Senior Lecturer

Department of Mathematics, Strand campus, London WC2R 2LS

Room S4.02.1, Strand campus,

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

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

- 7CCMCS07
**Research Methods and Advanced Topics in Complex Systems**(in 2022/23) - 7CCMCS04
**Dynamical Analysis of Complex Systems**(from 2011 to 2020) - 7CCMCS02
**Theory of Complex Networks**(in 2017/18) - 7CCMNE04
**Advanced Topics in Non-equilibrium systems**(in 2014/15) - 7CCM451A
**Neural Networks**(from 2007 to 2010)

- 6CCMCS05
**Mathematical Biology**(in 2022/23) - 4CCM131A/5CCM131B
**Introduction to Dynamical Systems**(from 2007 to 2017) - 6CCMCS02
**Theory of Complex Networks**(in 2017/18)

L Albanese, A Barra, A Annibale

About the de Almeida-Thouless line in neural networks (2023); preprint

*under review*

Evan Tzanis, Pierpaolo Vivo, Yanik-Pascal Förster, Luca Gamberi, Alessia Annibale

Graphie: A network-based visual interface for UK's Primary Legislation (2022); preprint

**F1000Research 2023, 12:236**

Luca Gamberi, Pierpaolo Vivo, Yanik-Pascal Förster, Evan Tzanis and Alessia Annibale

Rationalizing systematic discrepancies between election outcomes and opinion polls (2022); preprint

**J. Stat. Mech. (2022) 123403**(selected by JSTAT Scientific Directors for the Highlights collection)

Vladimir Koskin, Adam Kells, Joe Clayton, Alexander K. Hartmann, Alessia Annibale, and Edina Rosta

Variational Kinetic Clustering of Complex Networks (2022) ;

*in press in***Journal of Chemical Physics**journal link

Christian John Hurry, Alexander Mozeika, Alessia Annibale

Dynamics of sparse Boolean networks with multi-node and self-interactions (2022) ; preprint

**J. Phys. A: Math. Theor. 55 415003**journal link

Yanik-Pascal Förster, Alessia Annibale, Luca Gamberi, Evan Tzanis, Pierpaolo Vivo

Information retrieval and structural complexity of legal trees (2022); preprint

**J. Phys. Complex. 3 035008**journal link

G Torrisi, R. Kühn, A Annibale

Uncovering the non-equilibrium stationary properties in sparse Boolean networks (2022); preprint

**J. Stat. Mech. (2022) 053303**

DT Robson, ACW Baas, A Annibale

Reproducing size distributions of swarms of barchan dunes on Mars and Earth using a mean-field model (2022)

**Physica A: Statistical Mechanics and its Applications, 128042**; journal link

C. Hurry, A. Mozeika, A Annibale

Vaccination with partial transmission and social distancing on contact networks preprint

**J. Stat. Mech. (2022) 033302**; journal link

Yanik-Pascal Förster, Luca Gamberi, Evan Tzanis, Pierpaolo Vivo, Alessia Annibale

Exact and Approximate Mean First Passage Times on Trees and other Necklace Structures: a Local Equilibrium Approach preprint

**J. Phys. A: Math. Theor. 55 115001 (2022)**; journal link

G Torrisi, A Annibale, R. Kühn

Unlocking heterogeneity of node activation in Boolean networks through dynamical programming (2021); preprint

**Phys. Rev. E 104, 045313**; journal link

DT Robson, ACW Baas, A Annibale

A combined model of aggregation, fragmentation, and exchange processes: insights from analytical calculations (2021) preprint

**J. Stat. Mech. (2021) 053203**; journal link

L Gamberi, YP Förster, E Tzanis, A Annibale, P Vivo

Maximal modularity and the optimal size of parliaments (2021) preprint

**Scientific Reports, 11, 14452 (2021)**; journal link

CJ Hurry, A Mozeika, A Annibale

Modelling the interplay between the CD4+/CD8+ T-cell ratio and the expression of MHC-I in tumours (2021);

**Journal of Mathematical Biology, 83, 2 (2021)**journal link

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**journal link

Giuseppe Torrisi, Reimer Kühn, Alessia Annibale

Percolation on the gene regulatory network (2020); preprint

**J. Stat. Mech. (2020) 083501**journal link

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**, link

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

Controlled Markovian dynamics of graphs: 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 pp25-34**(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

"Modelling cellular attractors in gene-regulatory networks", Workshop Physics-informed machine learning -- Explainable artificial intelligence via glassy statistical mechanics and biologically-inspired computing, Alan Turing Institute, 23 January 2023

"Non-equilibrium dynamics of Sparse Boolean Networks", SEMPS18: A one-day Workshop on Out-of-Equilibrium Dynamics, City, University of London, 16 November 2022

"Dynamics of Gene Regulatory Networks – dealing with sparsity and cooperativity out of equilibrium", Seminar Series of the Institute of Theoretical and Computational Physics, University of Granada, 14 June 2022

"Statistical Mechanics perspectives on Cell Differentiation and Reprogramming", Chimera Seminar Series, Sapienza University of Rome, 16 March 2022

"Non-equilibrium dynamics of Sparse Boolean Networks", Chimera Seminar Series, Sapienza University of Rome, 16 February 2022

" Gene expression: insights from Neural networks and graph theoretical approaches " Seminar in Physics of Machine Learning and Complex Systems, Radboud University, Nijmegen, 6 October 2021

" Gene regulatory networks versus Neural networks and Bipartite Graphs: what we can learn on cellular (re)programming? " Statistical Physics and Complexity Seminar Series, University of Edinburgh, 23 June 2021

" 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

"Immune networks: multi-tasking capabilities near saturation" (pdf) 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

"Modelling biological networks via tailored random graphs: a study of sampling", Queen's Mary University London, 17 January 2013

"Protein Interaction Networks via tailored random graph ensembles: a study of sampling" (pdf) Workshop on interdisciplinary Complex Adaptive Networks and Systems (iCANS), King's College London, 15 June 2012

"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" (pdf) EMBO Cancer Proteomics Conference, the Burlington Hotel, Dublin, 20-23 June 2011

"Network resilience against intelligent attacks", Randall Regtreat, 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

11th Mathematics in Life Sciences (MiLS) meeting

**Inverse problems in Neurosciences and Biology**

University of Nottingham, Department of Mathematics, 5 December 2019

See details on the MiLS website

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