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)

Member of the

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

London, **28 June 2019**

Register via EventBrite

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

Past Years

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

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

" 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

Ninth 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