2026
Correction: MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning (International Journal of Molecular Sciences, (2021), 22, 8, (4217), 10.3390/ijms22084217)
Nosi, Vladimir; Luca, Alessandrì; Milan, Melissa; Arigoni, Maddalena; Benvenuti, Silvia; Cacchiarelli, Davide; Cesana, Marcella; Riccardo, Sara; Di Filippo, Lucio; Cordero, Francesca; Beccuti, Marco; Comoglio, Paolo M.; Calogero, Raffaele A.
International Journal of Molecular Sciences (2026-01-01)
COMPARATIVE ASSESSMENT OF TARGETED NEXT-GENERATION SEQUENCING PANELS AND ALGORITHMS FOR OPTIMAL MOLECULAR SUBTYPING OF DIFFUSE LARGE B-CELL LYMPHOMA IN CLINICAL PRACTICE
Gallucci, D.; Vegliante, M. C.; Gargano, G.; Ferri, A.; Pasini, L.; Lonardi, S.; Mandelli, G.; Medicina, D.; Balzarini, P.; Pellegrini, V.; Vermi, W.; Re, C.; Bossini, P.; Sanzogni, A.; Albertini, E.; Tucci, A.; Re, A.; Pizzi, M.; Di Napoli, A.; Cordero, F.; Lorenzi, L.; Ciavarella, S.
Haematologica (2026-03-03)
Image-Guided Microwave Ablation of Liver Tumours Using a 150-W Generator: Ex Vivo and Multicenter in Vivo Predictability Assessment
Calandri, Marco; Van Der Lei, Susan; Cignini, Valentina; Neuss, Timothy; Serafini, Alessandro; Risi, Gaetano; Menchini, Francesca; Ciferri, Fernanda; Gatti, Marco; Gazzera, Carlo; Fonio, Paolo; Sirovich, Roberta; Meijerink, Martijn Ruben
Cardiovascular and Interventional Radiology (2026-03-01)
Space debris detection from orbit: a prototype detector study
Reynaud, Federico; Abrate, Matteo; Coretti, Antonio Giulio; Bertaina, Mario Edoardo; Frasson, Andrea; Montanaro, Antonio; Bonino, Raffaella; Sirovich, Roberta
Journal of Space Safety Engineering (2026-01-01)
2025
Forge4Flame: An intuitive dashboard for designing GPU agent-based models to simulate infectious disease spread
Baccega, Daniele; Terrone, Irene; Heywood, Peter; Chisholm, Robert; Richmond, Paul; Contaldo, Sandro Gepiro; Bosio, Lorenzo; Pernice, Simone; Beccuti, Marco
Simulation Modelling Practice and Theory (2025-12-01)
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)
BookedSlurm: meeting user needs for advanced resource reservations in Slurm
Contaldo, Sandro Gepiro; Bosio, Lorenzo; Rea, Janneth Estefania Hoyos; Li Perottino, Elisa; Rabellino, Sergio; Aldinucci, Marco; Beccuti, Marco; Colonnelli, Iacopo
Proceedings 2025 IEEE International Conference on E Science Escience 2025 (2025-01-01)
Epidemic Modelling Frameworks for Studying Infectious Disease Dynamics
Baccega, Daniele; Beccuti, Marco; Pernice, Simone; Terrone, Irene
Proceedings 2025 IEEE 13th International Conference on Healthcare Informatics Ichi 2025 (2025-01-01)
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; Contaldo, Sandro Gepiro; 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)
Implementation of the Stack-CNN Algorithm for Space Debris Detection on FPGA Board
Abrate, Matteo; Reynaud, Federico; Bertaina, Mario Edoardo; Coretti, Antonio Giulio; Frasson, Andrea; Montanaro, Antonio; Bonino, Raffaella; Sirovich, Roberta
Applied Sciences Switzerland (2025-09-01)
Study Protocol DEDICATE: Italian Multicenter Study on the Treatment of Visceral Aneurysms with the Derivo Peripher and Derivo 2 Flow Diverter Stent
Discalzi, Andrea; Nardelli, Floriana; Ficara, Bruno; Comelli, Simone; de Donato, Gianmarco; Fanelli, Fabrizio; Quaretti, Pietro; Sallemi, Claudio; Semeraro, Vittorio; Sirovich, Roberta; Calandri, Marco; Vallone, Mario; Stanca, Carmelo; Solcia, Marco; Rossato, Denis; Pelle, Giuseppe; Patanè, Domenico; Pampana, Enrico; Muratore, Pierluigi; Moramarco, Lorenzo Paolo; Moniaci, Diego; Maresca, Silvio; Mancini, Andrea; Ierardi, Anna Maria; Fazzini, Stefano; Epifani, Enrico; Di Bartolomeo, Francesco; Doriguzzi Breatta, Andrea; Corona, Mario; Coi, Fabrizio; Chegai, Fabrizio; Casadei, Andrea; Cappucci, Matteo; Boi, Luca; Beneventi, Alessandro; Beleú, Alessandro; Beghetto, Mario; Arpesani, Roberto; Allegritti, Massimiliano
Cardiovascular and Interventional Radiology (2025-05-01)
Combined single-photon emission computed tomography-myocardial perfusion imaging with coronary calcium score for assessing coronary disease
Calandri, Enrico; Verdoia, Monica; Sirovich, Roberta; Giraudo, Maria Teresa; Pultrone, Mirco; Frantellizzi, Viviana; Viola, Orazio; Crivelli, Francesca; Gallina, Sonya; Serralunga, Monica; Rognoni, Andrea; De Vincentis, Giuseppe
Nuclear Medicine Communications (2025-01-01)
Dynamic Resources Management for Exascale in ADMIRE Framework
Carretero, Jesus; Singh, David E.; Fernandez-Muñoz, Javier; Sedona, Rocco; Pernice, Simone; Cantalupo, Barbara; Aldinucci, Marco; Torquati, Massimo; Tarraf, Ahmad; Jeannot, Emmanuel; Wolf, Felix
Procedia Computer Science (2025-01-01)
A Simulation-Based Framework to Reduce I/O Contention in HPC
Pernice, Simone; Tarraf, Ahmad; Besnard, Jean Baptiste; Cantalupo, Barbara; Cascajo, Alberto; Singh, David E.; Wolf, Felix; Carretero, Jesus; Shende, Sameer; Aldinucci, Marco
Proceedings 2025 IEEE International Parallel and Distributed Processing Symposium Workshops Ipdpsw 2025 (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)
An in vitro neurobacterial interface reveals direct modulation of neuronal function by gut bacteria
Lombardo-Hernandez, Juan; Mansilla-Guardiola, Jesús; Aucello, Riccardo; Botta, Cristian; García-Esteban, Maria Teresa; Murciano-Cespedosa, Antonio; Muñoz-Rodríguez, David; Quarta, Elisa; Mateos González, Álvaro; Juan-Llamas, Carmen; Rantsiou, Kalliopi; Geuna, Stefano; Cocolin, Luca; Herrera-Rincon, Celia
Scientific Reports (2025-12-01)
The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition
Trunfio, Mattia; Scutari, Rossana; Fox, Valeria; Vuaran, Elisa; Dastgheyb, Raha Maryam; Fini, Vanessa; Granaglia, Annarita; Balbo, Francesca; Tortarolo, Dora; Bonora, Stefano; Perno, Carlo Federico; Di Perri, Giovanni; Alteri, Claudia; Calcagno, Andrea
Frontiers in Microbiology (2025-01-01)
Nonproteolytic ubiquitination regulates chromatin occupancy by the NCoR/SMRT/HDAC3 corepressor complex in MCF-7 breast cancer cells
Ferrero, Giulio; Cardamone, Maria Dafne; Luca, Francesca; Bourk, Eliot; Ricci, Laura; Liu, Wen; Gao, Yuan; Burrone, Giulia; Muhammad, Akhirah; Chan, Stefanie; Smith, Emma; Fan, Ting Yu Claire; Cutrupi, Santina; Garcia-Bassets, Ivan; De Bortoli, Michele; Rosenfeld, Michael G.; Perissi, Valentina
Proceedings of the National Academy of Sciences of the United States of America (2025-05-06)
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)
RICTOR/mTORC2 downregulation in BRAFV600E melanoma cells promotes resistance to BRAF/MEK inhibition
Ponzone, Luca; Audrito, Valentina; Landi, Claudia; Moiso, Enrico; Levra Levron, Chiara; Ferrua, Sara; Savino, Aurora; Vitale, Nicoletta; Gasparrini, Massimiliano; Avalle, Lidia; Vantaggiato, Lorenza; Shaba, Enxhi; Tassone, Beatrice; Saoncella, Stefania; Orso, Francesca; Viavattene, Daniele; Marina, Eleonora; Fiorilla, Irene; Burrone, Giulia; Abili, Youssef; Altruda, Fiorella; Bini, Luca; Deaglio, Silvia; Defilippi, Paola; Menga, Alessio; Poli, Valeria; Porporato, Paolo Ettore; Provero, Paolo; Raffaelli, Nadia; Riganti, Chiara; Taverna, Daniela; Cavallo, Federica; Calautti, Enzo
Molecular Cancer (2024-12-01)
Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation
Gao, Yuan; Kwan, Julian; Orofino, Joseph; Burrone, Giulia; Mitra, Sahana; Fan, Ting Yu; English, Justin; Hekman, Ryan; Emili, Andrew; Lyons, Shawn M.; Cardamone, Maria Dafne; Perissi, Valentina
Pharmacological Research (2024-09-01)