2023

Ryan, W. , Husmeier, D. , Rolinski, O. J. and Vyshemirsky, V. (2023) Bayesian Model Selection and Emulation for Protein Fluorescence. In: 5th International Conference on Statistics: Theory and Applications (ICSTA'23), London, UK, 3-5 Aug 2023, ISBN 9781990800252 (doi: 10.11159/icsta23.153)

2022

Alghamdi, A., Birch, D. J.S., Vyshemirsky, V. and Rolinski, O. J. (2022) Impact of the flavonoid quercetin on β-amyloid aggregation revealed by intrinsic fluorescence. Journal of Physical Chemistry B, 126(38), pp. 7229-7237. (doi: 10.1021/acs.jpcb.2c02763) (PMID:36121408) (PMCID:PMC9527748)

2021

Muir, R., Forbes, S., Birch, D. J.S., Vyshemirsky, V. and Rolinski, O. J. (2021) Collagen glycation detected by its intrinsic fluorescence. Journal of Physical Chemistry B, 125(39), pp. 11058-11066. (doi: 10.1021/acs.jpcb.1c05001) (PMID:34555903)

2019

Rolinski, O. J., Alghamdi, A., Wellbrock, T., Birch, D. J.S. and Vyshemirsky, V. (2019) Cu2+ effects on beta‐amyloid oligomerisation monitored by fluorescence of intrinsic tyrosine. ChemPhysChem, 20(23), pp. 3181-3185. (doi: 10.1002/cphc.201900565) (PMID:31539190)

Chung, L. H. C., Birch, D. J. S., Vyshemirsky, V. , Ryadnov, M. G. and Rolinski, O. J. (2019) Tracking insulin glycation in real time by time-resolved emission spectroscopy. Journal of Physical Chemistry B, 123(37), pp. 7812-7817. (doi: 10.1021/acs.jpcb.9b06363) (PMID:31441653)

2018

Alghamdi, A., Vyshemirsky, V. , Birch, D.J.S. and Rolinski, O.J. (2018) Detecting beta-amyloid aggregation from the time-resolved emission spectra. Methods and Applications in Fluorescence, 6(2), 024002. (doi: 10.1088/2050-6120/aa9f95) (PMID:29210673)

2017

Chung, L. H. C., Birch, D. J.S., Vyshemirsky, V. , Ryadnov, M. G. and Rolinski, O. J. (2017) Insulin aggregation tracked by its intrinsic TRES. Applied Physics Letters, 111(26), 263701. (doi: 10.1063/1.5008477)

Milotti, E., Vyshemirsky, V. , Stella, S., Dogo, F. and Chignola, R. (2017) Analysis of the fluctuations of the tumour/host interface. Physica A: Statistical Mechanics and its Applications, 486, pp. 587-594. (doi: 10.1016/j.physa.2017.06.005)

2016

Mavrogonatou, L. and Vyshemirsky, V. (2016) Sequential Importance Sampling for Online Bayesian Changepoint Detection. In: 22nd International Conference on Computational Statistics (COMPSTAT 2016), Oviedo, Spain, 23-26 Aug 2016, pp. 73-84. ISBN 9789073592360

Rolinski, O. J., McLaughlin, D., Birch, D. J.S. and Vyshemirsky, V. (2016) Resolving environmental microheterogeneity and dielectric relaxation in fluorescence kinetics of protein. Methods and Applications in Fluorescence, 4(2), 024001. (doi: 10.1088/2050-6120/4/2/024001)

Chignola, R., Sega, M., Stella, S., Vyshemirsky, V. and Milotti, E. (2016) From single-cell dynamics to scaling laws in oncology. In: Gerstman, Bernard S. (ed.) Research on the Physics of Cancer. World Scientific: Singapore ; New Jersey, pp. 97-108. ISBN 9789814730259 (doi: 10.1142/9789814730266_0006)

2015

Rolinski, O. J., Wellbrock, T., Birch, D. J.S. and Vyshemirsky, V. (2015) Tyrosine photophysics during the early stages of β-amyloid aggregation leading to Alzheimer’s. Journal of Physical Chemistry Letters, 6(15), pp. 3116-3120. (doi: 10.1021/acs.jpclett.5b01285) (PMID:26267211)

2014

Rolinski, O. J. and Vyshemirsky, V. (2014) Fluorescence kinetics of tryptophan in a heterogeneous environment. Methods and Applications in Fluorescence, 2(4), 045002. (doi: 10.1088/2050-6120/2/4/045002)

Chignola, R., Sega, M., Stella, S., Vyshemirsky, V. and Milotti, E. (2014) From single-cell dynamics to scaling laws in oncology. Biophysical Reviews and Letters, 9(3), pp. 273-284. (doi: 10.1142/S1793048014300035)

Milotti, E., Vyshemirsky, V. , Sega, M. and Chignola, R. (2014) Corrigendum: Interplay between distribution of live cells and growth dynamics of solid tumours. Scientific Reports, 4, 3387. (doi: 10.1038/srep03387) (PMCID:PMC3974140)

2013

Milotti, E., Vyshemirsky, V. , Sega, M., Stella, S., Dogo, F. and Chignola, R. (2013) Computer-aided biophysical modeling: a quantitative approach to complex biological systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(3), pp. 805-810. (doi: 10.1109/TCBB.2013.35) (PMID:24091412)

Milotti, E., Vyshemirsky, V. , Sega, M., Stella, S. and Chignola, R. (2013) Metabolic scaling in solid tumours. Scientific Reports, 3, 1938. (doi: 10.1038/srep01938) (PMID:23727729) (PMCID:PMC3670262)

2012

Milotti, E., Vyshemirsky, V. , Sega, M. and Chignola, R. (2012) Interplay between distribution of live cells and growth dynamics of solid tumours. Scientific Reports, 2, 990. (doi: 10.1038/srep00990) (PMID:23251776) (PMCID:PMC3524520)

2011

Chignola, R., Vyshemirsky, V. , Farina, M., Del Fabbro, A. and Milotti, E. (2011) Modular model of TNFα cytotoxicity. Bioinformatics, 27(13), pp. 1754-1757. (doi: 10.1093/bioinformatics/btr297) (PMID:21561921)

2010

Girolami, M., Calderhead, B. and Vyshemirsky, V. (2010) System identification and model ranking: the Bayesian perspective. In: Lawrence, Neil D., Girolami, Mark, Rattray, Magnus and Sanguinetti, Guido (eds.) Learning and Inference in Computational Systems Biology. MIT Press: Cambridge, Massachusetts ; London, pp. 201-230. ISBN 9780262013864

Sturm, O. E., Orton, R. , Grindlay, J., Birtwistle, M., Vyshemirsky, V. , Gilbert, D., Calder, M. , Pitt, A.R., Kholodenko, B. and Kolch, W. (2010) The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Science Signaling, 3(153), ra90. (doi: 10.1126/scisignal.2001212)

Xu, T. et al. (2010) Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Science Signaling, 3(113), ra20. (doi: 10.1126/scisignal.2000517)

2009

Calder, M. , Gilmore, S., Hillston, J. and Vyshemirsky, V. (2009) Formal methods for biochemical signalling pathways. In: Boca, P., Bowen, J. P. and Siddiqi, J. (eds.) Formal Methods: State of the Art and New Directions. Springer, pp. 185-215. ISBN 9781848827356

2008

Vyshemirsky, V. and Girolami, M. (2008) BioBayes: a software package for Bayesian inference in systems biology. Bioinformatics, 24(17), pp. 1933-1934. (doi: 10.1093/bioinformatics/btn338) (PMID:18632751)

Vyshemirsky, V. and Girolami, M. A. (2008) Bayesian ranking of biochemical system models. Bioinformatics, 24(6), pp. 833-839. (doi: 10.1093/bioinformatics/btm607)

2006

Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R. (2006) Analysis of signalling pathways using continuous time Markov chains. Lecture Notes in Computer Science, 4220, pp. 44-67. (doi: 10.1007/11880646_3)

Gilbert, D., Fuss, H., Gu, X., Orton, R. , Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S. and Dubitzky, W. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 7(4), pp. 339-353. (doi: 10.1093/bib/bbl043)

Vyshemirsky, V. , Girolami, M., Gormand, A. and Kolch, W. (2006) A Bayesian Analysis of the ERK Signalling Pathway. [Research Reports or Papers]

2005

Calder, M. , Vyshemirsky, V. , Gilbert, D. and Orton, R. (2005) Analysis of Signalling Pathways Using the PRISM Model Checker. In: Computational Methods in Systems Biology (CMSB'05), Edinburgh, United Kingdom, 03-05 Apr 2005, pp. 179-190.

Orton, R.J. , Sturm, O.E., Vyshemirsky, V., Calder, M., Gilbert, D.R. and Kolch, W. (2005) Computational modelling of the receptor-tyrosine-kinase-activated MAR pathway. Biochemical Journal, 392, pp. 249-261. (doi: 10.1042/BJ20050908)

Articles

Alghamdi, A., Birch, D. J.S., Vyshemirsky, V. and Rolinski, O. J. (2022) Impact of the flavonoid quercetin on β-amyloid aggregation revealed by intrinsic fluorescence. Journal of Physical Chemistry B, 126(38), pp. 7229-7237. (doi: 10.1021/acs.jpcb.2c02763) (PMID:36121408) (PMCID:PMC9527748)

Muir, R., Forbes, S., Birch, D. J.S., Vyshemirsky, V. and Rolinski, O. J. (2021) Collagen glycation detected by its intrinsic fluorescence. Journal of Physical Chemistry B, 125(39), pp. 11058-11066. (doi: 10.1021/acs.jpcb.1c05001) (PMID:34555903)

Rolinski, O. J., Alghamdi, A., Wellbrock, T., Birch, D. J.S. and Vyshemirsky, V. (2019) Cu2+ effects on beta‐amyloid oligomerisation monitored by fluorescence of intrinsic tyrosine. ChemPhysChem, 20(23), pp. 3181-3185. (doi: 10.1002/cphc.201900565) (PMID:31539190)

Chung, L. H. C., Birch, D. J. S., Vyshemirsky, V. , Ryadnov, M. G. and Rolinski, O. J. (2019) Tracking insulin glycation in real time by time-resolved emission spectroscopy. Journal of Physical Chemistry B, 123(37), pp. 7812-7817. (doi: 10.1021/acs.jpcb.9b06363) (PMID:31441653)

Alghamdi, A., Vyshemirsky, V. , Birch, D.J.S. and Rolinski, O.J. (2018) Detecting beta-amyloid aggregation from the time-resolved emission spectra. Methods and Applications in Fluorescence, 6(2), 024002. (doi: 10.1088/2050-6120/aa9f95) (PMID:29210673)

Chung, L. H. C., Birch, D. J.S., Vyshemirsky, V. , Ryadnov, M. G. and Rolinski, O. J. (2017) Insulin aggregation tracked by its intrinsic TRES. Applied Physics Letters, 111(26), 263701. (doi: 10.1063/1.5008477)

Milotti, E., Vyshemirsky, V. , Stella, S., Dogo, F. and Chignola, R. (2017) Analysis of the fluctuations of the tumour/host interface. Physica A: Statistical Mechanics and its Applications, 486, pp. 587-594. (doi: 10.1016/j.physa.2017.06.005)

Rolinski, O. J., McLaughlin, D., Birch, D. J.S. and Vyshemirsky, V. (2016) Resolving environmental microheterogeneity and dielectric relaxation in fluorescence kinetics of protein. Methods and Applications in Fluorescence, 4(2), 024001. (doi: 10.1088/2050-6120/4/2/024001)

Rolinski, O. J., Wellbrock, T., Birch, D. J.S. and Vyshemirsky, V. (2015) Tyrosine photophysics during the early stages of β-amyloid aggregation leading to Alzheimer’s. Journal of Physical Chemistry Letters, 6(15), pp. 3116-3120. (doi: 10.1021/acs.jpclett.5b01285) (PMID:26267211)

Rolinski, O. J. and Vyshemirsky, V. (2014) Fluorescence kinetics of tryptophan in a heterogeneous environment. Methods and Applications in Fluorescence, 2(4), 045002. (doi: 10.1088/2050-6120/2/4/045002)

Chignola, R., Sega, M., Stella, S., Vyshemirsky, V. and Milotti, E. (2014) From single-cell dynamics to scaling laws in oncology. Biophysical Reviews and Letters, 9(3), pp. 273-284. (doi: 10.1142/S1793048014300035)

Milotti, E., Vyshemirsky, V. , Sega, M. and Chignola, R. (2014) Corrigendum: Interplay between distribution of live cells and growth dynamics of solid tumours. Scientific Reports, 4, 3387. (doi: 10.1038/srep03387) (PMCID:PMC3974140)

Milotti, E., Vyshemirsky, V. , Sega, M., Stella, S., Dogo, F. and Chignola, R. (2013) Computer-aided biophysical modeling: a quantitative approach to complex biological systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(3), pp. 805-810. (doi: 10.1109/TCBB.2013.35) (PMID:24091412)

Milotti, E., Vyshemirsky, V. , Sega, M., Stella, S. and Chignola, R. (2013) Metabolic scaling in solid tumours. Scientific Reports, 3, 1938. (doi: 10.1038/srep01938) (PMID:23727729) (PMCID:PMC3670262)

Milotti, E., Vyshemirsky, V. , Sega, M. and Chignola, R. (2012) Interplay between distribution of live cells and growth dynamics of solid tumours. Scientific Reports, 2, 990. (doi: 10.1038/srep00990) (PMID:23251776) (PMCID:PMC3524520)

Chignola, R., Vyshemirsky, V. , Farina, M., Del Fabbro, A. and Milotti, E. (2011) Modular model of TNFα cytotoxicity. Bioinformatics, 27(13), pp. 1754-1757. (doi: 10.1093/bioinformatics/btr297) (PMID:21561921)

Sturm, O. E., Orton, R. , Grindlay, J., Birtwistle, M., Vyshemirsky, V. , Gilbert, D., Calder, M. , Pitt, A.R., Kholodenko, B. and Kolch, W. (2010) The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Science Signaling, 3(153), ra90. (doi: 10.1126/scisignal.2001212)

Xu, T. et al. (2010) Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Science Signaling, 3(113), ra20. (doi: 10.1126/scisignal.2000517)

Vyshemirsky, V. and Girolami, M. (2008) BioBayes: a software package for Bayesian inference in systems biology. Bioinformatics, 24(17), pp. 1933-1934. (doi: 10.1093/bioinformatics/btn338) (PMID:18632751)

Vyshemirsky, V. and Girolami, M. A. (2008) Bayesian ranking of biochemical system models. Bioinformatics, 24(6), pp. 833-839. (doi: 10.1093/bioinformatics/btm607)

Calder, M., Vyshemirsky, V., Gilbert, D. and Orton, R. (2006) Analysis of signalling pathways using continuous time Markov chains. Lecture Notes in Computer Science, 4220, pp. 44-67. (doi: 10.1007/11880646_3)

Gilbert, D., Fuss, H., Gu, X., Orton, R. , Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S. and Dubitzky, W. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 7(4), pp. 339-353. (doi: 10.1093/bib/bbl043)

Orton, R.J. , Sturm, O.E., Vyshemirsky, V., Calder, M., Gilbert, D.R. and Kolch, W. (2005) Computational modelling of the receptor-tyrosine-kinase-activated MAR pathway. Biochemical Journal, 392, pp. 249-261. (doi: 10.1042/BJ20050908)

Book Sections

Chignola, R., Sega, M., Stella, S., Vyshemirsky, V. and Milotti, E. (2016) From single-cell dynamics to scaling laws in oncology. In: Gerstman, Bernard S. (ed.) Research on the Physics of Cancer. World Scientific: Singapore ; New Jersey, pp. 97-108. ISBN 9789814730259 (doi: 10.1142/9789814730266_0006)

Girolami, M., Calderhead, B. and Vyshemirsky, V. (2010) System identification and model ranking: the Bayesian perspective. In: Lawrence, Neil D., Girolami, Mark, Rattray, Magnus and Sanguinetti, Guido (eds.) Learning and Inference in Computational Systems Biology. MIT Press: Cambridge, Massachusetts ; London, pp. 201-230. ISBN 9780262013864

Calder, M. , Gilmore, S., Hillston, J. and Vyshemirsky, V. (2009) Formal methods for biochemical signalling pathways. In: Boca, P., Bowen, J. P. and Siddiqi, J. (eds.) Formal Methods: State of the Art and New Directions. Springer, pp. 185-215. ISBN 9781848827356

Research Reports or Papers

Vyshemirsky, V. , Girolami, M., Gormand, A. and Kolch, W. (2006) A Bayesian Analysis of the ERK Signalling Pathway. [Research Reports or Papers]

Conference Proceedings

Ryan, W. , Husmeier, D. , Rolinski, O. J. and Vyshemirsky, V. (2023) Bayesian Model Selection and Emulation for Protein Fluorescence. In: 5th International Conference on Statistics: Theory and Applications (ICSTA'23), London, UK, 3-5 Aug 2023, ISBN 9781990800252 (doi: 10.11159/icsta23.153)

Mavrogonatou, L. and Vyshemirsky, V. (2016) Sequential Importance Sampling for Online Bayesian Changepoint Detection. In: 22nd International Conference on Computational Statistics (COMPSTAT 2016), Oviedo, Spain, 23-26 Aug 2016, pp. 73-84. ISBN 9789073592360

Calder, M. , Vyshemirsky, V. , Gilbert, D. and Orton, R. (2005) Analysis of Signalling Pathways Using the PRISM Model Checker. In: Computational Methods in Systems Biology (CMSB'05), Edinburgh, United Kingdom, 03-05 Apr 2005, pp. 179-190.