Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

Authors: Grassucci, Isabella, Sperandio, Eleonora, Ticconi, Fabio, Massacci, Alice, Baldinelli, Sara, Betti, Martina, Pallocca, Matteo

Source: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2023 IEEE International Conference on. :3638-3641 Dec, 2023

Relation: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

AI drives the assessment of lung cancer microenvironment composition

Authors: Gallo, Enzo, Guardiani, Davide, Betti, Martina, Arteni, Brindusa Ana Maria, Di Martino, Simona, Baldinelli, Sara, Daralioti, Theodora, Merenda, Elisabetta, Ascione, Andrea, Visca, Paolo, Pescarmona, Edoardo, Lavitrano, Marialuisa, Nisticò, Paola, Ciliberto, Gennaro, Pallocca, Matteo

Source: In Journal of Pathology Informatics December 2024 15

Clinical bioinformatics desiderata for molecular tumor boards.

Authors: Pallocca, Matteo¹ (AUTHOR) matteo.pallocca@cnr.it, Betti, Martina² (AUTHOR), Baldinelli, Sara² (AUTHOR), Palombo, Ramona¹ (AUTHOR), Bucci, Gabriele³ (AUTHOR), Mazzarella, Luca^4,5 (AUTHOR), Tonon, Giovanni⁶ (AUTHOR), Ciliberto, Gennaro⁷ (AUTHOR)

Source: Briefings in Bioinformatics. Sep2024, Vol. 25 Issue 5, p1-9. 9p.

Subject Terms: *MEDICAL informatics, *DIGITAL technology, *CANCER patients, *GENOMICS, *CANCER treatment

Correction to: Comprehensive genomic profiling on metastatic Melanoma: results from a network screening from 7 Italian Cancer Centres.

Authors: Pallocca, Matteo¹ (AUTHOR) matteo.pallocca@cnr.it, Molineris, Ivan^2,3 (AUTHOR), Berrino, Enrico^3,4 (AUTHOR), Marcozzi, Benedetta⁵ (AUTHOR), Betti, Martina⁵ (AUTHOR), Levati, Lauretta⁶ (AUTHOR), D'Atri, Stefania⁶ (AUTHOR), Menin, Chiara⁷ (AUTHOR), Madonna, Gabriele⁸ (AUTHOR), Ghiorzo, Paola^9,10 (AUTHOR), Bulgarelli, Jenny¹¹ (AUTHOR), Ferraresi, Virgina¹² (AUTHOR), Venesio, Tiziana³ (AUTHOR), Rodolfo, Monica¹³ (AUTHOR), Rivoltini, Licia¹³ (AUTHOR), Lanfrancone, Luisa¹⁴ (AUTHOR), Ascierto, Paolo Antonio⁸ (AUTHOR), Mazzarella, Luca¹⁴ (AUTHOR), Pelicci, Pier Giuseppe^14,15 (AUTHOR), De Maria, Ruggero¹⁶ (AUTHOR)

Source: Journal of Translational Medicine. 10/22/2024, Vol. 22 Issue 1, p1-3. 3p.

Subject Terms: *MOLECULAR oncology, *MEDICAL specialties & specialists, *LIFE sciences, *INTERNAL medicine, *CANCER genetics

Machine learning endometrial cancer risk prediction model: integrating guidelines of European Society for Medical Oncology with the tumor immune framework

Authors: Bruno, Valentina ^{1, *}, Betti, Martina ², D’Ambrosio, Lorenzo ³, Massacci, Alice ³, Chiofalo, Benito ¹, Pietropolli, Adalgisa ⁴, Piaggio, Giulia ³, Ciliberto, Gennaro ³, Nisticò, Paola ³, Pallocca, Matteo ³, Buda, Alessandro ⁵, Vizza, Enrico ¹

Source: In International Journal of Gynecological Cancer November 2023 33(11):1708-1714

Comprehensive genomic profiling on metastatic Melanoma: results from a network screening from 7 Italian Cancer Centres.

Authors: Pallocca, Matteo¹ (AUTHOR) matteo.pallocca@ifo.it, Molineris, Ivan^2,3 (AUTHOR), Berrino, Enrico^3,4 (AUTHOR), Marcozzi, Benedetta¹ (AUTHOR), Betti, Martina¹ (AUTHOR), Levati, Lauretta⁵ (AUTHOR), D'Atri, Stefania⁵ (AUTHOR), Menin, Chiara⁶ (AUTHOR), Madonna, Gabriele⁷ (AUTHOR), Ghiorzo, Paola^8,9 (AUTHOR), Bulgarelli, Jenny¹⁰ (AUTHOR), Ferraresi, Virgina¹¹ (AUTHOR), Venesio, Tiziana³ (AUTHOR), Rodolfo, Monica¹² (AUTHOR), Rivoltini, Licia¹² (AUTHOR), Lanfrancone, Luisa¹³ (AUTHOR), Ascierto, Paolo Antonio⁶ (AUTHOR), Mazzarella, Luca¹⁴ (AUTHOR), Pelicci, Pier Giuseppe^13,15 (AUTHOR), De Maria, Ruggero¹⁴ (AUTHOR)

Source: Journal of Translational Medicine. 1/6/2024, Vol. 22 Issue 1, p1-7. 7p.

Subject Terms: *MACHINE learning, *SINGLE nucleotide polymorphisms, *MEDICAL screening, *MELANOMA, *RANDOM forest algorithms, *PROGRESSION-free survival

ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data

Authors: D'Antonio, Mattia, D'Onorio De Meo, Paolo, Castrignano, Tiziana, Erbacci, Giovanni, Pallocca, Matteo, Pesole, Graziano

Source: 2014 International Conference on High Performance Computing & Simulation (HPCS) High Performance Computing & Simulation (HPCS), 2014 International Conference on. :608-615 Jul, 2014

Relation: 2014 International Conference on High Performance Computing & Simulation (HPCS)

Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking

Authors: Donzelli, Sara, Ciuffreda, Ludovica, Pontone, Martina, Betti, Martina, Massacci, Alice, Mottini, Carla, De Nicola, Francesca, Orlandi, Giulia, Goeman, Frauke, Giuliani, Eugenia, Sperandio, Eleonora, Piaggio, Giulia, Morrone, Aldo, Ciliberto, Gennaro, Fanciulli, Maurizio, Blandino, Giovanni, Pimpinelli, Fulvia, Pallocca, Matteo

Source: Computational and Structural Biotechnology Journal. 20:2558-2563

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190063196.0x000001&indx=1&recIds=ETOCvdc_100190063196.0x000001

Duration of humoral response to the third dose of BNT162b2 vaccine in patients with solid cancer: Is fourth dose urgently needed?

Authors: Di Noia, Vincenzo, Pimpinelli, Fulvia, Renna, Davide, Campo, Flaminia, Cosimati, Antonella, Torchia, Andrea, Marcozzi, Benedetta, Massacci, Alice, Pallocca, Matteo, Pellini, Raul, Morrone, Aldo, Cognetti, Francesco

Source: European journal of cancer. 176:164-167

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100175334777.0x000001&indx=1&recIds=ETOCvdc_100175334777.0x000001

Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in multiple myeloma

Authors: Bruno, Tiziana, De Nicola, Francesca, Corleone, Giacomo, Catena, Valeria, Goeman, Frauke, Pallocca, Matteo, Sorino, Cristina, Bossi, Gianluca, Amadio, Bruno, Cigliana, Giovanni, Ricciardi, Maria Rosaria, Petrucci, Maria Teresa, Spugnini, Enrico Pierluigi, Baldi, Alfonso, Cioce, Mario, Cortese, Giancarlo, Mattei, Elisabetta, Merola, Roberta, Gianelli, Umberto, Baldini, Luca, Pisani, Francesco, Gumenyuk, Svitlana, Mengarelli, Andrea, Höpker, Katja, Benzing, Thomas, Vincenzi, Bruno, Floridi, Aristide, Passananti, Claudio, Blandino, Giovanni, Iezzi, Simona, Fanciulli, Maurizio

Source: In Blood Advances 24 November 2020 4(22):5616-5630

Development of a somatic variant registry in a National Cancer Center: towards Molecular Real World Data preparedness

Authors: Betti, Martina, Maria Salzano, Chiara, Massacci, Alice, D'Antonio, Mattia, Grassucci, Isabella, Marcozzi, Benedetta, Canfora, Marco, Melucci, Elisa, Buglioni, Simonetta, Casini, Beatrice, Gallo, Enzo, Pescarmona, Edoardo, Ciliberto, Gennaro, Pallocca, Matteo

Source: Journal of biomedical informatics. 142

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191578876.0x000001&indx=1&recIds=ETOCvdc_100191578876.0x000001

Host Immune Response To HPV Infection: Deconvolution Analysis From Liquid-Based Cytology Low-Volume Rna-Seq Data For Tumor Microenvironment Profiling In Cervical Dysplasia/Cancer Progression And Risk Stratification: A Pilot Study

Authors: Bruno, Valentina ¹, Logoteta, Alessandra ^{2, 3}, Betti, Martina ⁴, De Nicola, Francesca ⁵, Ciuffreda, Ludovica ⁵, Ferretti, Margherita ⁵, Baiocco, Ermelinda ¹, Mancini, Emanuela ¹, Vincenzoni, Cristina ¹, Cutillo, Giuseppe ¹, Pallocca, Matteo ⁶, Fanciulli, Maurizio ⁵, Vizza, Enrico ¹

Source: In International Journal of Gynecological Cancer February 2025 35(2) Supplement 1

Mutations in the KEAP1-NFE2L2 Pathway Define a Molecular Subset of Rapidly Progressing Lung Adenocarcinoma

Authors: Goeman, Frauke, De Nicola, Francesca, Scalera, Stefano, Sperati, Francesca, Gallo, Enzo, Ciuffreda, Ludovica, Pallocca, Matteo, Pizzuti, Laura, Krasniqi, Eriseld, Barchiesi, Giacomo, Vici, Patrizia, Barba, Maddalena, Buglioni, Simonetta, Casini, Beatrice, Visca, Paolo, Pescarmona, Edoardo, Mazzotta, Marco, De Maria, Ruggero, Fanciulli, Maurizio, Ciliberto, Gennaro, Maugeri-Saccà, Marcello

Source: In Journal of Thoracic Oncology November 2019 14(11):1924-1934

Targeting of mutant-p53 and MYC as a novel strategy to inhibit oncogenic SPAG5 activity in triple negative breast cancer.

Authors: Canu, Valeria, Vaccarella, Sebastiano, Sacconi, Andrea, Pulito, Claudio, Goeman, Frauke, Pallocca, Matteo, Rutigliano, Daniela, Lev, Sima, Strano, Sabrina, Blandino, Giovanni

Source: Cell Death & Disease; Aug2024, Vol. 15 Issue 8, p1-15, 15p

Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases

Authors: Grassi, Ludovica, Alfonsi, Romina, Francescangeli, Federica, Signore, Michele, Angelis, Maria, Addario, Antonio, Costantini, Manuela, Flex, Elisabetta, Ciolfi, Andrea, Pizzi, Simone, Bruselles, Alessandro, Pallocca, Matteo, Simone, Giuseppe, Haoui, Mustapha, Falchi, Mario, Milella, Michele, Sentinelli, Steno, Matteo, Paola, Stellacci, Emilia, Gallucci, Michele, Muto, Giovanni, Tartaglia, Marco, Maria, Ruggero, Bonci, Désirée

Source: Cell death and disease. 10(3):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125109907.0x000001&indx=1&recIds=ETOCvdc_100125109907.0x000001

Combinations of immuno-checkpoint inhibitors predictive biomarkers only marginally improve their individual accuracy

Authors: Pallocca, Matteo, Angeli, Davide, Palombo, Fabio, Sperati, Francesca, Milella, Michele, Goeman, Frauke, Nicola, Francesca, Fanciulli, Maurizio, Nisticò, Paola, Quintarelli, Concetta, Ciliberto, Gennaro

Source: Journal of translational medicine. 17(1):1-8

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100187124478.0x000001&indx=1&recIds=ETOCvdc_100187124478.0x000001

Poly-specific neoantigen-targeted cancer vaccines delay patient derived tumor growth

Authors: Aurisicchio, Luigi, Salvatori, Erika, Lione, Lucia, Bandini, Silvio, Pallocca, Matteo, Maggio, Roberta, Fanciulli, Maurizio, Nicola, Francesca, Goeman, Frauke, Ciliberto, Gennaro, Conforti, Antonella, Luberto, Laura, Palombo, Fabio

Source: Journal of experimental & clinical cancer research. 38(1):1-13

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185615149.0x000001&indx=1&recIds=ETOCvdc_100185615149.0x000001

Identification of a set of genes potentially responsible for resistance to ferroptosis in lung adenocarcinoma cancer stem cells.

Authors: Ascenzi, Francesca, Esposito, Antonella, Bruschini, Sara, Salvati, Valentina, De Vitis, Claudia, De Arcangelis, Valeria, Ricci, Giulia, Catizione, Angiolina, di Martino, Simona, Buglioni, Simonetta, Bassi, Massimiliano, Venuta, Federico, De Nicola, Francesca, Massacci, Alice, Grassucci, Isabella, Pallocca, Matteo, Ricci, Alberto, Fanciulli, Maurizio, Ciliberto, Gennaro, Mancini, Rita

Source: Cell Death & Disease; Apr2024, Vol. 15 Issue 4, p1-13, 13p

Targeting a phospho-STAT3-miRNAs pathway improves vesicular hepatic steatosis in an in vitro and in vivo model

Authors: Belloni, Laura, Di Cocco, Silvia, Guerrieri, Francesca, Nunn, Abigail, Piconese, Silvia, Salerno, Debora, Testoni, Barbara, Pulito, Claudio, Mori, Federica, Pallocca, Matteo, Sacconi, Andrea, Vivoli, Elisa, Marra, Fabio, Strano, Sabrina, Blandino, Giovanni, Levrero, Massimo, Pediconi, Natalia

Source: Scientific reports. 8(1):1-12

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181176702.0x000001&indx=1&recIds=ETOCvdc_100181176702.0x000001

Deep sequencing and pathway-focused analysis revealed multigene oncodriver signatures predicting survival outcomes in advanced colorectal cancer

Authors: De Nicola, Francesca, Goeman, Frauke, Pallocca, Matteo, Sperati, Francesca, Pizzuti, Laura, Melucci, Elisa, Casini, Beatrice, Amoreo, Carla, Gallo, Enzo, Diodoro, Maria, Buglioni, Simonetta, Mazzotta, Marco, Vici, Patrizia, Sergi, Domenico, Di Lauro, Luigi, Barba, Maddalena, Pescarmona, Edoardo, Ciliberto, Gennaro, De Maria, Ruggero, Fanciulli, Maurizio, Maugeri-Saccà, Marcello

Source: Oncogenesis. 7(7):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171476915.0x000001&indx=1&recIds=ETOCvdc_100171476915.0x000001