2025
UnifiedGreatMod: A new holistic modelling paradigm for studying biological systems on a complete and harmonious scale
Aucello, Riccardo; Pernice, Simone; Tortarolo, Dora; Calogero, Raffaele A.; Herrera-Rincon, Celia; Ronchi, Giulia; Geuna, Stefano; Cordero, Francesca; Lió, Pietro; Beccuti, Marco
Bioinformatics (2025-03-01)
Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node
Contaldo, Sandro Gepiro; d’Acierno, Antonio; Bosio, Lorenzo; Venice, Francesco; Perottino, Elisa Li; Hoyos Rea, Janneth Estefania; Varese, Giovanna Cristina; Cordero, Francesca; Beccuti, Marco
Frontiers in Bioinformatics (2025-01-01)
Living Along COVID-19: Assessing Contention Policies Through Agent-Based Models
Baccega, Daniele; Pernice, Simone; Castagno, Paolo; Sereno, Matteo; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Synergy Between Mechanistic Modelling and Ensemble Feature Selection Approaches to Explore Multiscale Biological Heterogeneity
Aucello, Riccardo; Licheri, Nicola; Rosso, Elena; Ferrero, Giulio; Gepiro Contaldo, Sandro; Pernice, Simone; Lió, Pietro; Cordero, Francesca; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Functional Data Analysis and Clustering of Haematological Parameters in SARS-CoV-2 Patients
Volpatto, Daniela; Frattarola, Marco; Pernice, Simone; Cordero, Francesca; Beccuti, Marco; Mengozzi, Giulio; De Angelis, Stefano; Sirovich, Roberta
Lecture Notes in Computer Science (2025-01-01)
Stochastic Modeling and Dosage Optimization of a Cancer Vaccine Exploiting the EpiMod Framework
Beccuti, Marco; Franceschinis, Giuliana; Pennisi, Marzio; Pernice, Simone; Terrone, Irene
Lecture Notes in Computer Science (2025-01-01)
Extension of the GreatMod Modeling Framework to Simulate Non-Markovian Processes with General-Distributed Events
Terrone, Irene; Volpatto, Daniela; Pernice, Simone; Amparore, Elvio; Sirovich, Roberta; Cordero, Francesca; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
PHeP: TrustAlert Open-Source Platform for Enhancing Predictive Healthcare with Deep Learning
Contaldo, Sandro Gepiro; Pietropaolo, Emanuele; Bosio, Lorenzo; Pernice, Simone; Terrone, Irene; Baccega, Daniele; Wang, Yuting; Sahoo, Rahul Kumar; Rizzo, Giuseppe; Visconti, Alessia; Berchialla, Paola; Beccuti, Marco
Lecture Notes in Computer Science (2025-01-01)
Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer
Piccinno, Gianmarco; Thompson, Kelsey N.; Manghi, Paolo; Ghazi, Andrew R.; Thomas, Andrew Maltez; Blanco-Míguez, Aitor; Asnicar, Francesco; Mladenovic, Katarina; Pinto, Federica; Armanini, Federica; Punčochář, Michal; Piperni, Elisa; Heidrich, Vitor; Fackelmann, Gloria; Ferrero, Giulio; Tarallo, Sonia; Nguyen, Long H.; Yan, Yan; Keles, Nazim A.; Tuna, Bilge G.; Vymetalkova, Veronika; Trompetto, Mario; Liska, Vaclav; Hucl, Tomas; Vodicka, Pavel; Bencsiková, Beatrix; Čarnogurská, Martina; Popovici, Vlad; Marmorino, Federica; Cremolini, Chiara; Pardini, Barbara; Cordero, Francesca; Song, Mingyang; Chan, Andrew T.; Derosa, Lisa; Zitvogel, Laurence; Huttenhower, Curtis; Naccarati, Alessio; Budinska, Eva; Segata, Nicola
Nature Medicine (2025-07-01)
Impact of the ONCOBIOME network in cancer microbiome research
Zitvogel, Laurence; Derosa, Lisa; Routy, Bertrand; Loibl, Sibylle; Heinzerling, Lucie; de Vries, I. Jolanda M.; Engstrand, Lars; Zeller, Georg; Trochon, Jean Jacques; Trinchieri, Giorgio; Sow, Cissé; Szallasi, Zoltan; Schuler, Gerold; Schuler-Thurner, Beatrice; Tarallo, Sonia; Rachid, Maan Haj; Popovici, Vlad; Pizzato, Eugénie; Piccinno, Gianmarco; Pinto, Federica; Pardini, Barbara; Naccarati, Alessio; Monville, Florence; Messaoudene, Meriem; Martineau, Magalie; Lehtio, Janne; Iebba, Valerio; Guindo, Cheick Oumar; Gariboldi, Manuela; Gaborit, Jérôme; Fidelle, Marine; Ferrere, Gladys; Felder, Baerbel; Fall, Katja; Elkrief, Arielle; Eisinger, François; Ehrlich, Stanislav; Durand, Sylvere; Denkert, Carsten; Daillère, Romain; Cremolini, Chiara; Cordero, Francesca; Caldas, Carlos; Budinska, Eva; Brusselaers, Nele; Bol, Kalijn; Boleij, Annemarie; Barbieri, Daniela; Silva, Carolina Alves Costa; Segata, Nicola; Kroemer, Guido
Nature Medicine (2025-04-01)
Luminescent sensing of conformational integrin activation in living cells
Villari, Giulia; Gioelli, Noemi; Gino, Marta; Zhang, Heng; Hodge, Kelly; Cordero, Francesca; Zanivan, Sara; Zhu, Jieqing; Serini, Guido
Cell Reports (2025-02-25)
Dynamic regulation of Rgs16 and its correlation with Neuregulin1 expression in acute and chronic nerve injury
García-Bejarano, Marina; Aucello, Riccardo; Zen, Federica; El Soury, Marwa; Cordero, Francesca; de la Fuente, Jesús M.; Perroteau, Isabelle; Ronchi, Giulia; Gambarotta, Giovanna
Frontiers in Cell and Developmental Biology (2025-01-01)
Exploiting GPU computing for effective Agent-Based simulation: initial experiments
Pennisi, Marzio; Franceschinis, Giuliana; Baccega, Daniele; Pernice, Simone; Terrone, Irene
Proceedings 33rd Euromicro International Conference on Parallel Distributed and Network Based Processing Pdp 2025 (2025-01-01)
Social Compliance with NPIs, Mobility Patterns, and Reproduction Number: Lessons from COVID-19 in Europe
Baccega, Daniele; Aguilar, Jose; Baquero, Carlos; Anta, Antonio Fernandez; Ramirez, Juan Marcos
IEEE Access (2025-01-01)
2024
A novel machine-learning framework based on early embryo morphokinetics identifies a feature signature associated with blastocyst development
Canosa, S.; Licheri, N.; Bergandi, L.; Gennarelli, G.; Paschero, C.; Beccuti, M.; Cimadomo, D.; Coticchio, G.; Rienzi, L.; Benedetto, C.; Cordero, F.; Revelli, A.
Journal of Ovarian Research (2024-12-01)
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
Alessandri, Simone; Ratto, Maria L.; Rabellino, Sergio; Piacenti, Gabriele; Contaldo, Sandro Gepiro; Pernice, Simone; Beccuti, Marco; Calogero, Raffaele A.; Alessandri, Luca
BMC Bioinformatics (2024-12-01)
A single cell RNAseq benchmark experiment embedding “controlled” cancer heterogeneity
Arigoni, Maddalena; Ratto, Maria Luisa; Riccardo, Federica; Balmas, Elisa; Calogero, Lorenzo; Cordero, Francesca; Beccuti, Marco; Calogero, Raffaele A.; Alessandri, Luca
Scientific Data (2024-12-01)
Tamoxifen Activates Transcription Factor EB and Triggers Protective Autophagy in Breast Cancer Cells by Inducing Lysosomal Calcium Release: A Gateway to the Onset of Endocrine Resistance
Boretto, Cecilia; Actis, Chiara; Faris, Pawan; Cordero, Francesca; Beccuti, Marco; Ferrero, Giulio; Muzio, Giuliana; Moccia, Francesco; Autelli, Riccardo
International Journal of Molecular Sciences (2024-01-01)
Synchronies and asynchronies in the development of COVID-19 pandemic in Italy
Giraudo, Maria Teresa; Falcone, Manuele; Cislaghi, Cesare; Cordero, Francesca; Pernice, Simone; Sirovich, Roberta
Epidemiologia E Prevenzione (2024-05-01)
Modulation of faecal miRNAs highlights the preventive effects of a Mediterranean low-inflammatory dietary intervention
Illescas, Oscar; Ferrero, Giulio; Belfiore, Antonino; Pardini, Barbara; Tarallo, Sonia; Ciniselli, Chiara M.; Noci, Sara; Daveri, Elena; Signoroni, Stefano; Cattaneo, Laura; Mancini, Andrea; Morelli, Daniele; Milione, Massimo; Cordero, Francesca; Rivoltini, Licia; Verderio, Paolo; Pasanisi, Patrizia; Vitellaro, Marco; Naccarati, Alessio; Gariboldi, Manuela
Clinical Nutrition (2024-04-01)
In pancreatic cancer patients, chemotherapy reshapes the gene expression profile and antigen receptor repertoire of T lymphocytes and enhances their effector response to tumor-associated antigens
Brugiapaglia, Silvia; Bulfamante, Sara; Curcio, Claudia; Arigoni, Maddalena; Calogero, Raffaele; Bonello, Lisa; Genuardi, Elisa; Spadi, Rosella; Satolli, Maria Antonietta; Campra, Donata; Giordano, Daniele; Cappello, Paola; Cordero, Francesca; Novelli, Francesco
Frontiers in Immunology (2024-01-01)
Enhancing COVID-19 forecasting precision through the integration of compartmental models, machine learning and variants
Baccega, Daniele; Castagno, Paolo; Fernández Anta, Antonio; Sereno, Matteo
Scientific Reports (2024-12-01)
Convolutional neural network (CNN)-enabled electrocardiogram (ECG) analysis: a comparison between standard twelve-lead and single-lead setups
Saglietto, Andrea; Baccega, Daniele; Esposito, Roberto; Anselmino, Matteo; Dusi, Veronica; Fiandrotti, Attilio; De Ferrari, Gaetano Maria
Frontiers in Cardiovascular Medicine (2024-01-01)