Publications

@article{podda2024classification,

title = {Classification of Neisseria meningitidis genomes with a bag-of-words approach and machine learning},

author = {Marco Podda and Simone Bonechi and Andrea Palladino and Mattia Scaramuzzino and Alessandro Brozzi and Guglielmo Roma and Alessandro Muzzi and Corrado Priami and Alina Sîrbu and Margherita Bodini},

url = {https://www.cell.com/iscience/pdf/S2589-0042(24)00478-4.pdf},

year  = {2024},

date = {2024-02-16},

journal = {iScience},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pingitore2024machine,

title = {Machine learning to identify a composite indicator to predict cardiac death in ischemic heart disease},

author = {Alessandro Pingitore and Chenxiang Zhang and Cristina Vassalle and Paolo Ferragina and Patrizia Landi and Francesca Mastorci and Rosa Sicari and Alessandro Tommasi and Cesare Zavattari and Giuseppe Prencipe and others},

url = {https://www.sciencedirect.com/science/article/pii/S016752732400531X},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {International Journal of Cardiology},

volume = {404},

pages = {131981},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cignoni2024pd,

title = {PD-L1 Classification of Weakly-Labeled Whole Slide Images of Breast Cancer},

author = {Giacomo Cignoni and Cristian Scatena and Chiara Frascarelli and Nicola Fusco and Antonio Giuseppe Naccarato and Giuseppe Nicoló Fanelli and Alina Sîrbu},

url = {https://arxiv.org/abs/2404.10175},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {arXiv preprint arXiv:2404.10175},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BBF24,

title = {A framework for monitored dynamic slicing of Reaction Systems},

author = {Linda Brodo and Roberto Bruni and Moreno Falaschi},

doi = {https://doi.org/10.1007/s11047-024-09976-3},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Natural Computing},

abstract = {Reaction systems (RSs) are a computational framework inspired by biochemical mechanisms. A RS defines a finite set of reactions over a finite set of entities. Typically each reaction has a local scope, because it is concerned with a small set of entities, but complex models can involve a large number of reactions and entities, and their computation can manifest unforeseen emerging behaviours. When a deviation is detected, like the unexpected production of some entities, it is often difficult to establish its causes, e.g., which entities were directly responsible or if some reaction was misconceived. Slicing is a well-known technique for debugging, which can point out the program lines containing the faulty code. In this paper, we define the first dynamic slicer for RSs and show that it can help to detect the causes of erroneous behaviour and highlight the involved reactions for a closer inspection. To fully automate the debugging process, we propose to distil monitors for starting the slicing whenever a violation from a safety specification is detected. We have integrated our slicer in BioResolve, written in Prolog which provides many useful features for the formal analysis of RSs. We define the slicing algorithm for basic RSs and then enhance it for dealing with quantitative extensions of RSs, where timed processes and linear processes can be represented. Our framework is shown at work on suitable biologically inspired RS models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PERNICE2023104546,

title = {A new computational workflow to guide personalized drug therapy},

author = {Simone Pernice and Alessandro Maglione and Dora Tortarolo and Roberta Sirovich and Marinella Clerico and Simona Rolla and Marco Beccuti and Francesca Cordero},

url = {https://www.sciencedirect.com/science/article/pii/S1532046423002678},

doi = {https://doi.org/10.1016/j.jbi.2023.104546},

issn = {1532-0464},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Journal of Biomedical Informatics},

volume = {148},

pages = {104546},

abstract = {Objective: 

Computational models are at the forefront of the pursuit of personalized medicine thanks to their descriptive and predictive abilities. In the presence of complex and heterogeneous data, patient stratification is a prerequisite for effective precision medicine, since disease development is often driven by individual variability and unpredictable environmental events. Herein, we present GreatNectorworkflow as a valuable tool for (i) the analysis and clustering of patient-derived longitudinal data, and (ii) the simulation of the resulting model of patient-specific disease dynamics. 

Methods: 

GreatNectoris designed by combining an analytic strategy composed of CONNECTOR, a data-driven framework for the inspection of longitudinal data, and an unsupervised methodology to stratify the subjects with GreatMod, a quantitative modeling framework based on the Petri Net formalism and its generalizations. 

Results: 

To illustrate GreatNectorcapabilities, we exploited longitudinal data of four immune cell populations collected from Multiple Sclerosis patients. Our main results report that the T-cell dynamics after alemtuzumab treatment separate non-responders versus responders patients, and the patients in the non-responders group are characterized by an increase of the Th17 concentration around 36 months. 

Conclusion: 

GreatNectoranalysis was able to stratify individual patients into three model meta-patients whose dynamics suggested insight into patient-tailored interventions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sirbu2021early,

title = {Early outcome detection for COVID-19 patients},

author = {Alina Sîrbu and Greta Barbieri and Francesco Faita and Paolo Ferragina and Luna Gargani and Lorenzo Ghiadoni and Corrado Priami},

url = {https://www.nature.com/articles/s41598-021-97990-1},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Scientific Reports},

volume = {11},

number = {1},

pages = {18464},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Prezza2020,

title = {Variable-order reference-free variant discovery with the Burrows-Wheeler Transform},

author = {Nicola Prezza and Nadia Pisanti and Marinella Sciortino and Giovanna Rosone},

doi = {10.1186/s12859-020-03586-3},

year  = {2020},

date = {2020-09-01},

journal = {BMC Bioinformatics},

volume = {21},

number = {S8},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guerrini2020,

title = {Metagenomic analysis through the extended Burrows-Wheeler transform},

author = {Veronica Guerrini and Felipe A Louza and Giovanna Rosone},

doi = {10.1186/s12859-020-03628-w},

year  = {2020},

date = {2020-09-01},

journal = {BMC Bioinformatics},

volume = {21},

number = {S8},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kocian2020b,

title = {Bayesian Sigmoid-Type Time Series Forecasting with Missing Data for Greenhouse Crops},

author = {Alexander Kocian and Giulia Carmassi and Fatjon Cela and Luca Incrocci and Paolo Milazzo and Stefano Chessa},

doi = {10.3390/s20113246},

year  = {2020},

date = {2020-01-01},

journal = {Sensors},

volume = {20},

number = {11},

pages = {3246},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kocian2020c,

title = {Dynamic Bayesian network for crop growth prediction in greenhouses},

author = {Alexander Kocian and Daniele Massa and Samantha Cannazzaro and Luca Incrocci and Sara Di Lonardo and Paolo Milazzo and Stefano Chessa},

doi = {10.1016/j.compag.2019.105167},

year  = {2020},

date = {2020-01-01},

journal = {Computers and Electronics in Agriculture},

volume = {169},

pages = {105167},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barbuti2020,

title = {Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation},

author = {Roberto Barbuti and Roberta Gori and Paolo Milazzo},

doi = {10.1016/j.tcs.2020.07.031},

year  = {2020},

date = {2020-01-01},

journal = {Theoretical Computer Science},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ferragina2020,

title = {The PGM-index: a fully-dynamic compressed learned index with provable worst-case bounds},

author = {Paolo Ferragina and Giorgio Vinciguerra},

doi = {10.14778/3389133.3389135},

year  = {2020},

date = {2020-01-01},

journal = {Proceedings of the VLDB Endowment},

volume = {13},

number = {10},

pages = {1162--1175},

publisher = {VLDB Endowment},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rossi2020,

title = {A Public Dataset of 24-h Multi-Levels Psycho-Physiological Responses in Young Healthy Adults},

author = {Alessio Rossi and Eleonora Da Pozzo and Dario Menicagli and Chiara Tremolanti and Corrado Priami and Alina Sirbu and David A Clifton and Claudia Martini and Davide Morelli},

doi = {10.3390/data5040091},

year  = {2020},

date = {2020-01-01},

journal = {Data},

volume = {5},

number = {4},

pages = {91},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ferrari2020,

title = {Measuring the effects of confounders in medical supervised classification problems: the Confounding Index (CI)},

author = {Elisa Ferrari and Alessandra Retico and Davide Bacciu},

doi = {10.1016/j.artmed.2020.101804},

year  = {2020},

date = {2020-01-01},

journal = {Artificial Intelligence in Medicine},

volume = {103},

pages = {101804},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kocian2020,

title = {Monitoring Practitioner's Skills in Pure-Tone Audiometry},

author = {Alexander Kocian and Stefano Chessa and Wilko Grolman},

doi = {10.4018/ijehmc.2020040103},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of E-Health and Medical Communications},

volume = {11},

number = {2},

pages = {38--63},

publisher = {IGI Global},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pappalardo2019b,

title = {PlayeRank: Data-driven Performance Evaluation and Player Ranking in Soccer via a Machine Learning Approach},

author = {Luca Pappalardo and Paolo Cintia and Paolo Ferragina and Emanuele Massucco and Dino Pedreschi and Fosca Giannotti},

doi = {10.1145/3343172},

year  = {2019},

date = {2019-11-01},

journal = {ACM Transactions on Intelligent Systems and Technology},

volume = {10},

number = {5},

pages = {1--27},

publisher = {Association for Computing Machinery (ACM)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Misselbeck2019,

title = {A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome},

author = {Karla Misselbeck and Silvia Parolo and Francesca Lorenzini and Valeria Savoca and Lorena Leonardelli and Pranami Bora and Melissa J Morine and Maria Caterina Mione and Enrico Domenici and Corrado Priami},

doi = {10.1038/s41467-019-13208-z},

year  = {2019},

date = {2019-11-01},

journal = {Nature Communications},

volume = {10},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Morelli2019,

title = {Analysis of the Impact of Interpolation Methods of Missing RR-intervals Caused by Motion Artifacts on HRV Features Estimations},

author = {Davide Morelli and Alessio Rossi and Massimo Cairo and David A Clifton},

doi = {10.3390/s19143163},

year  = {2019},

date = {2019-07-01},

journal = {Sensors},

volume = {19},

number = {14},

pages = {3163},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ciuffoletti2019,

title = {Design of an Open Remote Electrocardiogram (ECG) Service},

author = {Augusto Ciuffoletti},

doi = {10.3390/fi11040101},

year  = {2019},

date = {2019-01-01},

journal = {Future Internet},

volume = {11},

number = {4},

pages = {101},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rossi2019,

title = {Relationship between External and Internal Workloads in Elite Soccer Players: Comparison between Rate of Perceived Exertion and Training Load},

author = {Alessio Rossi and Enrico Perri and Luca Pappalardo and Paolo Cintia and Fedon Marcello Iaia},

doi = {10.3390/app9235174},

year  = {2019},

date = {2019-01-01},

journal = {Applied Sciences},

volume = {9},

number = {23},

pages = {5174},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pappalardo2019,

title = {A public data set of spatio-temporal match events in soccer competitions},

author = {Luca Pappalardo and Paolo Cintia and Alessio Rossi and Emanuele Massucco and Paolo Ferragina and Dino Pedreschi and Fosca Giannotti},

doi = {10.1038/s41597-019-0247-7},

year  = {2019},

date = {2019-01-01},

journal = {Scientific Data},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Simoni2019,

title = {A comparison of deterministic and stochastic approaches for sensitivity analysis in computational systems biology},

author = {Giulia Simoni and Hong Thanh Vo and Corrado Priami and Luca Marchetti},

doi = {10.1093/bib/bbz014},

year  = {2019},

date = {2019-01-01},

journal = {Briefings in Bioinformatics},

volume = {21},

number = {2},

pages = {527--540},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Podda2018,

title = {A machine learning approach to estimating preterm infants survival: development of the Preterm Infants Survival Assessment (PISA) predictor},

author = {Marco Podda and Davide Bacciu and Alessio Micheli and Roberto Bellu and Giulia Placidi and Luigi Gagliardi},

doi = {10.1038/s41598-018-31920-6},

year  = {2018},

date = {2018-09-01},

journal = {Scientific Reports},

volume = {8},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bacciu2018,

title = {Randomized neural networks for preference learning with physiological data},

author = {Davide Bacciu and Michele Colombo and Davide Morelli and David Plans},

doi = {10.1016/j.neucom.2017.11.070},

year  = {2018},

date = {2018-07-01},

journal = {Neurocomputing},

volume = {298},

pages = {9--20},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cappanera2018,

title = {Demand uncertainty in robust Home Care optimization},

author = {Paola Cappanera and Maria Grazia Scutellà and Federico Nervi and Laura Galli},

url = {https://doi.org/10.1016/j.omega.2017.08.012},

doi = {10.1016/j.omega.2017.08.012},

year  = {2018},

date = {2018-01-01},

journal = {Omega},

volume = {80},

pages = {95--110},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rossi2018,

title = {Effective injury forecasting in soccer with GPS training data and machine learning},

author = {Alessio Rossi and Luca Pappalardo and Paolo Cintia and Fedon Marcello Iaia and Javier Fernandez and Daniel Medina},

editor = {Jaime Sampaio},

doi = {10.1371/journal.pone.0201264},

year  = {2018},

date = {2018-01-01},

journal = {PLOS ONE},

volume = {13},

number = {7},

pages = {e0201264},

publisher = {Public Library of Science (PLoS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Palumbo2017,

title = {Reliability and human factors in Ambient Assisted Living environments},

author = {Filippo Palumbo and Davide La Rosa and Erina Ferro and Davide Bacciu and Claudio Gallicchio and Alessio Micheli and Stefano Chessa and Federico Vozzi and Oberdan Parodi},

doi = {10.1007/s40860-017-0042-1},

year  = {2017},

date = {2017-06-01},

journal = {Journal of Reliable Intelligent Environments},

volume = {3},

number = {3},

pages = {139--157},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PanGenomics2016,

title = {Computational pan-genomics: status, promises and challenges},

author = {The Computational Pan-Genomics Consortium},

doi = {10.1093/bib/bbw089},

year  = {2016},

date = {2016-10-01},

journal = {Briefings in Bioinformatics},

pages = {bbw089},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barbuti2016,

title = {Investigating dynamic causalities in reaction systems},

author = {Roberto Barbuti and Roberta Gori and Francesca Levi and Paolo Milazzo},

doi = {10.1016/j.tcs.2015.11.041},

year  = {2016},

date = {2016-01-01},

journal = {Theoretical Computer Science},

volume = {623},

pages = {114--145},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sameen2016,

title = {Mathematical modeling of drug resistance due to KRAS mutation in colorectal cancer},

author = {Sheema Sameen and Roberto Barbuti and Paolo Milazzo and Antonio Cerone and Marzia Del Re and Romano Danesi},

doi = {10.1016/j.jtbi.2015.10.019},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Theoretical Biology},

volume = {389},

pages = {263--273},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yalnda2016,

title = {Pattern-based decompositions for human resource planning in home health care services},

author = {Semih Yalçindağ and Paola Cappanera and Maria Grazia Scutellà and Evren Şahin and Andrea Matta},

url = {https://doi.org/10.1016/j.cor.2016.02.011},

doi = {10.1016/j.cor.2016.02.011},

year  = {2016},

date = {2016-01-01},

journal = {Computers & Operations Research},

volume = {73},

pages = {12--26},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grossi2016,

title = {Circular sequence comparison: algorithms and applications},

author = {Roberto Grossi and Costas S Iliopoulos and Robert Mercas and Nadia Pisanti and Solon P Pissis and Ahmad Retha and Fatima Vayani},

doi = {10.1186/s13015-016-0076-6},

year  = {2016},

date = {2016-01-01},

journal = {Algorithms for Molecular Biology},

volume = {11},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Patterson2015,

title = {WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads},

author = {Murray Patterson and Tobias Marschall and Nadia Pisanti and Leo van Iersel and Leen Stougie and Gunnar W Klau and Alexander Schönhuth},

doi = {10.1089/cmb.2014.0157},

year  = {2015},

date = {2015-06-01},

journal = {Journal of Computational Biology},

volume = {22},

number = {6},

pages = {498--509},

publisher = {Mary Ann Liebert Inc},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cappanera2015,

title = {Joint Assignment, Scheduling, and Routing Models to Home Care Optimization: A Pattern-Based Approach},

author = {Paola Cappanera and Maria Grazia Scutellà},

url = {https://doi.org/10.1287/trsc.2014.0548},

doi = {10.1287/trsc.2014.0548},

year  = {2015},

date = {2015-01-01},

journal = {Transportation Science},

volume = {49},

number = {4},

pages = {830--852},

publisher = {Institute for Operations Research and the Management Sciences (INFORMS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cappanera2013,

title = {Home Care optimization: impact of pattern generation policies on scheduling and routing decisions},

author = {Paola Cappanera and Maria Grazia Scutellà},

url = {https://doi.org/10.1016/j.endm.2013.05.075},

doi = {10.1016/j.endm.2013.05.075},

year  = {2013},

date = {2013-01-01},

journal = {Electronic Notes in Discrete Mathematics},

volume = {41},

pages = {53--60},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barbuti2012,

title = {Probabilistic model checking of biological systems with uncertain kinetic rates},

author = {Roberto Barbuti and Francesca Levi and Paolo Milazzo and Guido Scatena},

doi = {10.1016/j.tcs.2011.10.022},

year  = {2012},

date = {2012-02-01},

journal = {Theoretical Computer Science},

volume = {419},

pages = {2--16},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}