Alessia Annibale

Senior Lecturer
Department of Mathematics, Strand campus, London WC2R 2LS
Room S4.02.7, Strand campus,    Tel: +44 (0)20 7848 2877

Institute of Mathematical and Molecular Biomedicine
Room HB4.3N, Hodgkin Bldg, Guy's campus, London WC2R

Email: alessia.annibale (followed by @kcl.ac.uk)

  

  Modelling Challenges in Cancer and Immunology

   A one-day meeting of the LMS Mathematics in Life Science (MiLS)


   London, 28 June 2019


   Register via EventBrite

TEACHING

2017-2018

• 7CCMCS04    Dynamical Analysis of Complex Systems
• 6CCMCS02 - 7CCMCS02    Theory of Complex Networks

Past Years

• 4CCM131A - 5CCM131B    Introduction to Dynamical Systems
• 7CCMNE04    Advanced Topics in Non-equilibrium systems
• 7CCM451A    Neural Networks

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PUBLICATIONS/PREPRINTS

• R Hannam, R, Kuhn, A Annibale
     Sustaining like: Percolation in Gene Regulatory Networks (2019)
     under review

• A Kells, ZE Mihalka, A Annibale, E Rosta
     Mean First Passage Times in Variational Coarse Graining using Markov State Models (2019)
     J. Chem. Phys. 150, 134107   (Editor's pick)   journal link

• A Annibale, LA Dziobek-Garrett, H Tari
     The role of the T-helper/T-suppressor ratio on the adaptive immune response: a dynamical model (2018)
     J. Phys. A: Math. Theor. 51 505602   preprint

• A Kells, A Annibale, E Rosta
     Limiting relaxation times from Markov state models (2018)
     J. Chem. Phys. 149, 072324

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Retrieving an infinite number of patterns in a spin glass model of immune network (2017)
     European Physics Letters 117:28003, (Editor's choice 2017)

• R Hannam, A Annibale, R Kuehn
     Cell reprogramming modelled as transitions in a hierarchy of cell cycles (2017)
     J. Phys. A: Math. Theor. 50 425601, (Journal of Physics A Highlights of 2017) preprint

• Silvia Bartolucci, Alexander Mozeika, Alessia Annibale
     The role of idiotypic interactions in the adaptive immune system: a belief-propagation approach (2016)
     J. Stat. Mech. (2016) 083402 ,   preprint

• A Annibale, ACC Coolen, N. Planell-Morrell
     Quantifying noise in mass spectrometry and yeast two-hybrid protein interaction detection experiments (2015)
     J. R. Soc. Interface 12(110):0573,   preprint

• S Bartolucci, A Annibale
     A dynamical model of the adaptive immune system: effects of cells promiscuity, antigens and B-B interactions (2015)
     J. Stat. Mech. (2015) P08017,   preprint

• A Annibale, O Courtney
     The two-star model: exact solution in the sparse regime and condensation transition (2015)
     J. Phys. A: Math. Theor. 48 (2015) 365001,   preprint

• S Sook Chung, A Pandini, A Annibale, ACC Coolen, N S Thomas, F Fraternali
     Bridging Topological and Functional Information in Protein Interaction Networks by Short Loops Profiling (2015)
     Scientific Reports 5:8540

• P Sollich, D Tantari, A Annibale, A Barra
     Extensive Parallel Processing on Scale-Free Networks (2014)
     Phys. Rev. Lett. 113 (23), 238106

• S Bartolucci, A Annibale
     Associative networks with diluted patterns: dynamical analysis at low and medium load (2014)
     J. Phys. A: Math. Theor. 47 415001 (on the Front Cover)     preprint

• E Roberts, A Annibale, ACC Coolen
     Unbiased algorithms for the generation of random graphs with controlled topological properties in Nonlinear Maps and their Applications (2014)
     Springer Proceedings in Mathematical and Statistics Volume 57 pp81-94 (pdf)

• C Gracio, ACC Coolen, A Annibale
     Cycle Statistics in Complex Networks and Ihara's Zeta Function in Nonlinear Maps and their Applications (2014)
     Springer Proceedings in Mathematical and Statistics Volume 57 pp81-94

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Immune networks: multi-tasking capabilities near saturation (2013)
     J. Phys. A: Math. Theor: 46 (41) 2013, (IOP Select: Highlights 2013)   preprint

• E Agliari, A Annibale, A Barra, ACC Coolen, D Tantari
     Immune networks: multi-tasking capabilities at medium load (2013)
     J. Phys. A: Math. Theor: 46 (33) 2013, (News item on "Insights")   preprint

• ES Roberts, A Annibale, ACC Coolen
     Tailored Random Graph Ensembles (2013)
     Journal of Physics Conference Series 410 012097

• ACC Coolen, F Fraternali, A Annibale, LP Fernandes, J Kleinjung
     Modelling biological networks via tailored random graphs (2011)
     in Handbook of statistical systems biology  ISBN: 978-0-470-71086-9   (pdf)

• A Annibale, ACC Coolen
     What you see is not what you get: how sampling affects macroscopic features of biological networks (2011)
     Interface Focus 2011, 1(6) , (on the Front Cover)   (pdf)

• A Annibale, ACC Coolen, G Bianconi
     Network resilience against intelligent attacks constrained by degree dependent node removal cost (2010)
     J. Phys. A: Math. Theor: 43 (39) 2010,   arXiv:1005.4283

• LP Fernandes, A Annibale, J Kleinjung, ACC Coolen and F Fraternali
     Protein networks reveal detection bias and species consistency when viewed through information-theoretic glasses (2010)
     PLoSONE 5(8) e12083 (2010),   (pdf)

• A Annibale, ACC Coolen, LP Fernandes, F Fraternali, J Kleinjung
     Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure (2009)
     J. Phys. A: Math. Theor. 42 485001 (Top 10% most dowloaded of the quarter)  arXiv:0908.1759

• ACC Coolen, A De Martino, A Annibale
     Constrained Markovian dynamics of random graphs (2009)
     J. Stat. Phys. 136 (2009), 1035-1067 , arXiv:0905.4155

• A Annibale, P Sollich
     Dynamic heterogeneities in critical coarsening: Exact results for correlation and response fluctuations in finite-sized spherical models (2009)
     J Stat Mech P02064 (2009), arXiv:0811.3168

• A Annibale, P Sollich
     Fluctuation-dissipation relations in critical coarsening: crossover from unmagnetized to magnetized initial states (2008)
     J.Phys.A: Math.Theor: 41 (2008) 135001 (IOP Select)  arXiv:0801.1381

• A Annibale, P Sollich
     Spin, bond and global fluctuation-dissipation relations in the non-equilibrium spherical ferromagnet,
     J.Phys.A: Math.Gen: 39 (2006) 2853-2907 arXiv:cond-mat/0510731

• A Annibale, G Gualdi, A Cavagna
     Coexistence of supersymmetirc and supersymmetry-breaking states in spherical spin-glasses,
     J.Phys.A: Math.Gen: 37 (2004) 11311-11320 arXiv:cond-mat/0406466

• A Annibale, A Cavagna, I Giardina, G Parisi, E Trevigne
     The role of the Becchi-Rouet-Stora-Tyutin supersymmetry in the calculation of the complexity for the Sherrington-Kirkpatrick model,
     J.Phys.A: Math.Gen.36 (2003) 10937 arXiv:cond-mat/0307465

• A Annibale, A Cavagna, I Giardina, G Parisi
     Supersymmetric quenched complexity in the Sherrington-Kirkpatrick model,
     Phys.Rev.E 68, 061103 (2003) arXiv:cond-mat/0304698

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RECENT PRESENTATIONS

• " A statistical physics view of cellular (re)programming ", Computational Approaches in Mathematical Biology, Dundee, 17 May 2019

• " Markov State models: Limiting relaxation time and Dimensionality Reduction ", ZIF Wokshop, Bielefeld, 4-9 March 2019

• " Modelling cellular gene expression via neural networks and bipartite graphs ", The Cambridge University Mathematical Society, 22th February 2019

• " Cell differentiation and reprogramming: insights from neural networks and graph theoretical approaches ", Disordered serendipity: a glassy path to discovery, Sapienza University (Rome), 20th September 2018

• " Cell reprogramming modelled as transitions in a hierarchy of cell cycles " Northumbria University (Newcastle), 18th April 2018

• " The role of the T-helper/T-regulator lymphocyte ratio on the adaptive immune system ", Mathematical Innovation for Biomedicine one-day meeting, 13th September 2017

• "Quantifying Noise in Y2H and Mass-spectrometry Datasets: A Mathematical Approach ", 7th Annual World Congress of Molecular and Cell Biology, 26 April 2017, Xi'An

• "Cell differentiation modelled as transitions in a hierarchy of cell cycles ", The Crick Institute London - Computational and Physical Biology Workshop 5 Dec 2016

• "Protein interaction networks and biology: towards a connection?", NIMR (National Institute for Medical Research), London, 11 Feb 2015 (pdf)

• "Immune system: multi-tasking capabilities near the saturation regime", University of Birmingham, 20 Oct 2013

• "Modelling biological networks via tailored random graphs", University College London, Intelligent Systems Seminars, 23 Apr 2012 (pdf)

• "Effects of sampling on macroscopic features of biological networks", Symposium of Synthetic and Systems Biology, Imperial College London, 16 Nov 2011 (pdf)

• "Network resilience against intelligent attacks", University of Chichester, 1-3 September 2010

• "Quantifying and comparing complexity of cellular networks", University College Dublin, 15-17 June 2009

• "Signaling networks and random graphs", King's College London, 26 June 2009 The key role of mathematics in 21st century biology and medicine

• "Cellular networks: structure beyond degree statistics", King's College London, 26 May 2009

• "Fluctuation-dissipation relations and heterogeneities in coarsening systems", The University of Manchester, 22 October 2008

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ORGANISED EVENTS