@article{Marchesi2025.05.08.652855,

title = {Toward Reliable Synthetic Omics: Statistical Distances for Generative Models Evaluation},

author = {Raffaele Marchesi and Nicolò Lazzaro and Gianluca Leonardi and Federica Rignanese and Stefano Bovo and Marco Chierici and Giuseppe Jurman},

doi = {10.1101/2025.05.08.652855},

year  = {2025},

date = {2025-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{poretto2025machine,

title = {Machine Learning Analysis Applied to Prediction of Early Progression Independent of Relapse Activity in Multiple Sclerosis Patients},

author = {Valentina Poretto and Walter Endrizzi and Matteo Betti and Stefano Bovo and Angelo Bellinvia and Flavio Ragni and Caterina Lapucci and Monica Moroni and Sabrina Marangoni and Emilio Portaccio and others},

year  = {2025},

date = {2025-01-01},

journal = {European Journal of Neurology},

volume = {32},

number = {12},

pages = {e70417},

publisher = {Wiley Online Library},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{melaiu2025mapping,

title = {Mapping B cells and the immune landscape of tertiary lymphoid structures reveals their clinical impact in neuroblastoma},

author = {Ombretta Melaiu and Marco Chierici and Paula Gragera and Nicolò Lazzaro and Lucia L Petrilli and Judith Wienke and Francisca J Bergsma and Bronte Manouk Verhoeven and Cristiano De Stefanis and Valentina DÓria and others},

year  = {2025},

date = {2025-01-01},

journal = {Journal for Immunotherapy of Cancer},

volume = {13},

number = {11},

pages = {e012860},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bezzina2025bottlenecks,

title = {Bottlenecks in advancing and applying multiomic data integration—common data resources as rate-limiting drivers—the high-impact use case of atherosclerotic cardiovascular disease},

author = {Stephanie Bezzina Wettinger and Kanita Karaduzovic-Hadziabdic and Ritienne Attard and Rosienne Farrugia and Brooke N Wolford and Marco Chierici and Giuseppe Jurman and Panagiotis Alexiou and José L Peñalvo and Rafael S Costa and others},

year  = {2025},

date = {2025-01-01},

journal = {Briefings in Bioinformatics},

volume = {26},

number = {5},

pages = {bbaf526},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{riello2025neuropsychological,

title = {Neuropsychological and clinical variables associated with cognitive trajectories in patients with Alzheimer's disease},

author = {Marianna Riello and Monica Moroni and Stefano Bovo and Flavio Ragni and Manuela Buganza and Raffaella Di Giacopo and Marco Chierici and Lorenzo Gios and Matteo Pardini and Federico Massa and others},

year  = {2025},

date = {2025-01-01},

journal = {Frontiers in Aging Neuroscience},

volume = {17},

pages = {1565006},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{malaguti2025machine,

title = {Machine Learning Predicts Risk of Falls in Parkison's Disease Patients in a Multicenter Observational Study},

author = {Maria Chiara Malaguti and Chiara Longo and Monica Moroni and Flavio Ragni and Stefano Bovo and Marco Chierici and Lorenzo Gios and Laura Avanzino and Roberta Marchese and Francesca Di Biasio and others},

year  = {2025},

date = {2025-01-01},

journal = {European Journal of Neurology},

volume = {32},

number = {5},

pages = {e70118},

publisher = {Wiley Online Library},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{martorell2025explainable,

title = {Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics},

author = {Jordi Martorell-Marugán and Raúl López-Domínguez and Juan Antonio Villatoro-García and Daniel Toro-Domínguez and Marco Chierici and Giuseppe Jurman and Pedro Carmona-Sáez},

doi = {10.1093/bib/bbae673},

issn = {1467-5463},

year  = {2025},

date = {2025-01-01},

journal = {Briefings in Bioinformatics},

volume = {26},

number = {1},

pages = {bbae673},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cazzolli2025neuro,

title = {Neuropsychological tests and machine learning: identifying predictors of MCI and dementia progression},

author = {Carlotta Cazzolli and Marco Chierici and Monica Dallabona and Chiara Guella and Giuseppe Jurman},

doi = {10.1007/s40520-025-02962-4},

issn = {1594-0667},

year  = {2025},

date = {2025-01-01},

journal = {Aging Clinical and Experimental Research},

volume = {37},

number = {1},

pages = {79},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lazzaro2024generative,

title = {Generative models validation via manifold recapitulation analysis},

author = {Nicolo’ Lazzaro and Gianluca Leonardi and Raffaele Marchesi and Massimiliano Datres and Anna Saiani and Jacopo Tessadori and Alejandro Granados and Johan Henriksson and Marco Chierici and Giuseppe Jurman and others},

year  = {2024},

date = {2024-01-01},

journal = {bioRxiv},

pages = {2024–10},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{malaguti2024artificial,

title = {Artificial intelligence of imaging and clinical neurological data for predictive, preventive and personalized (P3) medicine for Parkinson Disease: The NeuroArtP3 protocol for a multi-center research study},

author = {Maria Chiara Malaguti and Lorenzo Gios and Bruno Giometto and Chiara Longo and Marianna Riello and Donatella Ottaviani and Maria Pellegrini and Raffaella Di Giacopo and Davide Donner and Umberto Rozzanigo and Marco Chierici and Monica Moroni and Giuseppe Jurman and Giorgia Bincoletto and Matteo Pardini and Ruggero Bacchin and Flavio Nobili and Francesca Di Biasio and Laura Avanzino and Roberta Marchese and Paola Mandich and Sara Garbarino and Mattia Pagano and Cristina Campi and Michele Piana and Manuela Marenco and Antonio Uccelli and Venet Osmani},

doi = {10.1371/journal.pone.0300127},

year  = {2024},

date = {2024-01-01},

journal = {PLOS ONE},

volume = {19},

number = {3},

pages = {e0300127},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{minnai2023genetic,

title = {Genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients’ non‐involved lung tissue},

author = {Francesca Minnai and Sara Noci and Marco Chierici and Chiara Cotroneo and Barbara Bartolini and Matteo Incarbone and Davide Tosi and Giovanni Mattioni and Giuseppe Jurman and Tommaso A. Dragani and Francesca Colombo},

year  = {2023},

date = {2023-01-01},

journal = {Cancer Science},

volume = {114},

number = {1},

pages = {281--294},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{martorell2023differential,

title = {Differential diagnosis of systemic lupus erythematosus and Sjögren's syndrome using machine learning and multi-omics data},

author = {Jordi Martorell Marugán and Marco Chierici and Giuseppe Jurman and Marta E. Alarcón-Riquelme and Pedro Carmona-Sáez},

year  = {2023},

date = {2023-01-01},

journal = {Computers in biology and medicine},

volume = {152},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{datres2023endoscopy-based,

title = {Endoscopy-based IBD identification by a quantized deep learning pipeline},

author = {Massimiliano Datres and Elisa Paolazzi and Marco Chierici and Matteo Pozzi and Antonio Colangelo and Marcello Dorian Donzella and Giuseppe Jurman},

year  = {2023},

date = {2023-01-01},

journal = {BioData Mining},

volume = {16},

number = {1},

pages = {33},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{martorell2023machine,

title = {Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review},

author = {Jordi Martorell Marugán and Marco Chierici and Bandres-Ciga Sara and Giuseppe Jurman and Carmona-Sáez Pedro},

year  = {2023},

date = {2023-01-01},

journal = {CURRENT BIOINFORMATICS},

volume = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chierici2022automatically,

title = {Automatically detecting Crohn’s disease and Ulcerative Colitis from endoscopic imaging},

author = {Marco Chierici and Nicolae Puica and Matteo Pozzi and Antonello Capistrano and Marcello Dorian Donzella and Antonio Colangelo and Venet Osmani and Giuseppe Jurman},

year  = {2022},

date = {2022-01-01},

journal = {BMC Medical Informatics and Decision Making},

volume = {22},

number = {Suppl 6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{buonaiuto2022prioritization,

title = {Prioritization of putatively detrimental variants in euploid miscarriages},

author = {Silvia Buonaiuto and Immacolata Di Biase and Valentina Aleotti and Amin Ravaei and Adriano De Marino and Gianluca Damaggio and Marco Chierici and Madhuri Pulijala and Palmira D’Ambrosio and Gabriella Esposito and others},

year  = {2022},

date = {2022-01-01},

journal = {Scientific reports},

volume = {12},

number = {1},

pages = {1--12},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{levimortera2022metaproteomic,

title = {A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders},

author = {Stefano Levi Mortera and Pamela Vernocchi and Ilaria Basadonne and Alessandro Zandon`a and Marco Chierici and Martina Durighello and Valeria Marzano and Simone Gardini and Antonio Gasbarrini and Andrea Urbani and Stefano Vicari and Paola Roncada and Cesare Furlanello and Paola Venuti and Lorenza Putignani},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Proteomics},

volume = {251},

pages = {104407},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{buonaiuto2021prioritization,

title = {Prioritization of putatively detrimental variants in euploid miscarriages},

author = {Silvia Buonaiuto and Immacolata Di Biase and Valentina Aleotti and Amin Ravaei and Adriano De Marino and Gianluca Damaggio and Marco Chierici and Madhuri Pulijala and Palmira D’Ambrosio and Gabriella Esposito and Qasim Ayub and Cesare Furlanello and Pantaleo Greco and Antonio Capalbo and Michele Rubini and Sebastiano Di Biase and Vincenza Colonna},

doi = {10.1101/2021.01.02.20248961},

year  = {2021},

date = {2021-01-01},

journal = {medRxiv},

publisher = {Cold Spring Harbor Laboratory Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rustici2020transcriptomics,

title = {Transcriptomics data availability and reusability in the transition from microarray to next-generation sequencing},

author = {Gabriella Rustici and Eleanor Williams and Mitra Barzine and Alvis Brazma and Roger Bumgarner and Marco Chierici and Cesare Furlanello and Liliana Greger and Giuseppe Jurman and Michael Miller and B. F. Francis Ouellette and John Quackenbush and Michael Reich and Christian J. Stoeckert and Ronald C. Taylor and Stephen Chervitz Trutane and Jennifer Weller and Brian Wilhelm and Neil Winegarden},

doi = {10.1101/2020.12.31.425022},

year  = {2021},

date = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grapotte2021discovery,

title = {Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network},

author = {Mathys Grapotte and Manu Saraswat and Chloé Bessi`ere and Christophe Menichelli and Jordan A Ramilowski and Jessica Severin and Yoshihide Hayashizaki and Masayoshi Itoh and Michihira Tagami and Mitsuyoshi Murata and others},

year  = {2021},

date = {2021-01-01},

journal = {Nature communications},

volume = {12},

number = {1},

pages = {1--18},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}