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Publications in peer-reviewed journals

100.- D. Stepanova, M. Brunet-Guasch, H.M. Byrne, T. Alarcon. Understanding how chromatin folding and enzyme competition affect rugged epigenetic landscapes. Submitted (2024). Preprint version posted in arXiv. 

99.- M. Fucho-Rius, S. Maretvadakethop, A. Haro, R. Perez-Carrasco, T. Alarcon, J. Sardanyes. Local Nearby Bifurcations Lead to Synergies in Critical Slowing Down: the Case of Mushroom Bifurcations. Submitted (2024). Preprint version posted in bioRxiv. 

98.- T. Alarcon, N. Brinas-Pascual, J. Calvo, P. Guerrero, D. Stepanova. Hybrid methods for reaction-diffusion systems. The Mathematics of Movement: an Interdisciplinary Approach to Mutual Challenges in Animal Ecology and Cell Biology. Eds. L. Giuggioli & P.K. Maini. Springer-Verlag. To Appear. Preprint version posted in arXiv.

97.- M. Conte, V.C. Fernandez, F.J. Oliver, T. Alarcon, J. Soler. Emergence of cyclic hypoxia and the impact of PARP inhibitors on tumor progression. npj Systems Biology and Applications. 10, 122 (2024). https://doi.org/10.1038/s41540-024-00453-2.

96.- S. Verdura, S. Pedarra, M.A. Pardo, R. Espin-Garcia, E. Serrano-Hervás, A. Llop-Hernández, E. Teixidor, J. Bosch-Barrera, E. López-Bonet, B. Martin-Castillo, R. Lupu, J. Sardanyès, M.A. Pujana, T. Alarcón, E. Cuyàs, J.A. Menendez. Fatty acid synthase (FASN) is a tumor-cell-intrinsic metabolic checkpoint restricting T-cell immunity. Cell Death Discovery. 10, 417 (2024). doi: https://doi.org/10.1038/s41420-024-02184-z

95.- J.T. Lazaro, A. Albo, T. Alarcon, S.F. Elena, J. Sardanyes. No two without three: Modelling dynamics of the trio RNA virus-defective interfering genomes-RNA satellite. Communications in Nonlinear Sciences and Numerical Simulation. 133,  107987 (2024). doi: https://doi.org/10.1016/j.cnsns.2024.107987. Preprint version posted in arXiv

94.- D.Stepanova, H.M. Byrne, P.K. Maini, T. Alarcon.  Computational modelling of angiogenesis: The importance of cell rearrangements during vascular growth. WIREs Mechanisms of Disease. 16, e1634 (2023). doi: https://doi.org/10.1002/wsbm.1634. Preprint version posted in arXiv.

93.- J.T. Lazaro, T. Alarcon, C.P. Garay, J. Sardanyes. Semiclassical theory explains stochastic ghosts scaling. Proceedings of the Royal Society A Proceedings of the Royal Society A.  479, 20220621 (2023). doi: https://doi.org/10.1098/rspa.2023.0210. We made the cover! Preprint version posted in arXiv.

92.- A. Carrasco-Mantis, T. Alarcon, J.A. Sanz-Herrera. An in silico study on the influence of extracellular matrix mechanics on vasculogenesis. Computer Methods and Programs in Biomedicine. 231, 107369 (2023). https://doi.org/10.1016/j.cmpb.2023.107369

91.- D.Stepanova, H.M. Byrne, P.K. Maini, T. Alarcon. A method to coarse-grain multi-agent stochastic systems with regions of multistability. SIAM Multiscale Modeling and Simulation. 20, 404 (2022). Preprint version posted in arXiv.

90.- S. Salinas-Almaguer, M. Mell, V.G. Almendro-Vedia, K.C.M. Robledo-Sanchez, C. Ruiz-Suarez, T. Alarcon, R.A. Barrio, A. Hernandez-Machado, F. Monroy. Membrane rigidity regulates E. coli proliferation rates. Scientific Reports. 12, 933 (2022). doi: 10.1038/s41598-022-04970-0

89.- E. Fontich, A. Guillamon, J. Tomas Lazaro, T. Alarcon, B. Vidiella, J. Sardanyes. Critical slowing down close to a global bifurcation of a curve of quasi-neutral equilibria. Comm. Nonlin. Sci. Numer. Sim. 104, 106032 (2022). https://doi.org/10.1016/j.cnsns.2021.106032

88- A. Elizalde-Torrent, C. Trejo-Soto, L. Mendez-Mora, M. Nicolau, O. Ezama, M. Gualdron-Lopez, C. Fernandez-Becerra, T. Alarcon, A. Hernandez-Machado, H. del Portillo Obando. Pitting of malaria-infected red blood cells in microfluidic devices mimicking spleen interendothelial slits. Scientific Reports. 11, 22099 (2021). doi: https://doi.org/10.1038/s41598-021-01568-w

87- L.E. Mendez-Mora, M. Cabello-Fusares, J. Ferre-Torres, C. Riera-Llobet, E. Krishnevskaya, C. A. Trejo-Soto, S. Payan-Pernía, I. Hernandez-Rodriguez, C. Morales-Indiano, T. Alarcon, J.L. Vives-Corrons, A. Hernandez-Machado. Blood rheological characterization of beta-thalassemia trait and iron deficiency anemia using front microrheometry. Frontiers in Physiology. 12, 1860 (2021). doi: 10.3389/fphys.2021.761411

86.- T. Alarcon, J. Sardanyes, A. Guillamon, J.A. Menendez. Bivalent chromatin as a therapeutic target in cancer: An in silico predictive approach for combining epigenetic drugs. PLoS Comp. Biol. 17, e1008408 (2021). https://doi.org/10.1371/journal.pcbi.1008408. Preprint version posted in bioRxiv.  

85.- A.I. Rodriguez-Villarreal, L. Ortega-Tana, J. Cid, A. Hernendez-Machado, T. Alarcon, P. Miribel-Catala, J. Colomer-Farrarons. An integrated detection method for flow viscosity measurements in microdevices. IEEE Transactions on Biomedical Engineering. 68, 2049-2057 (2021). doi: 10.1109/TBME.2020.3013519.

84.- L. Mendez-Mora, M. Cabello-Fusares, J. Ferre-Torres, C. Riera-Llobet, S. Lopez, C. Trejo-Soto, T. Alarcon, A. Hernandez-Machado. Microrheometer for biofluidic analysis: Electronic detection of the fluid-front advancement. Micromachines. 12, 726 (2021). https://doi.org/10.3390/mi12060726

83.- D.Stepanova, H.M. Byrne, P.K. Maini, T. Alarcon. A multiscale model of complex endothelial cell dynamics in early angiogenesis. PLoS Comp. Biol. 17, e1008055 (2021). doi: https://doi.org/10.1371/journal.pcbi.1008055. Preprint version posted in bioRxiv.

82.- M.O. Bernabeu, J. Kory, J.A. Grogan, B. Markelc, A. Beardo-Ricol, M. d'Avezac, J. Kaeppler, N. Daly, J. Hetherington, T. Krueger, P.K. Maini, J.M. Pitt-Francis, R.J. Muschel, T. Alarcon, H.M. Byrne. Abnormal morphology biases haematocrit distribution in tumour vasculature and contributes to heterogeneity in tissue oxygenation. Proc. Natl. Adad. Sci. 117, 27811-27819 (2020). doi:  https://doi.org/10.1073/pnas.2007770117. Preprint version posted in bioRxiv.

81.- J. Sardanyes, C. Raich, T. Alarcon. Noise-induced stabilisation of saddle-node ghosts. New J. Phys. 22, 093064 (2020). doi: https://doi.org/10.1088/1367-2630/abb549

80.- E. Cuyas, S. Verdura, B. Martin-Castillo, T. Alarcon, R. Lupu, J. Bosch-Barrera, J.A. Menendez. Tumor-cell-intrinsic immunometabolism and precision nutrition in cancer immunotherapy. Cancers. 12, 1757 (2020). doi: 10.3390/cancers12071757

79.- E. Cuyas, J. Gumizio, S. Verdura, J. Brunet, J. Bosch-Barrera, B. Martin-Castillo, T. Alarcon, J.A. Encinar, A. Martin, and J.A. Menendez. The LSD1 inhibitor iadademstat (ORY-1001) targets SOX2-driven breast cancer stem cells: A potential epigenetic therapy in luminal-B and HER2-positive breast cancer subtypes. Aging.  12, 4794-4814 (2020). doi: 10.18632/aging.102887

78.- R.A. Barrio, T. Alarcon, A. Hernandez-Machado. The dynamics of shapes of vesicle membranes with time dependent spontaneous curvature. PLoS One. 15, e0227562 (2020). doi: 10.1371/journal.pone.0227562

77.- J.A. Menendez, E. Cuyas, N. Folguera-Blasco, S. Verdura, B. Martin-Castillo, T. Alarcon. In silico clinical trials for anti-aging therapies. Aging. 11, 6591-6601 (2019). doi: 10.18632/aging.102180

76.- A.V. Ponce-Bobadilla, T. Carraro, H.M. Byrne, P.K. Maini, T. Alarcon. Age-structure can account for delayed logistic proliferation of scratch assays. Bull. Math. Biol. 81, 2706-2724 (2019). Preprint version available from bioRxiv 

75.- N. Folguera-Blasco, R. Perez-Carrasco, E. Cuyas, J.A. Menendez, T. Alarcon. A multiscale model of epigenetic heterogeneity reveals the kinetic routes of pathological cell fate reprogramming. PLos Comp. Biol. 15, e1006592 (2019). Preprint version available from bioRxiv

74.- A.V. Ponce-Bobadilla, J. Arevalo, E. Sarro, H.M. Byrne, P.K. Maini, T. Carraro, S. Balocco, A. Meseguer, T. Alarcon. Local migration quantification method for scratch assays. J. R. Soc. Interface. 16, 20180709 (2019). doi: 10.1098/rsif.2018.0709. Preprint version avialable from arXiv

73.- J. Forners, J. Sardanyes, T. Lazaro, T. Alarcon, S.F. Elena. Viral replication modes in single-peak fitness landscapes: a dynamical systems analysis. J. Theor. Biol. 460, 170-183 (2019). doi: 10.1016/j.jtbi.2018.10.007. Preprint version available from bioRxiv

72.- E. Cuyas, S. Verdura, N. Folguera-Blasco, C. Bastidas-Velez, A.G. Martin, T. Alarcon, J.A. Menendez. Mitostemness. Cell Cycle. 17, 918-926 (2018) doi: 10.1080/15384101.2018.1467679 (2018).

71.- C.A. Trejo-Soto, E. Costa-Miracle, A.I. Rodríguez-Villarreal, J. Cid, M. Castro, T. Alarcón and A. Hernández-Machado. Front Microrheology of Biological Fluids. J. Phys: Conference Series. 1043, 012058 (2018)

70.- J. Sardanyes, A. Arderiu, S.F. Elena, T. Alarcon. Noise-induced bistability in the quasineutral coexistence of viral RNA under different replication modes.  J. R. Soc. Interface. 15, 20180129 (2018). Preprint version available from bioRxiv

69.- N. Folguera-Blasco, E. Cuyas, J.A. Menendez, T. Alarcon. Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model. PLoS Comp. Biol. 14, e1006052 (2018). doi: 10.1371/journal.pcbi.1006052

68.- R. de la Cruz, R. Perez-Carrasco, P. Guerrero, T. Alarcon, K.M. Page. Minimum Action Path theory reveals the details of stochastic biochemical transitions out of oscillatory states. Phys. Rev. Lett. 120, 128102 (2018). Preprint version available from arXiv:1705.08683. Comment by Meerson and Smith here. Our reply here.

67.- J. Sardanyes and T. Alarcon. Noise-induced bistability in the fate of cancer phenotypic quasispecies: a bit-strings approach. Scientific Reports. 8, 1027 (2018). doi:10.1038/s41598-018-19552-2..

66.- R. de la Cruz, P. Guerrero, J. Calvo, T. Alarcon. Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth. J. Comp. Phys. 350, 974-991 (2017). doi: 10.1016/j.jcp.2017.09.019

65.- J.A. Menendez, T. Alarcon. Senescence-inflammatory regulation of reparative cellular reprogramming in aging and cancer. Frontiers in Cell and Developmental Biology. 5, 49 (2017). doi: 10.3389/fcell.2017.00049

64.- C. Trejo-Soto, E. Costa-Miracle, I. Rodriguez-Villarreal, J. Cid, M. Castro, T. Alarcon, A. Hernandez-Machado. Front microrheology of the non-Newtonian behaviour of blood: Scaling theory of erythrocyte aggregation by aging. Soft Matter. 13, 3042-3047 (2017). doi: 10.1039/C6SM02412B

63.- H. Perfahl, B.D. Hughes, T. Alarcon, P.K. Maini, M.C. Lloyd, M. Reuss, H.. Byrne. 3D Hybrid Modelling of Vascular Network Formation. J. Theor. Biol. 414, 254-268 (2017). doi: 10.1016/j.jtbi.2016.11.013

62.- J.A. Menendez, T. Alarcon. Nuclear reprogramming of cancer stem cells: Corrupting the epigenetic code of cell identity with oncometabolites. Mol. Cell. Oncol.  3, e1160854 (2016). doi: 10.1080/23723556.2016.1160854

61.- T. Alarcon, J. Castillo, B. García-Ponce, M.A. Herrero, and P. Padilla. Growth rate and shape as possible control mechanisms for the selection of mode development in optimal biological branching processes. Eur. Phys. J. Special Topics. 225, 2581-2589 (2016). doi: 10.1140/epjst/e2016-60032-0

60.- A.M. Gonzalez-Guerrico, I. Espinoza, B. Schroeder, C.H. Park, Chandra Mohan KVP, A. Khurana, B. Corominas-Faja, E. Cuyas, T. Alarcon, C. Kleer, J.A. Menendez, Ruth Lupu. Suppression of endogenous lipogenesis induces reversion of the malignant phenotype and normalized differentiation in breast cancer. Oncotarget. 4, 71151 (2016). doi: 10.18632/oncotarget.9463

59.-  E. Cuyas, S. Fernandez-Arroyo, T. Alarcon, R. Lupu, J. Joven, J.A. Menendez. Germline BRCA1 mutation reprograms breast epithelial cell metabolism towards mitochondrial-dependent biosynthesis: Evidence for metformin-based “starvation” strategies in BRCA1 carriers. Oncotarget. 7, 52974-52992. (2016). doi: 10.18632/oncotarget.9732

58.- D. Sanchez-Taltavull, A. Vieiro, T. Alarcon. Stochastic modelling of the eradication of the HIV-1 infection by stimulation of latently infected cells in patients under highly active anti-retroviral therapy. J. Math. Biol. 73, 919–946 (2016). doi: 10.1007/s00285-016-0977-5

57.- R. de la Cruz, P. Guerrero, F. Spill, T. Alarcon. Stochastic multi-scale models of competition within heterogeneous cellular populations: simulation methods and mean-field analysis. J. Theor. Biol. 407, 161-183 (2016). doi:10.1016/j.jtbi.2016.07.028. Preprint version available from arXiv:1607.01449

56.- C. Trejo-Soto, E. Costa-Miracle, I. Rodriguez-Villarreal, J. Cid, T. Alarcon, A. Hernandez-Machado. Capillary filling at the microscale: Control of fluid front using geometry.  PLoS ONE 11, e0153559 (2016). doi: 10.1371/journal.pone.0153559 (2016).

55.- J.A. Menendez, E. Cuyas, N. Folguera-Blasco, S. Fernandez-Arroyo, J. Joven, T. Alarcon. Accelerated geroncogenesis in hereditary breast-ovarian cancer syndrome. Oncotarget. 7, 11959-11971 (2016). doi: 10.18632/oncotarget.7867

54.- J.A. Menendez, B. Corominas-Faja, E. Cuyas, M.G. García, S. Fernandez-Arroyo, A.F. Fernandez, J. Joven, M.F. Fraga, T. Alarcon. Oncometabolic nuclear reprogramming of cancer stemness. Stem Cell Reports. 6, 273-283 (2016). doi: 10.1016/j.stemcr.2015.12.012

53.- E. Ibanez-Marcelo, T. Alarcon. Evolutionary escape on complex genotype-phenotype networks. J. Theor. Biol. 394, 18-31 (2016). doi: 10.1016/j.jtbi.2015.12.033

52.- E. Ibanez-Marcelo, T. Alarcon. Surviving evolutionary escape on complex genotype-phenotype networks. J. Math. Biol. 72, 623-647 (2016). doi: 10.1007/s00285-015-0896-x

51.- P. Guerrero, H.M. Byrne, P.K. Maini, T. Alarcon. From invasion to latency: Intracellular noise and cell motility as key controls of the competition between resource-limited cellular populations. J. Math. Biol. 72, 123-156 (2016). doi: 10.1007/s00285-015-0883-2

50.- S. Fernández-Arroyo, E. Cuyas, J. Bosch-Barrera, T. Alarcon, J. Joven, J.A. Menendez. Activation of the methylation cycle in cells reprogrammed into a stem cell-like state. Oncoscience. 2, 958-967 (2015).

49.- R. de la Cruz, P. Guerrero, F. Spill, T. Alarcon. The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions. J. Chem. Phys. 143, 074105 (2015). Preprint version available from arxiv:1508.02895

48.- F. Spill, P. Guerrero, T. Alarcon, P.K. Maini, H.M. Byrne. Hybrid approaches for multiple-species stochastic reaction-diffusion models. J. Comp. Phys. 299, 429-445 (2015). Preprint version available from arxiv:1507.07992

47.- C.B. Picallo, R.A. Barrio, C. Varea, T. Alarcon, A. Hernandez-Machado. Phase-field modelling of the dynamics of Z-ring formation in liposomes: Onset of constriction and coarsening. Eur. Phys. J. E. 38, 61 (2015). doi: 10.1140/epje/i2015-15061-0

46.- D. Sanchez-Taltavull and T. Alarcon. Stochastic modelling of viral blips in HIV-1-infected patients: Effects of inhomogeneous density fluctuations. J. Theor. Biol. 371, 79-89 (2015). doi:10.106/j.tbi.2015.02.001

45.- F. Spill, P. Guerrero, T. Alarcon, P.K. Maini, H.M. Byrne. Mesoscopic and continuum modelling of angiognesis. J. Math. Biol. 70, 485–532 (2015). doi: 10.1007/s00285-014-0771-1. Preprint version available from arxiv:1401.5701. 

44.- P. Guerrero, T. Alarcon. Stochastic multiscale models of cell population dynamics: asymptotic and numerical methods. Math. Model. Nat. Phenom. 10, 64-93. (2015).

43.- J.A. Menendez, B. Corominas-Faja, E. Cuyas, T. Alarcon. Metabostemness: metaboloepigenetic reprogramming of cancer stem-cell functions. Oncoscience. 1, 803-806. (2014).

42.- J.A. Menendez, T. Alarcon. Metabostemness: a new cancer hallmark. Front. Oncol. 4, 262 (2014). doi:10.3389/fonc.2014.00262.

41.- T. Alarcon, Ph. Getto, Y. Nakata. Stability analysis of a renewal equation for cell population dynamics with quiescence. SIAM J. Appl. Math. 74, 1266-1297 (2014).

40.- E. Ibanez-Marcelo and T. Alarcon. The topology of robustness and evolvability in evolutionary systems with genotype-phenotype map. J. Theor. Biol. 356, 144-162 (2014)

39.- T. Alarcon. Stochastic quasi-steady state approximations for asymptotic solutions of the Chemical Master Equation. J. Chem. Phys. 140, 184109 (2014)

38.- D. Sanchez-Taltavull and T. Alarcon. Robustness of differentiation cascades with symmetric stem cell division. J. R. Soc. Interface. 11, 20140264 (2014). DOI: 10.1098/rsif.2014.0264

37.- J.A. Menendez, T. Alarcon, J. Joven. Gerometabolites: The pseudohypoxic aging side of cancer. Cell Cycle. 13, 699-709 (2014).

36.- J.A. Menendez, T. Alarcon, B. Corominas-Faja, E. Cuyas, E. Lopez-Bonet, A.G. Martin, L. Vellon. Xenopatients 2.0: Reprogarmming the epigenetic landscape of patient-derived cancer genomes. Cell Cycle. 13, 358-370 (2014).

35.- T. Alarcon. Comment on "Morphogenetic action through flux-limited spreading". Phys. Life Rev. 10, 493 (2013). Invited comment to Morphogenetic action through flux-limited spreading by Verbeni et al. Phys. Life Rev. 10, 457 (2013).

34.- L. Willis, T.A. Graham, T. Alarcon, M.R. Alison, I.P.M. Tomlinson, K.M. Page. What can be learnt about disease progression in breast cancer dormancy from disease-free survival data?. PLoS One. 8, e62320 (2013).

33.- J.A. Menendez, J. Joven, S. Cufi, B. Corominas-Faja, C. Oliveras-Ferraros, E. Cuyas, B. Martin-Castillo, E. Lopez-Bonet, T. Alarcon, A. Vazquez-Martin. The Warburg effect version 2.0: Metabolic reprogramming of cancer stem cells. Cell Cycle. 12, 1166 -1179, (2013).

32.- Y. Nakata, P. Getto, A. Marciniak-Czochra, T. Alarcon. Stability analysis of multi-compartment models for cell production systems. J. Biol. Dyn. 6(Supp. 1), 2-18 (2012).

31.- T. Alarcon, H.J. Jensen. Invasion in multi-type populations: The role of robustness and fluctuations. IMA J. Math. Med. Biol. 29, 3-20 (2012). Invited contribution to the special issue on Computational Cancer Modelling, A.R.A. Anderson and K. Rejniak, eds.

30.- H. Perfahl, H.M. Byrne, T. Chen, V. Estrella, T. Alarcon, A. Lapin, R.A. Gatenby, R.J. Gillies, M.C. Lloyd, P.K. Maini, M. Reuss, M.R. Owen. Multiscale modelling of vascular tumour growth in 3D: The roles of domain size and boundary conditions. PLoS One. 6(4), e14790 (2011).

29.- T. Alarcon, Ph. Getto, A. Marciniak-Czochra, MdM. Vivanco. A model for stem cell population dynamics with maturation-regulated delay. Disc. Cont. Dyn. Sys. B. Special Issue 2011, 32-43 (2011).

28.- T. Alarcon and H.J. Jensen. Quiescence: a mechanism for escaping the effects of drug on cell populations. J. R. Soc. Interface. 8, 99-106 (2010). doi:10.1098/rsif.2010.0130

27.- L. Willis, T. Alarcon, G. Elia, J.L. Jones, N. Wright, T.A. Graham, I.P.M. Tomlinson, K.M. Page. Breast cancer dormancy can be maintained by a small number of micrometastases. Cancer Research. 70, 4310-4317 (2010). Supplementary material available here.

26.- T. Alarcon and H.J. Jensen. From gene regulatory networks to population dynamics: robustness, diversity and their role in progression to cancer. arXiv:1003.2366

25.- T. Alarcon. Modelling tumour-induced angiogenesis: A review of individual-based models and multiscale approaches. In The Mathematics of Cancer and Developmental Biology. M.A. Herrero, F. Giraldez, Eds. Contemporary Mathematics. 492, 45-74 (2009)

24.- T Alarcon, H.J. Jensen.  Spreading on a complex network avoiding certain motifs. arXiv:0903.1199.

23.-  M.R. Owen, T. Alarcon, P.K. Maini, H.M. Byrne. Angiogenesis and vascular remodelling in normal and cancerous tissues. J. Math. Biol. 58, 689-721 (2009). DOI: 10.1007/s00285-008-0213-z. Online supplementary material available here.

22.- T. Alarcon, K.M. Page. Mathematical models of the VEGF receptor and its role in cancer therapy. J. R. Soc. Interface. 4, 283-304 (2007). Online supplementary material available here.

21.- T. Alarcon, M.J. Tindall. Modelling cell growth and its modulation of the G1/S transition. Bull. Math. Biol. 69, 197-214 (2007).

20.-  T. Alarcon, M.R. Owen, H.M. Byrne, P.K. Maini. Multiscale modelling of tumour growth and therapy: the influence of vessels normalisation and chemotherapy. Computational Mathematical Methods in Medicine. 7, 85-119 (2006).

19.- P. Betteridge, M.R. Owen,  H.M. Byrne, T. Alarcon, P.K. Maini. The impact of cell crowding and cell movement on vascular tumour growth. Networks and Heterogeneous Materials. 1, 515-535 (2006).

18.- H.M. Byrne, M.R. Owen, T. Alarcon, J. Murphy, P.K. Maini. Modelling the response of vascular tumours to anticancer therapies: a multiscale approach. Math. Mod. Meth. App. Sci. 16, 1-25 (2006). 

17.- H.M. Byrne, T. Alarcon, M.R. Owen, S.D. Webb, P.K. Maini. Modelling aspects of cancer dynamics: a review.  Phil. Trans. Roy. Soc. A. 364, 1563-1568 (2006).

16.- T. Alarcon, R. Marches, K.M. Page. Mathematical models of the fate of lymphoma B-cells after antigen receptor ligation with specific antibodies. J. theor. Biol. 240, 54-71 (2006).

15.- T. Alarcon, K.M. Page. Stochastic models of receptor oligomerisation by bivalent ligands. J. R. Soc. Interface. 3, 545-559 (2006).

14.- T. Alarcon, H.M. Byrne, P.K. Maini. A design principle for vascular beds: the role of complex blood rheology. Microvasc. Res. 69, 156-172 (2005).

13.- T. Alarcon, H.M. Byrne, P.K. Maini. A multiple scale model of tumour growth. Multiscale Model. Sim. 3, 440-475, (2005).

12.- B. Ribba, K. Marron, Z. Agur, T. Alarcon, P.K. Maini. A mathematical model of Doxorubicin treatment efficacy on non-Hodgkin lymphoma: investigation of current protocol through theoretical modelling results. Bull. Math. Biol. 67, 79-99 (2005).

11.- B. Ribba, T. Alarcon, K. Marron, P.K. Maini, Z. Agur. The use of hybrid cellular automata for improving cancer therapy. Lecture Notes in Computer Science. 3305, 444-453 (2005).

10.- T. Alarcon, H.M. Byrne, P.K. Maini. A mathematical model of the effect of hypoxia on the cell-cycle of normal and cancer cells. J. theor. Biol. 229, 395-411 (2004).

9.- T. Alarcon, H.M. Byrne, P.K. Maini. Towards a whole-organ model of tumour growth. Progr. Biophys. Mol. Biol. 85, 451-472 (2004).

8.- T. Alarcon, H.M. Byrne, P.K. Maini. A cellular automaton model for tumour growth in an inhomegeneous environment. J. theor. Biol. 225, 257-274 (2003).

7.- A. Perez-Madrid, T. Alarcon, J.M. Rubi. Vorticity ratchet. Physica A, 325, 55-61 (2003).

6.- T. Alarcon, A. Perez-Madrid. Stochastic resonance in a suspension of magnetic dipoles under shear flow. Phys. Rev. E. 63, 041112 (2001). 

5.- T. Alarcon, A. Perez-Madrid, J.M. Rubi. Energy transduction in peridiocally driven non-Hermitian systems. Phys. Rev. Lett.  85, 3995 (2000).

4.- A. Perez-Madrid, T. Alarcon, J.M.G. Vilar, J.M. Rubi. A mesoscopic approach to the negative viscosity effect in ferrofluids. Physica A. 270, 403 (1999).

3.- T. Alarcon, A. Perez-Madrid, J.M. Rubi. Periodic modulation induced increase of reaction rates in autocatilytic systems. J. Chem. Phys. 108, 7367 (1998). 

2.- T. Alarcon, A. Perez-Madrid, J.M. Rubi. Stochastic resonance in nonpotential systems. Phys. Rev. E. 57, 4979 (1998).

1.- T. Alarcon, A. Perez-Madrid, J.M. Rubi. Low temperature viscosity in elongated ferrofluids. J. Chem. Phys. 107, 10253 (1997).

Book chapters 

5.- H. Perfahl, H.M. Byrne, T. Chen, V. Estrella, T. Alarcon, A. Lapin, R.A. Gatenby, R.J. Gillies, M.C. Lloyd, P.K. Maini, M. Reuss, M.R. Owen. 3D Multiscale Modelling of Angiogenesis and Vascular Tumour Growth. Nano and Micro Flow Systems for Bioanalysis. Eds. M.W.Collins & C.S.Konig. Springer-Verlag. (2013).

4.- T. Alarcon and K.M. Page. Mathematical modelling of the VEGF receptor.  In Modelling tumour vasclature: Molecular, cellular, and tissue level aspects and implications. Ed. T.L. Jackson. Springer-Verlag, New York, USA. (2011).

3.- H.M. Byrne, I.M.M. Van Leeuwen, M.R. Owen, T. Alarcon, P.K. Maini. Multiscale modelling of solid tumour growth. In Selected topics in cancer modelling: Genesis, evolution, immune competition, therapy. N. Bellomo, E. De Angelis, M.A.J. Chaplain, Eds. Modelling and Simulation in Science, Engineering and Technology, Birkhauser, Boston. (2008).

2.- P.K. Maini, T. Alarcon, H.M. Byrne, M.R. Owen, J. Murphy. Structural adaptation in normal and cancerous vasculature. In Math Everywhere: Deterministic and stochastic modelling in biomedicine economics and industry. G. Aletti, M. Burger, A. Micheletti, D. Morale, eds. Springer, Heidelberg (2007).

1.- T. Alarcon, H.M. Byrne, P.K. Maini, J. Panovska. Mathematical modelling of angiogenesis and vascular adaptation. In Multidisciplinary approaches to theory in medicine. Ray Patton and Laura McNamara, eds. Studies in multidisciplinarity, vol. 3, Elsevier (2005).

Peer-reviewed proceedings 

2.-  H.M. Byrne, M.R. Owen, T. Alarcon, P.K. Maini. Cancer disease: Integrative modelling approaches. IEEE International symposium on biomedical imaging: From Nano to Macro, 806-806, (2006).

1.- P.K. Maini, T. Alarcon, H.M. Byrne. Modelling aspects of vascular cancer development. Internationals symposium on mathematical and computational biology. December 3-8, 2005. Petropolis, Brazil. R.P. Mondaini, R. Dilao, eds. World Scientific (2006)

Abstracts 

1.- H.M. Byrne, T. Alarcon, P.K. Maini. Cancer modelling: getting to the heart of the problem. J. Physiol. 561P, SA9 (2005).

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