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)
Inverse problems in Neurosciences and Biology
will be held at the University of Nottingham, 5 December 2019
Register on the MiLS website
Non-equilibrium statistical physics
Complex biological systems, mathematical immunology and cell differentiation
Markov models of stochastic trajectories, dimensionality reduction, projection techniques
Glassy dynamics, coarsening processes, fluctuation-dissipation violations
Complex Networks
null models, entropies and characterization of distances between networks
network dynamics and generation of networks ensembles
sampling and inference
Equilibrium statistical physics
Processes on networks (spin models, Kuramoto oscillators, percolation)
Spin-glasses, complexity and structure of metastable states, supersymmetric approaches
Modelling biological networks via tailored random graphs, in Handbook of Statistical Systems biology
Information for potential PhD applicants
I am interested in taking PhD students to work in the field of Complex Systems Modelling and their biological applications.
For general information on research and graduate positions available in the Mathematics department, please refer to MPhil/PhD Mathematics Research (applied) programmes.
Information for prospective MSc applicants
For information on our Master Programme Complex Systems Modelling: from Biomedical and Natural to Economic and Social Science, please refer to the departmental page and online prospectus
L Gamberi, M Colnaghi, F Fraternali, A Annibale
Inferring sampling biases in protein interaction networks (2021)
in preparation
DT Robson, ACW Baas, A Annibale
A combined model of aggregation, fragmentation, and exchange processes: insights from analytical calculations (2021)
under review
L Gamberi, YP Förster, E Tzanis,
A Annibale, P Vivo
Maximal modularity and the optimal size of parliaments
(2020);
preprint
under review
CJ Hurry, A Mozeika, A Annibale
Modelling the interplay between the CD4+/CD8+ T-cell ratio and the expression of MHC-I in tumours (2020);
preprint
under review
F Sicard, V Koskin, A Annibale, E Rosta
Assessing Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis
(2020);
preprint
J. Chem. Theory Comput 2021, 17, 4, 2022–2033
Giuseppe Torrisi, Reimer Kühn, Alessia Annibale
Percolation on the gene regulatory network (2020);
J. Stat. Mech. (2020) 083501
preprint
A Kells, V. Koskin E Rosta, A Annibale
Correlation functions, mean first passage times and the Kemeny constant (2020)
J. Chem. Phys. 152, 104108 (2020) journal link
R Hannam, R, Kühn, A Annibale
Percolation in Gene Regulatory Networks and its role in sustaining life (2019)
J. Phys. A: Math. Theor. 52 334002 journal link
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 journal link
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) journal link
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
ACC Coolen, A Annibale, ES Roberts
Generating randomg networks and graphs (2017)
Oxford University Press, ISBN: 9780198709893
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 journal link
P Sollich, D Tantari, A Annibale,
A Barra
Extensive Parallel Processing on Scale-Free
Networks (2014)
Phys. Rev. Lett. 113 (23),
238106 journal link
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
" Variational coarse-graining and Mean First Passage Times in Markov State Models " Warwick Centre for Predictive Modelling, 11 May 2020
" Quantifying sampling bias in protein interaction networks " Symposium on Networks and Machine Learning in Biology, Francis Crick Institute, 3 February 2020
" Modelling Gene Expression Dynamics via Neural Networks and Bipartite Boolean Graphs " University of Leeds - Non-linear Applied Dynamics Seminar Series, 3 December 2019
" A mathematical perspective on cellular reprogramming "Image and Data - Analysis, Research and Translation, The Francis Crick Institute, 2 September 2019
" 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 (pdf)
" 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
10th Mathematics in Life Sciences (MiLS) meeting
Modelling challenges in cancer and immunology
King's College London, Department of Mathematics, 28 June 2019
See details on the
MiLS website
9th Mathematics in Life Sciences (MiLS) meeting
Multiscale modelling techniques and their applications in biology and medicine
Oxford, Mathematical Institute, 2 April 2019
See details on the
MiLS website
Second International Conference in Non-Equilibrium Systems (CONES)
London, 25-27 June 2018
For more information, see the conference website
One-day workshop on Modelling the Complexity of the Immune System
A satellite of the European Conference on Complex Systems
(ECCS'13)
Barcelona, World Trade Center, 19 September 2013
For details see the event
website