Hugo Antonius van den Berg, lecturer in Theoretical Biology

University of Warwick




Books

Evolutionary Dynamics: The Mathematics of Genes and Traits (2015) Institute of Physics

Mathematical Models of Biological Systems (2011) Oxford University Press

Mathematics for Multidisciplinary Masters (2007) Warwick University


Papers

82. E. J. Lutton, W. J. E. P. Lammers, S. James, H. A. van den Berg and A. M. Blanks (2018) Identification of uterine pacemaker regions at the myometrial-placental interface J. Physiol. additional animated graphics

81. H. A. van den Berg (2018) Occam's razor: from Ockham's via moderna to modern data science Science Progress

80. H. A. van den Berg (2018) Darwin endures, despite disparagement Science Progress 101 32-51

79. O. A. Nev and H. A. van den Berg (2018) Holling Type I versus Holling Type II functional responses in Gram-negative bacteria Tr. Math. Appl. tny001

78. O. A. Nev and H. A. van den Berg (2018) Microbial metabolism and growth under conditions of starvation modelled as the sliding mode of a differential inclusion Dynamical Systems 33 93-112

76. O. A. Nev, O. A. Nev and H. A. van den Berg (2017) Optimal management of nutrient reserves in microorganisms under time-varying environmental conditions J. Theor. Biol. 429 124-141

76. O. A. Nev and H. A. van den Berg (2017) Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources J. Math. Biol. 74 409-445

75. O. A. Nev and H. A. van den Berg (2017) Mathematical models of microbial growth and metabolism: a whole-organism perspective Science Progress 100 343-362

74. E. J. Lutton, W. J. E. P. Lammers, S. James, H. A. van den Berg and A. M. Blanks (2017) A computational method for three-dimensional reconstruction of the microarchitecture of myometrial smooth muscle from histological sections PLoS ONE 12 e0173404

73. H. A. van den Berg (2017) Inceptions of biomathematics from Lotka to Thom Science Progress 100 45-62

72. D. K. Cole, H. A. van den Berg, A. Lloyd, M. D. Crowther, K. Beck, J. Ekeruche-Makinde, J. J. Miles, A. M. Bulek, G. Dolton, A. A.J. Schauenburg, A. Wall, A. Fuller, M. Clement, B. Laugel, P. J. Rizkallah, L. Wooldridge and A. K. Sewell (2017) Structural mechanism underpinning cross-reactivity of a CD8+ T-cell clone that recognises a peptide derived from human telomerase reverse transcriptase J. Biol. Chem. 292 802-813

71. T. Dockree, C. J. Holland, M. Clement, K. Ladell, J. E. McLaren, H. A. van den Berg, E. Gostick, S. Llewellyn-Lacey, S. Man, M. Bailey, S. R. Burrows, D. A. Price, L. Wooldridge (2017) CD8+ T-cell specificity is compromised at a defined major histocompatibility complex class I/CD8 affinity threshold Immunol. Cell Biol. 95 68-76

70. M. Clement, J. A. Pearson, S. Gras, H. A. van den Berg, A. Lissina, S. Llewellyn-Lacey, M. D. Willis, T. Dockree, J. E. McLaren, J. Ekeruche-Makinde, E. Gostick, N. P. Robertson, J. Rossjohn, S. R. Burrows, D. A. Price, F. S. Wong, M. Peakman, A. Skowera, L. Wooldridge (2016) Targeted suppression of autoreactive CD8+ T-cell activation using blocking anti-CD8 antibodies Scientific Reports 6, Article number 35332

69. B. Szomolay, J. Liu, P. E. Brown, J. J. Miles, M. Clement, S. Llewellyn-Lacey, G. Dalton, J. Ekeruche-Makinde, A. Lissina, A. J. Schauenburg, A. K. Sewell, S. R. Burrows, M. Roederer, D. A. Price, L. Wooldridge and H. A. van den Berg (2016) Identification of human viral protein derived ligands recognized by individual MHCI-restricted T-cell receptors Immunol. Cell Biol. 94 573-582

68. J. Atia, C. McCloskey, A. S. Shmygol, D. A. Rand, H. A. van den Berg and A. M. Blanks (2016) Reconstruction of cell surface densities of ion pumps, exchangers and channels from mRNA expression, conductance kinetics, whole-cell calcium and current-clamp voltage recordings, with an application to human uterine smooth muscle cells. PLoS Comput Biol 12 e1004828

67. C. E. Dow, D. I. Roper, H. A. van den Berg and A. Rodger (2016) Beyond the Discovery Void: New targets for antibacterial compounds Science Progress 99 153-182

66. C. E. Dow, H. A. van den Berg, D. I. Roper and A. Rodger (2015) Biological insights from a simulation model of the critical FtsZ accumulation required for prokaryotic cell division Biochemistry 54 3803-3813

65. C. E. Broughton, D. I. Roper, H. A. van den Berg and A. Rodger (2015) Bacterial cell division: experimental and theoretical approaches to the divisome Science Progress 98 313-345

64. H. A. van den Berg, Y. N. Kiselev and M. V. Orlov (2015) Homeostatic regulation in physiological systems: a versatile Ansatz Math. Biosci. 268 92-101

63. R. E. Sheldon, A. Shmygol, H. A. van den Berg and A. M. Blanks (2015) Functional and morphological development of the womb throughout life Science Progress 98 103-127

62. R. E. Sheldon, C. Mashayamombe, S.-Q. Shi, R. E. Garfield, A. Shmygol, A. M. Blanks and H. A. van den Berg (2014) Alterations in gap junction connexin43/connexin45 ratio mediate a transition from quiescence to excitation in a mathematical model of the myometrium J. R. Soc. Interface 11 20140726

61. C. McCloskey, C. Rada, E. Bailey, S. McCavera, H. A. van den Berg, J. Atia, D. A. Rand, A. S. Shmygol, Y.-W. Chan, S. Quenby, J. J. Brosens, M. Vatish, J. Zhang, J. Denton, M. J. Taggart, C. Kettleborough, D. Tickle, J. Jerman, P. Wright, T. Dale, S. Kanumilli, D. Trezise, S. Thornton, P. Brown, R. Catalano, N. Lin, S. K. England and A. M. Blanks (2014) The inwardly rectifying K+ channel KIR7.1 controls uterine excitability throughout pregnancy EMBO Mol. Med. 6 1161-1174

60. Y.-W. Chan, H. A. van den Berg, J. D. Moore, S. Quenby and A. M. Blanks (2014) Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq Exp. Physiol. 99 510-524

59. B. J. Hill, P. A. Darrah, Z. Ende, D. R. Ambrozak, K. M. Quinn, S. Darko, E. Gostick, L. Wooldridge, H. A. van den Berg, V. Venturi, M. Larsen, M. P. Davenport, R. A. Seder, D. A. Price and D. C. Douek (2014) Epitope specificity delimits the functional capabilities of vaccine-induced CD8 T cell populations J. Immunol. 193 5626-5636

58. B. Szomolay and H. A. van den Berg (2014) Modulation of T-cell receptor functional sensitivity via the opposing actions of protein tyrosine kinases and phosphatases: a mathematical model Integr. Biol. 6 1183

57. B. Szomolay, T. Williams, L. Wooldridge and H. A. van den Berg (2013) Co-receptor CD8-mediated modulation of T-cell receptor functional sensitivity and epitope recognition degeneracy Frontiers Immunol. 4 article 329

56. H. A. van den Berg, K. Ladell, K. Miners, B. Laugel, S. Llewellyn-Lacey, M. Clement, D. K. Cole, E. Gostick, L. Wooldridge, A. K. Sewell, J. S. Bridgeman and D. A. Price (2013) Cellular-level versus receptor-level response threshold hierarchies in T-cell activation Frontiers Immunol. 4 article 250

55. R. E. Sheldon, M. Baghdadi, C. McCloskey, A. M. Blanks, A. Shmygol and H. A. van den Berg (2013) Spatial heterogeneity enhances and modulates excitability in a mathematical model of the myometrium J. R. Soc. Interface 10 20130458

54. J. Ekeruche-Makinde, J. J. Miles, H. A. van den Berg, A. Skowera, D. K. Cole, G. Dolton, A. J. Schauenburg, M. P. Tan, J. M. Pentier, S. Llewellyn-Lacey,K. M. Miles, A. M. Bulek, M. Clement, T. Williams, A. Trimby, M. Bailey, P. Rizkallah, J. Rossjohn, M. Peakman, D. A. Price, S. R. Burrows, A. K. Sewell and L. Wooldridge (2013) Peptide length determines the outcome of TCR/peptide-MHCI engagement Blood 121 1112-1123

53. C. E. Dow, A. Rodger, D. I. Roper and H. A. van den Berg (2013) A model of membrane contraction predicting initiation and completion of bacterial cell division Integr. Biol. 5 117-795

52. Y.-F. Wang, M. Khan and H. A. van den Berg (2012) Interaction of fast and slow dynamics in endocrine control systems with an application to β-cell dynamics Math. Biosci. 235 8-18

51. I. R. Humphreys, M. Clement, M. Marsden, K. Smart, J. P. Hindley, H. M. Bridgeman, H. A. van den Berg, A. Ager, L. Wooldridge, A. Godkin and A. M. Gallimore (2012) Avidity of influenza-specific memory CD8 T cell responses decays over time compromising antiviral immunity J. Immunol. 42 1-8

50. O. Aslanidi, J. Atia, A.P. Benson, H. A. van den Berg, A. M. Blanks, C. Choi, S. H. Gilbert, I. Goryanin, B. R. Hayes-Gill, A. V. Holden, P. Li, J. E. Norman, A. Shmygol, N. A. B. Simpson, M. J. Taggart, W. C. Tong and H. Zhang (2011) Towards a computational reconstruction of the electrodynamics of premature and full term human labour Progress Biophys. Mol. Biol. 107 183-192

49. L. Wooldridge, J. Ekeruche-Makinde, H. A. van den Berg, A. Skowera, J. J. Miles, M. P. Tan, G. Dolton, M. Clement, S. Llewellyn-Lacey, D. A. Price, M. Peakman and A. K. Sewell (2011) A single autoimmune T cell receptor recognizes more than a million different peptides J. Biol. Chem. 287 1168-1177

48. H. A. van den Berg, C. Molina-ParÝs and A. K. Sewell (2011) Specific T-cell activation in an unspecific T-cell repertoire Science Progress 94 245-264

47. H. A. van den Berg and A. K. Sewell (2011) Dynamic tuning of T cell receptor specificity by co-receptors and costimulation Chapter in: Mathematical Models and Immune Cell Biology, C. Molina-ParÝs, G. Lythe, eds, Springer

46. G. King, J. Oates, D. Patel, H. A. van den Berg and A. M. Dixon (2010) Towards a structural understanding of the smallest known oncoprotein: Investigation of the bovine papillomavirus E5 protein using solution-state NMR Biochimica et Biophysica Acta 1808 1493-1501

45. L. Wooldridge, B. Laugel, J. Ekeruche, M. Clement, H. A. van den Berg, D. A. Price and A. K. Sewell (2010) CD8 controls T cell cross-reactivity J. Immunol. 185 4625-4632

44. H. A. van den Berg and Z. A. Duncombe (2010) Eradication-resolution dynamics with stochastic flare-ups J. Theor. Biol. 264, 962-970

43. K. Hassani-Pak, R. Legaie, C. Cavenet, H. A. van den Berg, J. D. Moore and C. J. Rawlings (2010) Enhancing data integration with text analysis to find proteins implicated in plant stress response J. Integrative Bioinf. 7 121

42. E. R. Stirk, C. Molina-ParÝs, G. Lythe, G. A. D. Hurst and H. A. van den Berg (2010) The limiting conditional distribution in a stochastic model of T cell repertoire maintenance Math. Biosci. 224 74-86

41. E. R. Stirk, G. Lythe, H. A. van den Berg and C. Molina-ParÝs (2010) Stochastic competitive exclusion in the maintenance of the na´ve T cell repertoire J. Theor. Biol. 265 396-410

40. B. Smith, C. Hill, E. L. Godfrey, D. Rand, H. A. van den Berg, S. Thornton, M. Hodgkin, J. Davey and G. Ladds (2009) Dual positive and negative regulation of GPCR signalling by GTP hydrolysis Cellular Signalling 21 1151-1160

39. L. Wooldridge, A. Lissina, D. K. Cole, H. A. van den Berg, D. A. Price and A. K. Sewell (2009) Tricks with tetramers: how to get the most from multimeric peptide-MHC J. Immunol. 126 147-164

38. A. Lissina, K. Ladell, A. Skowera, M. Clement, E. Edwards, R. Seggewiss, H. A. van den Berg, E. Gostick, K. Gallagher, E. Jones, J. J. Melenhorst, A. J. Godkin, M. Peakman, D. A. Price, A. K. Sewell and L. Wooldridge (2009) Protein kinase inhibitors substantially improve the physical detection of T-cells with peptide-MHC tetramers J. Immunol. Meth. 340 11-24

37. R. Pattaranit and H. A. van den Berg (2008) Mathematical models of energy homeostasis Interface 5 1119-1135

36. R. Pattaranit and H. A. van den Berg (2008) Diabetes and mechanisms of insulin resistance Science Progress 91 285-316

35. H. A. van den Berg (2008) Design principles of adaptive cellular immunity for artificial immune systems Soft Comput. 13 1073-1080

34. E. R. Stirk, C. Molina-ParÝs and H. A. van den Berg (2008) Stochastic niche structure and maintenance in the T cell repertoire J. Theor. Biol. 255 237-249

33. J. J. Melenhorst, P. Scheinberg, P. K. Chattopadhyay, A. Lissina, E. Gostick, D. K. Cole, L. Wooldridge, H. A. van den Berg, E. Bornstein, N. F. Hensel, D. C. Douek, M. Roederer, A. K. Sewell, A. J. Barrett and D. A. Price (2008) Detection of low avidity CD8+ T cell populations with coreceptor-enhanced peptide-major histocompatibility complex class I tetramers J. Immunol. Meth. 338 31-39

32. H. A. van den Berg, M. V. Orlov and Yu. N. Kiselev (2008) The Malthusian parameter in microbial ecology and evolution: An optimal control treatment Comp. Maths. Modell. 19 406-428

31. H. A. van den Berg, L. Wooldridge, B. Laugel and A. K. Sewell (2007) Coreceptor CD8-driven modulation of T cell antigen receptor specificity J. Theor. Biol. 249 395-408

30. B. Laugel, H. A. van den Berg, E. Gostick, D. K. Cole, L. Wooldridge, J. M. Boulter, A. Milicic, D. A. Priceand A. K. Sewell (2007) Different T cell receptor affinity thresholds and CD8 coreceptor dependency govern cytotoxic T lymphocyte activation and tetramer binding properties J. Biol. Chem. 282 23799-23810

29. L. Wooldridge, A. Lissina, J. Vernazza, E. Gostick, B. Laugel, S. L. Hutchinson, F. Mirza, P. R. Dunbar, J. M. Boulter, M. Glick, V. Cerundolo, H. A. van den Berg, D. A. Price, A. K. Sewell (2007) Enhanced immunogenicity of CTL antigens through mutation of the CD8 binding MHC class I invariant region Eur. J. of Immunol. 37 1323-1333

28. A. N. W. Hone and H. A. van den Berg (2007) Modelling a cytokine network. Proceedings of the 2007 IEEE Symposium on Foundations of Computational Intelligence (FOCI 2007)

27. A. N. W. Hone and H. A. van den Berg (2007) Mathematical analysis of dynamics and performance of Artificial Immune Systems Chapter in: In Silico Immunology D. Flower and J. Timmis, eds, Springer

26. H. A. van den Berg and D. A. Rand (2007) Quantitative theories of T cell responsiveness Immunological Reviews 216 81-92

25. L. Wooldridge, H. A. van den Berg, M. Glick, E. Gostick, J. M. Brenchley, D. C. Douek, D. A. Price and A. K. Sewell (2005) Interaction between the CD8 coreceptor and MHC class I stabilizes TCR-antigen complexes at the cell surface J. Biol. Chem. 280 27491-27501

24. H. A. van den Berg (2004) Control of T cell immunity: design principles without the wetware. Preprint UKC/IMS/04/36 University of Kent

23. H. A. van den Berg and D. A. Rand (2004) Foreigness as a matter of degree: The relative immunogenicity of peptide/MHC ligands. J. Theor. Biol. 231 535-548

22. H. A. van den Berg and D. A. Rand (2004) Dynamics of T cell activation threshold tuning. J. Theor. Biol. 228 397-416

21. H. A. van den Berg and Yu. N. Kiselev (2004) Expansion and contraction of the cytotoxic T lymphocyte response - an optimal control approach. Bull. Math. Biol. 66 1345-1369

20. H. A. van den Berg and C. Molina-ParÝs (2003) How thymic presentation determines the target of negative selection. J. Theor. Med. 5 1-22

19. H. A. van den Berg, Yu. N. Kiselev and M. V. Orlov (2003) Studying mathematical models of resource allocation among a cell's assimilator mechanisms. J. Math. Sci. 116 3683-3732

18. M. H. Wooders and H. A. van den Berg (2003) Female competition, evolution and the battle of the sexes. The Warwick Economics Research Paper Series 620

17. H. A. van den Berg and D. A. Rand (2003) Antigen presentation as a diversity filter that enhances immune efficacy. J. Theor. Biol. 224 249-267

16. H. A. van den Berg, N. J. Burroughs and D. A. Rand (2002) Quantifying the strength of ligand antagonism in TCR triggering. Bull. Math. Biol. 64 781-808

15. H. A. van den Berg, Yu. N. Kiselev and M. V. Orlov (2002) Optimal allocation of building blocks between nutrient uptake systems in a microbe. J. Math. Biol. 44 276-296

14. H. A. van den Berg, D. A. Rand and N. J. Burroughs (2001) A reliable and safe T cell repertoire based on low-affinity T cell receptors. J. Theor. Biol. 209 465-486

13. H. A. van den Berg, Yu. N. Kiselev and M. V. Orlov (2001) Analysis of trajectories of a nonlinear system of differential equations. Differential Equations 37 1515-1525

12. H. A. van den Berg (2001) How microbes can achieve balanced growth in a fluctuating environment. Acta Biotheor. 49 1-21

11. M. H. Wooders and H. A. van den Berg (2001) The battle of the sexes over the distribution of male surplus Economics Bulletin 3 1-9

10. W. J. van der Steen and H. A. van den Berg (1999) Dissolving disputes over genic selectionism. J. Evol. Biol. 12 177-183

9. H. A. van den Berg, H. M. Jonkers, S. van Bergeijk and S. A. L. M. Kooijman (1998) Biotransformation of dimethylsulfoniopropionate (DMSP) in a sedimental microbial ecosystem subject to diel variations of oxic and anoxic conditions: a simple mathematical model. FEMS Microbiol. Ecol. 26 1-16

8. H. A. van den Berg (1998) Propagation of permanent perturbations in food chains and food webs. Ecol. Model. 107 225-235

7. H. A. van den Berg (1998) Multiple nutrient limitation in unicellulars: reconstructing Liebig's law. Math. Biosci. 149 1-22

6. H. A. van den Berg (1998) A generic view of classic microbial growth models. Acta Biotheor. 46 117-130

5. H. A. van den Berg, Yu. N. Kiselev, M. V. Orlov and S. A. L. M. Kooijman (1998) Optimal allocation between nutrient uptake and growth in a microbial trichome. J. Math. Biol. 37 28-48

4. H. A. van den Berg (1998) Modelling the metabolic versatility of a microbial trichome. Bull. Math. Biol. 60 131-150

3. C. Zonneveld, H. A. van den Berg and S. A. L. M. Kooijman (1997) Modelling carbon cell quota in light-limited phytoplankton. J. Theor. Biol. 188 215-226

2. N. D. de With and H. A. van den Berg (1992) Neuroendocrine control of hydromineral metabolism in molluscs, with special emphasis on the pulmonate freshwater snail, Lymnaea stagnalis. Adv. Comp. Endocrin. 1 83-99

1. H. A. van den Berg (1992) Model for mechanics of mollusc systemic heart. J. Comp. Biochem. Physiol. 101A 835-844


Animated representations of 3D-reconstructed myometrial smooth muscle micro-architecture

Placental-myometrial bridges (with E. J. Lutton and A. M. Blanks); selected circular (brown) and longitudinal (pink) muscle fibres, together with spaces-filling representations (green and yellow) of fibrous connections (bridges) that connect the circular and longitudinal layers of the uterine wall and mediate the linkage between local constriction (circular fibres) and global activation/contraction of the myometrium (longitudinal fibres).

Placental-myometrial bridges (with E. J. Lutton and A. M. Blanks); the z-direction has been exaggerated by a factor 5 to visualise the published histological cut planes.

Placental-myometrial bridges connecting longitudinal and circular layers (with E. J. Lutton and A. M. Blanks); the longitudinal and circular layers of myometrial smooth muscle (in an tissue volume of approximately 5 mm3) are represented by their convex envelopes and these are moves apart as the bridges are stretched to reveal how the latter are anchored in both layers.

Placental-myometrial connecting bridges: z-sections (with E. J. Lutton and A. M. Blanks); these are the sections as originally cut.

Placental-myometrial connecting bridges: x-sections (with E. J. Lutton and A. M. Blanks); these are the virtual sections in the x-direction.

Placental-myometrial connecting bridges: y-sections (with E. J. Lutton and A. M. Blanks); these are the virtual sections in the y-direction.


Current commentary

H. A. van den Berg (2016) X makes nine: a distant ice giant in the Solar system Science Progress 99 220-224

H. A. van den Berg (2018) Doing away with variables Science Progress 101 76-82


Illustration art

Portfolio


PhD students

R. Pattaranit (2009) Glucose sensing in the hypothalamic arcuate nucleus: electrophysiological and mathematical studies

B. Smith (2009) A Systems Biology analysis of G protein-mediated signalling in eukaryotic cells

Y.-F. Wang (2011) Experimental and mathematical studies on changes in beta-cell mass and activity following c-myc-mediated perturbations of insulin expression

J. Atia (2014) A comprehensive mathematical model of the myometrial smooth muscle cell: excitability, Ca2+ dynamics, and network interactions

L. W. Somathilake (2014) On the stability and growth forms of a mathematical model for growth of coral reefs

R. E. Sheldon (2015) The role of gap junctions in the excitability of the myometrial smooth muscle network

C. E. Dow (2015) Kinetics and mechanics of prokaryotic cell division

C. Mashayamombe (2016) The role of progesterone in transcriptomics of smooth muscle cells in the uterus

E. J. Lutton (2016) Propagation of excitability through myometrial tissue

O. A. Nev (2017) Regulation of nutrient uptake, substrate conversion, and bio-production in micro-organisms

J. Dunford (expected 2020) The role of calcium-gated anion channels in the regulation of the myometrial smooth muscle action potential