Professor Nick Monk

All publications

Books

• Monk NAM & Maroto M (2008) Cellular Oscillatory Mechanisms. Springer.

Journal articles

• Kadiyala U, Sprinzak D, Monk NAM, Taylor SE, Verd B, Sonnen KF, Moon L, Roeder AHK, Perez-Carrasco R & Formosa-Jordan P (2025) From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms. Development, 152(14). View this article in WRRO
• Holland BL, Monk NAM, Clayton RH & Osborne CP (2025) Implementing a framework of carbon and nitrogen feedback responses into a plant resource allocation model. in silico Plants, 7(1). View this article in WRRO
• Chaffin S, Monk NAM, Rees JM & Zimmerman WB (2024) Dissolved nutrient gas uptake and fluid mixing by bubble-mediated mass transfer in tall fermenters — a theoretical study. Food and Bioproducts Processing, 145, 136-147. View this article in WRRO
• Jaeger J & Monk N (2022) The flow of substance: a reply to Horsting & Hartjes. EMBO reports, 23(8).
• Chaffin S, Monk N, Rees J & Zimmerman W (2021) Re-entrant corner for a White-Metzner fluid. Fluids, 6(7). View this article in WRRO
• Jaeger J & Monk N (2021) Dynamical modules in metabolism, cell and developmental biology. Interface Focus, 11(3).
• Economou AD, Monk NAM & Green JBA (2020) Perturbation analysis of a multi-morphogen Turing reaction-diffusion stripe patterning system reveals key regulatory interactions. Development, 147(20).
• Verd B, Monk NAM & Jaeger J (2019) Modularity, criticality, and evolvability of a developmental gene regulatory network. eLife, 8, ---.
• Holland BL, Monk NAM, Clayton RH & Osborne CP (2019) A theoretical analysis of how plant growth is limited by carbon allocation strategies and respiration. in silico Plants (isP), 1(1).
• Hartwell RD, England SJ, Monk NAM, van Hateren NJ, Baxendale S, Marzo M, Lewis KE & Whitfield TT (2019) Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression. PLOS Genetics, 15(4). View this article in WRRO
• Jaeger J & Monk N (2015) Everything flows. EMBO reports, 16(9), 1064-1067.
• Kasprzewska A, Carter R, Swarup R, Bennett M, Monk N, Hobbs JK & Fleming A (2015) Auxin influx importers modulate serration along the leaf margin. The Plant Journal, 83(4), 705-718. View this article in WRRO
• Hale R, Brittle AL, Fisher KH, Monk NAM & Strutt D (2015) Cellular interpretation of the long-range gradient of Four-jointed activity in the Drosophila wing. eLife, 4. View this article in WRRO
• Jaeger J & Monk N (2014) Bioattractors: dynamical systems theory and the evolution of regulatory processes.. J Physiol, 592(11), 2267-2281.
• Shimizu H, Woodcock SA, Wilkin MB, Trubenová B, Monk NAM & Baron M (2014) Compensatory flux changes within an endocytic trafficking network maintain thermal robustness of Notch signaling.. Cell, 157(5), 1160-1174.
• Whitfield TT & Monk N (2014) Julian Hart Lewis, FRS (1946-2014) Obituary. DEVELOPMENTAL CELL, 29(5), 507-509.
• Savage N, Yang TJW, Chen CY, Lin KL, Monk NAM & Schmidt W (2013) Positional Signaling and Expression of ENHANCER OF TRY AND CPC1 Are Tuned to Increase Root Hair Density in Response to Phosphate Deficiency in Arabidopsis thaliana. Plos One, 8(10).
• Fischer S, Houston P, Monk NAM & Owen MR (2013) Is a persistent global bias necessary for the establishment of planar cell polarity?. PLoS One, 8(4), e60064.
• Jaeger J, Irons D & Monk N (2012) The Inheritance of Process: A Dynamical Systems Approach. Journal of Experimental Zoology Part B Molecular and Developmental Evolution, 318(8), 591-612.
• Gaffney EA, Monk NAM, Baker RE & Seirin Lee S (2012) Reply to Correspondence: No Oscillations in Real Activator-Inhibitor Systems in Accomplishing Pattern Formation. Bulletin of Mathematical Biology, 1-4.
• Kuwabara A, Backhaus A, Malinowski R, Bauch M, Hunt L, Nagata T, Monk N, Sanguinetti G & Fleming A (2011) A shift toward smaller cell size via manipulation of cell cycle gene expression acts to smoothen Arabidopsis leaf shape.. Plant Physiol, 156(4), 2196-2206.
• Benitez M, Monk NAM & Alvarez-Buylla ER (2011) Epidermal Patterning in Arabidopsis: Models Make a Difference. J EXP ZOOL PART B, 316B(4), 241-253.
• Backhaus A, Kuwabara A, Bauch M, Monk N, Sanguinetti G & Fleming A (2010) LEAFPROCESSOR: a new leaf phenotyping tool using contour bending energy and shape cluster analysis.. New Phytol, 187(1), 251-261.
• Irons DJ, Wojcinski A, Glise B & Monk NAM (2010) Robustness of positional specification by the Hedgehog morphogen gradient. Developmental Biology, 342(2), 180-193.
• Lee SS, Gaffney EA & Monk NAM (2010) The Influence of Gene Expression Time Delays on Gierer-Meinhardt Pattern Formation Systems. B MATH BIOL, 72(8), 2139-2160.
• Schamberg S, Houston P, Monk NAM & Owen MR (2010) Modelling and analysis of planar cell polarity.. Bull Math Biol, 72(3), 645-680.
• Momiji H & Monk NAM (2009) Oscillatory Notch-pathway activity in a delay model of neuronal differentiation.. Phys Rev E Stat Nonlin Soft Matter Phys, 80(2 Pt 1), 021930.
• Marato M & Monk NAM (2008) Advances in Experimental Medicine and Biology: Preface. Advances in Experimental Medicine and Biology, 641, v-vi.
• Momiji H & Monk NAM (2008) Oscillatory expression of Hes family transcription factors: insights from mathematical modelling.. Adv Exp Med Biol, 641, 72-87.
• Savage NS, Walker T, Wieckowski Y, Schiefelbein J, Dolan L & Monk NAM (2008) A mutual support mechanism through intercellular movement of CAPRICE and GLABRA3 can pattern the Arabidopsis root epidermis.. PLoS Biol, 6(9), e235.
• Jaeger J, Irons D & Monk N (2008) Regulative feedback in pattern formation: towards a general relativistic theory of positional information. DEVELOPMENT, 135(19), 3175-3183.
• Momiji H & Monk NAM (2008) Dissecting the dynamics of the Hes1 genetic oscillator.. J Theor Biol, 254(4), 784-798.
• Bennett M & Monk N (2008) The flowering of systems approaches in plant and crop biology.. New Phytol, 179(3), 567-568.
• Monk N (2008) Using mathematical models to probe dynamic expression data.. SEB Exp Biol Ser, 61, 93-111.
• Irons DJ & Monk NAM (2007) Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network.. BMC Bioinformatics, 8, 413.
• Page KM, Monk NAM & Maini PK (2007) Speed of reaction diffusion in embryogenesis. Physical Review E Statistical Nonlinear and Soft Matter Physics, 76(1).
• Gaffney EA & Monk NAM (2006) Gene expression time delays and turing pattern formation systems. Bulletin of Mathematical Biology, 68(1), 99-130.
• Veflingstad SR, Plahte E & Monk NAM (2005) Effect of time delay on pattern formation: Competition between homogenisation and patterning. Physica D Nonlinear Phenomena, 207(3-4), 254-271.
• Page KM, Maini PK & Monk NAM (2005) Complex pattern formation in reaction-diffusion systems with spatially varying parameters. Physica D Nonlinear Phenomena, 202(1-2), 95-115.
• Monk N (2004) Development: dissecting the dynamics of segment determination.. Curr Biol, 14(17), R705-R707.
• Monk N (2004) Developmental biology - Asymmetric fixation. NATURE, 427(6970), 111-112.
• Thomas A, Cannings R, Monk NAM & Cannings C (2003) On the structure of protein-protein interaction networks. Biochemical Society Transactions, 31(6), 1491-1496.
• Monk NAM (2003) Unravelling Nature's networks.. Biochem Soc Trans, 31(Pt 6), 1457-1461.
• Monk N & Lawrence N (2003) Unravelling Nature's Networks: From Microarray and Proteomic Analysis to Systems Biology: University of Sheffield, 21–22 July 2003. The Biochemist, 25(6), 40-41.
• Monk NAM (2003) Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays.. Curr Biol, 13(16), 1409-1413.
• Page K, Maini PK & Monk NAM (2003) Pattern formation in spatially heterogeneous Turing reaction-diffusion models. Physica D Nonlinear Phenomena, 181(1-2), 80-101.
• Page KM, Maini PK, Monk NAM & Stern CD (2001) A model of primitive streak initiation in the chick embryo. Journal of Theoretical Biology, 208(4), 419-438.
• Monk NA (2000) Elegant hypothesis and inelegant fact in developmental biology.. Endeavour, 24(4), 170-173.
• Monk NAM & Hiley BJ (1998) A unified algebraic approach to quantum theory. Foundations of Physics Letters, 11(4), 371-377.
• Monk NAM (1998) Towards a quantum pregeometric description of space-time. Endeavour, 22(1), 27-30.
• Monk NA (1998) Restricted-range gradients and travelling fronts in a model of juxtacrine cell relay.. Bull Math Biol, 60(5), 901-918.
• Monk NAM (1997) The community effect and ectoderm-mesoderm interaction inXenopus muscle differentiation. Bulletin of Mathematical Biology, 59(3), 409-425.
• Monk NAM (1997) Conceptions of space-time: Problems and possible solutions. Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics, 28(1), 1-34.
• Monk NAM (1997) Cell communities and robustness in development. Bulletin of Mathematical Biology, 59(6), 1183-1189.
• Collier JR, Monk NAM, Maini PK & Lewis JH (1996) Pattern Formation by Lateral Inhibition with Feedback: a Mathematical Model of Delta-Notch Intercellular Signalling. Journal of Theoretical Biology, 183(4), 429-446.
• Alachkar N, Opoku NK-DO, Monk NAM & Thurley K () Decoding cellular population dynamics through mechanistic modelling and statistical data analysis. npj Systems Biology and Applications, 12(1).

Book chapters

• Jaeger J & Monk N (2021) Dynamical Modularity of the Genotype-Phenotype Map, Evolutionary Systems Biology (pp. 245-280). Springer International Publishing
• Jaeger J & Monk NA (2013) Keeping the gene in its place In Lambert D & Chetland C (Ed.), The Intuitive Way of Knowing. A Tribute to Brian Goodwin Floris Books
• Monk N (2004) Spatial Patterning in Explicitly Cellular Environments: Activity-Regulated Juxtacrine Signalling, Natural Computing Series (pp. 211-225). Springer Berlin Heidelberg
• Monk NAM, Sherratt JA & Owen MR (2001) Spatiotemporal Patterning in Models of Juxtacrine Intercellular Signalling with Feedback, The IMA Volumes in Mathematics and its Applications (pp. 165-192). Springer New York

Conference proceedings

• Irons D & Monk N (2009) Glypicans enhance robustness in Hedgehog gradient formation. MECHANISMS OF DEVELOPMENT, Vol. 126 (pp S285-S285)
• Monk N & Momiji H (2009) Delay-driven oscillations in the Notch signalling network. MECHANISMS OF DEVELOPMENT, Vol. 126 (pp S287-S287)
• Monk N (2008) Modelling the mutual support of differential cell fates in the Arabidopsis root epidermis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, Vol. 150(3) (pp S45-S45)

Preprints

• Holland BL, Monk NAM, Clayton RH & Osborne CP (2023) Implementing a framework of carbon and nitrogen feedback responses into a plant resource allocation model, Cold Spring Harbor Laboratory.
• Petangoda J, Deisenroth MP & Monk NAM (2021) Learning to Transfer: A Foliated Theory, arXiv.
• Jaeger J & Monk N (2021) Dynamical Modules in Metabolism, Cell and Developmental Biology, Center for Open Science.
• Jaeger J & Monk N (2021) Dynamical Modularity of the Genotype-Phenotype Map, Center for Open Science.
• Hartwell RD, England SJ, Monk NAM, van Hateren NJ, Baxendale S, Marzo M, Lewis KE & Whitfield TT (2018) Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation ofhmx3aexpression, Cold Spring Harbor Laboratory.
• Momiji H & Monk NAM (2009) Oscillatory Notch pathway activity in a delay model of neuronal differentiation, arXiv.
• Thomas A, Cannings R, Monk NAM & Cannings C (2003) On the structure of proten-protein interaction networks, arXiv.
• Economou AD, Monk NAM & Green JBA () Perturbation analysis of a multi-morphogen Turing Reaction-Diffusion stripe patterning system reveals key regulatory interactions.