====== Case Studies ======

==== Immune System ====

  * Emanuela Merelli, Matteo Rucco, Peter M. A. Sloot, Luca Tesei. "Topological Characterization of Complex Systems: Using Persistent Entropy". Entropy 17(10): 6872-6892 (2015) [[http://dx.doi.org/10.3390/e17106872|Open Access Link]]
  * Emanuela Merelli, Marco Pettini, Mario Rasetti. "Topology driven modeling: the IS metaphor". Natural Computing 14(3): 421-430 (2015) [[http://dx.doi.org/10.1007/s11047-014-9436-7|Open Access Link]]
  * Matteo Rucco, Filippo Castiglione, Emanuela Merelli, Marco Pettini. "Characterisation of the Idiotypic Immune Network Through Persistent Entropy". Proceedings of ECCS 2014. Springer Proceedings in Complexity: 117-128 (2016) [[http://link.springer.com/chapter/10.1007/978-3-319-29228-1_11|Link]]

==== Epileptic Brain =====

  * Marco Piangerelli, Matteo Rucco, Luca Tesei, Emanuela Merelli. "Topological classifier for detecting the emergence of epileptic seizures". BMC Research Notes  2018 11:392 [[https://doi.org/10.1186/s13104-018-3482-7| Open Access Link]]
  * Emanuela Merelli, Marco Piangerelli, Matteo Rucco, Daniele Toller. "A topological approach for multivariate time series characterization: the epileptic brain". EAI Endorsed Trans. Self-Adaptive Systems 2(7): e5 (2016) [[http://dx.doi.org/10.4108/eai.3-12-2015.2262525|Open Access Link]]
  * 	Emanuela Merelli, Marco Piangerelli. "RNN-based Model for Self-adaptive Systems - The Emergence of Epilepsy in the Human Brain". IJCCI (NCTA) 2014: 356-361 [[http://dx.doi.org/10.5220/0005165003560361|Open Access Link]]

==== RNA =====

  * Michela Quadrini, Luca Tesei, Emanuela Merelli. "An algebraic representation for tree alignment of RNA pseudoknotted structures". PeerJ Preprints 5:e3327v1 [[https://doi.org/10.7287/peerj.preprints.3327v1|Open Access Link]]
  * Adane Letta Mamuye, Matteo Rucco, Luca Tesei, Emanuela Merelli. "Persistent Homology Analysis of RNA". Journal of Molecular Based Mathematical Biology, 2016, 4:14-25. [[https://doi.org/10.1515/mlbmb-2016-0002|Open Access Link]]
  * Adane Letta Mamuye, Emanuela Merelli, Luca Tesei. "A Graph Grammar for Modelling RNA Folding". CoRR abs/1612.01639 (2016) [[http://arxiv.org/abs/1612.01639|Open Access Link]]
  * Adane Letta Mamuye, Emanuela Merelli, Luca Tesei. "Towards a Shape Language for Interpreting RNA Folding". BICT 2015: 185-188 [[http://dl.acm.org/citation.cfm?id=2954836|Open Access Link]]
  * 	Adane Letta Mamuye, Matteo Rucco. "Persistent Homology on RNA Secondary Structure Space". BICT 2015: 189-192 [[http://dl.acm.org/citation.cfm?id=2954801|Open Access Link]]