Topological Interpretation of Interactive Computation.
In printing.

Simplicial models of social contagion.
Nature Communications 10(1),2485

Topology highlights mesoscopic functional equivalence between imagery and perception: The case of hypnotizability.
NeuroImage 200, pp. 437-449

Spectral and topological analyses of the cortical representation of the head position: Does hypnotizability matter?
Brain and Behavior 9(6),e01277

Process calculi may reveal the equivalence lying at the heart of RNA and proteins.
Nature, Scientific Reports 9(1), 559.

An algebraic language for RNA pseudoknots comparison.
BMC Bioinformatics 20(161).

A Persistent Entropy Automaton for the Dow Jones Stock Market.
In printing in LNCS 11761.


Simplicial Activity Driven Model.
Physical Review Letters 121(22),228301

Topological Classifier for Detecting the Emergence Epiletic Searures.
BMC Research Notes 11(1),392.


A new topological entropy-based approach for measuring similarities among piecewise linear functions.
Signal Processing 134.


Topological field theory of data: Mining data beyond complex networks.
Book Chapter in Advances in Disordered Systems, Random Processes and Some Applications. Cambridge University Press.


A Geometric Entropy Detecting the Erdos-Renyi Phase Transition. 
Europhysics Letters, 111, 20001.

Topological Characterization of Complex Systems: Using Persistent Entropy.
Entropy, 17(10), 6872-6892.

The Topological Field Theory of Data: a program towards a novel strategy for data mining through data language.
Journal of Physics: Conference Series, 626, 012005.

Adaptability Checking in Complex Systems.
Science of Computer Programming, 115-116, 23-46.

Topology driven modeling: the IS metaphor.
Natural Computing, 14(3), 421-430.NACO Version

Gaussian networks’ dynamics reflected into geometric entropy.
Entropy, 17, 5660-5672.

On the local genus distribution of graphs embeddings
BMC Research Note,8, 1554. 

The influence of memory on indoor environment exploration: A numerical study Vaisagh. 
Behavior Research Methods.

Using topological data analysis for diagnosis pulmonary embolism.
Journal of Theoretical and Applied Computer Science 9, 1.

Neural hypernetwork approach for pulmonary embolism diagnosis.   
BMC research notes. 8(1):617.

Unveiling patterns of international communities in a global city using mobile phone data. 
Paolo Bajardi, Matteo Delfino, André Panisson, Giovanni Petri & Michele Tizzoni.
EPJ Data Science, 4(1).

On the RNA-RNA interaction structures of fixed topological genus. 
Mathematical Biosciences 262, 88-104.

Possible role of electrodynamic interactions in long-distance biomolecular recognition. 
Physical Review E, 91, 052710.

Shapes of topological RNA structures. 
Mathematical biosciences 270 (2015): 57-65.

Complex agent networks: An emerging approach for modeling complex systems. 
Shan Mei, Narges Zarrabi, Michael Lees & Peter M.A. Sloot. 2015. Applied Soft Computing Journal, 37.

Investigating encounter dynamics of biomolecular reactions: long-range resonant interactions versus Brownian collisions. 
Jordane Preto, Ilaria Nardecchia, Sebastien Jaeger , Pierre Ferrier & Marco Pettini. 2015. Fields of the Cell, 215-228.

Characterization of the idiotypic network through persistent entropy. 
Matteo Rucco, Filippo Castiglione, Emanuela Merelli & Marco Pettini. 2015. Springer Proceedings in Complexity.

Topological classification of small DC motors. 
Matteo Rucco, E. Concettoni, Cristina Cristalli, Andrea Ferrante & Emanuela Merelli.2015. IEEE Proceedings on 1st International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI).

A topological approach for multivariate time series characterization: the epilepsy case study. 
Emanuela Merelli, Marco Piangerelli, Matteo Rucco & Daniele Toller. 2015. Proceedings of the 9th EAI Conference on Bio-inspired Information and Communications Technologies (BICT 2015).

Persistent Homology Analysis of the RNA Folding Space. 
Adane Mamuye & Matteo Rucco. 2015. Proceedings of the 9th EAI Conference on Bio-inspired Information and Communications Technologies (BICT 2015).

Towards a Shape Language for Interpreting RNA Folding. 
Adane Mamuye, Luca Tesei & Emanuela Merelli. 2015. Proceedings of the 9th EAI Conference on Bio-inspired Information and Communications Technologies (BICT 2015).

Investigation of Brownian Diffusion and Long-Distance Electrodynamic Interactions of Biomolecules. 
Matteo Gori, Ilaria Nardecchia, Marco Pettini, Jeremie Torres & Luca Varani. 2015. IEEE Proceedings on International Conference on Noise and Fluctuations (ICNF).


jHoles: A Tool for Understanding Biological Complex Networks via Clique Weight Rank Persistent Homology. 
Jacopo Binchi, Emanuela Merelli, Matteo Rucco, Giovanni Petri & Francesco Vaccarino. 2014. Electronic Notes in Theoretical Computer Science 306, 5-18. SD Version


Shapes of Interacting RNA Complexes. 
Benjamin M. Fu and Christian M. Reidys. 2014. Journal of Computational Biology 21.9. JCB Version

Combinatorics of γ-structures.
Hillary S.W. Han, Thomas J.X. Li & Christian M. Reidys. 2014.  J Comput Biol. 2014 Aug;21(8):591-608. JCB Version

Homological scaffolds of brain functional networks. 
Giovanni Petri, Paul Expert , Federico Turkheimer, Robin Carhart-Harris, D. Nutt , Peter J Hellyer & Francesco Vaccarino. 2014. Journal of The Royal Society Interface 11.101, 20140873. JOTRSI Version

Information geometric complexity of a trivariate Gaussian statistical model. 
Carlo Cafaro, Domenico Felice & Stefano Mancini. 2014. Entropy 16.6, 2944-2958. Entropy Version

Individual decision making can drive epidemics: a fuzzy cognitive map study. 
Shan Mei, Yifan Zhu, Xiaogang Qiu, Xuan Zhou, Zhenghu Zu, A.V. Boukhanovsky, & Peter M.A. Sloot. 2014. IEEE Transactions on Fuzzy Systems, 22, 2. IEEE Version

Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes. 
Siew Ann Cheong, Teck Liang Tan , Chien-Chih Chen, Wu-Lung Chang , Zheng Liu, Lock Yue Chew, Peter M. A. Sloot & Neil F. Johnson. 2014.  Scientific reports 4. NSR Version

The Relative Ineffectiveness of Criminal Network Disruption. 
Paul A. C. Duijn, Victor Kashirin & Peter M. A. Sloot. 2014. Scientific reports, 4. NSR Version

Applying information theory to neuronal networks: from theory to experiments. 
Thijs I. Jung, Filippos Vogiatzian, Omri Har-Shemesh, C. P. Fitzsimons & Rick Quax. 2014. Entropy, 16(11), 5721-5737. Entropy Version

1Shapes of Interacting RNA Complexes.
Benjamin M. Fu and Christian M. Reidys. 2014. Journal of Computational Biology 21.9.

Quantifying networks complexity from information geometric view point.
Domenico Felice, Stefano Mancini & Marco Pettini. 2014. Journal of Mathematical Physics 55.4, 043505.

Temporal stability of network partitions. 
Giovanni Petri & Paul Expert. 2014. Physical Review E 90.2 (2014): 022813.

The Nori-Hilbert scheme is not smooth for 2-Calabi Yau algebras. 
Raf Bocklandt, Federica Galluzzi & Francesco Vaccarino. 2014. J.Non Commutative Geometry, In press.

Inference of the Russian drug community from one of the largest social networks in the Russian Federation. 
L. J. Dijkstra, A. V. Yakushev, P. A. C. Duijn, A. V. Boukhanovsky & Peter M.A. Sloot. 2014. Quality & Quantity 48.5: 2739-2755.

Topology dependent epidemic spreading velocity in weighted networks. 
Wei Duan, Rick Quax, Michael Lees, Xiaogang Qiu & Peter M A Sloot. 2014. Journal of Statistical Mechanics: Theory and Experiment 2014.12, P12020.

Quantitative comparison between crowd models for evacuation planning and evaluation. 
Vaisagh Viswanthan, Michael Harold Lees, Chong Eu Lee, Siew Ann Cheong & Peter M. A. Sloot. 2014. The European Physical Journal B 87.2.

Q-analysis based clustering of online news. 
David Sousa-Rodrigues. 2014. Discontinuity, Nonlinearity, and Complexity 3.3.

Evolutionary dynamics of time-resolved social interactions. 
Alessio Cardillo, Giovanni Petri, Vincenzo Nicosia, Roberta Sinatra, Jesús Gómez-Gardeñes, & Vito Latora. 2014. Physical Review E 90.5, 052825.

Experimental detection of long-distance interactions between biomolecules through their diffusion behavior: Numerical study.
Ilaria Nardecchia, Lionel Spinelli, Jordane Preto, Matteo Gori, Elena Floriani, Sebastien Jaeger, Pierre Ferrier & Marco Pettini. 2014. Physical Review E 90, 022703.

Hypernetwork-based Peer Marking for Scalable Certificated Mass Education. 
Jeffrey Johnson, Cristian Jimenez-Romero, David Rodrigues & Jane M. Bromley. 2014. Proceedings of the European Conference on Complex Systems, ECCS’14.

Is quantum simulation of turbulence within reach? 
Mario Rasetti. 2014. International Journal of Quantum Information 12.07n08, 1560008.

Policy Design: a New area of design research and Practice. 
Jeffrey Johnson & Matthew Cook. 2014. Complex Systems Design & Management. Springer International Publishing.

Traversing News With Ant Colony Optimisation and Negative Pheromones. 
David M.S. Rodrigues & Vitorino Ramos .2014.


Non locality, topology, formal languages: new global tools to handle large data sets. 
Emanuela Merelli & Mario Rasetti. 2013. Procedia Computer Science 18, 90-99. SD Version

Topological Strata of Weighted Complex Networks.
Giovanni Petri , Martina Scolamiero, Irene Donato & Francesco Vaccarino. PloS one 8.6 (2013): e66506. PlosOne Version

Towards understanding the behavior of physical systems using information theory. 
Rick Quax, Andrea Apolloni & Peter M.A. Sloot. The European Physical Journal Special Topics 222.6 (2013): 1389-1401. TEPJST Version

Entangled communities and spatial synchronization lead to criticality in urban traffic.
Giovanni Petri , Paul Expert , Henrik J. Jensen & John W. Polak. 2013. Computer Performance Engineering. Springer Berlin Heidelberg. Sci Rep Version

Hypernetworks in the Science of Complex Systems. 
Jeffrey Johnson. 2013. Vol. 3. London: Imperial College Press.

Second Order Swarm Intelligence. 
Vitorino Ramos, David MS Rodrigues & Jorge Louça. 2013. Hybrid Artificial Intelligent Systems. Springer Berlin Heidelberg.

A Bijection for Tricellular Maps.
Hillary S. W. Han & Christian M. Reidys. 2013. SRN Discrete Mathematics.

A data-driven clinical prediction rule for pulmonary embolism. 
Lorenzo Falsetti, Emanuela Merelli, Matteo Rucco , Cinzia Nitti, T. Gentili, M. Pennacchioni & Aldo Salvi. 2013. European Heart Journal 34.suppl 1.

Advances in dynamic temporal networks: Understanding the temporal dynamics of complex adaptive networks. 
Peter M.A. Sloot, George Kampis & László Gulyás. 2013. The European Physical Journal Special Topics 222.6, 1287-1293.

Generation of RNA pseudoknot structures with topological genus filtration. 
Fenix W.D. Huang , Markus E. Nebel & Christian M. Reidys. 2013. Mathematical biosciences 245.2, 216-225.

Identifying news clusters using Q-analysis and Modularity. 
David Rodrigues. 2013. Lecture Notes in Computer Science, vol. 8073, 411-420.

Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM. 
Rick Quax, David A.M.C. van de Vijver and Dineke Frentz & Peter M.A. Sloot. 2013. European Physical Journal Special Topics 222, 1347-1358.

Information dissipation as an early-warning signal for the Lehman Brothers collapse in financial time series. 
Rick Quax, Drona Kandhai & Peter M. A. Sloot. 2013. Scientific Reports, 3(1898).

Noise enhances information transfer in hierarchical networks. 
Agnieszka Czaplick, Janusz A. Holyst & Peter M. A. Sloot 2013. Scientific Reports 3(1223).

The diminishing role of hubs in dynamical processes on complex networks. 
Rick Quax , Andrea Apolloni,and Peter M. A. Sloot. Journal of The Royal Society Interface 10.88, 20130568.

The importance of centralities in dark network value chains. 
Noemi Toth, László Gulyás, Richard O. Legendi, Paul Dujin, Peter M. A. Sloot & George Kampis. 2013. The European Physical Journal Special Topics, 222.6,1413-1439.

Encoding timed models as uniform labeled transition systems. 
Marco Bernardo & Luca Tesei. 2013. Computer Performance Engineering. Springer Berlin Heidelberg.


Challenges in Complex Systems Science. 
M. San Miguel, J.H. Johnson, J. Kertesz, K. Kaski, A. D´ıaz-Guilera, R.S. MacKay, V. Loreto P.Erdi & D. Helbing. 2012. The European Physical Journal Special Topics 214.1. TEPJST Version

Networks and Cycles: A Persistent Homology Approach to Complex Networks.
Giovanni Petri, Martina Scolamiero, Irene Donato and Francesco Vaccarino. Proceedings of the European Conference on Complex Systems 2012. Springer International Publishing.


Topological Field Theory of Data: mining data beyond complex networks. 
Mario Rasetti & Emanuela Merelli. Cambridge University Press. To appear in March 2016.

Global Systems Science and Policy. Jeffrey Johnson et al. in Non-Equilibrium Social Science,
Johnson et al (eds), Springer. To appear within 2016.

A Formal Approach to Multi-level Adaptive Systems. Modelling and Analysis. 
Narges Khakpour, Emanuela Merelli, Marjan Sirjani, Luca Tesei. CRC Press. To appear within 2016.

Book of abstracts of TOPDRIM Workshop and EATCS School.
Ed. Emanuela Merelli, In preparation. PDF.

Topological Data Analysis for Modeling Complex Systems
Matteo Rucco. PhD Thesis. To appear within 2016.

Hypernetworks in the Science of Complex Systems
J. Johnson, 2014, Imperial College Press, London