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)