 (2012) 231-238

• [Conference paper] B. Jelfs, J. Panovska-Griffiths, I. Tachtsidis, M. Banaji and C. Elwell Individualised Optimisation of Modelled Cerebral Oxygenation Near-Infrared Spectroscopy Signals, Biomedical Optics and 3-D Imaging, OSA Technical Digest (2012).

• [Conference paper] T. Moroz, M. Banaji, et al, Development of a model to aid NIRS data interpretation: Results from a hypercapnia study in healthy adults, Adv Exp Med Biol 737 (2012) 293-300.

• [Conference paper] M. Banaji, A. Mallet, et al, Modelling of mitochondrial oxygen consumption and NIRS detection of cytochrome oxidase redox state, Adv Exp Med Biol, 662 (2010) 285-292

• [open source software] M. Banaji, BRAINCIRC modelling environment. (http://braincirc.sourceforge.net/) (2004-2008)