Raffaele Calogero
Socio Ordinario
Professore ordinario
Università di Torino
Contact Information
phone
++390116706454
mobile
3333827080
website
RESEARCH AREA
algorithms,biological data integration,network systems,sequence analysis,system biology
RESEARCH ACTIVITY
Raffaele Calogero is the PI of the Bioinformatics and Genomics core lab (BGcore) at Molecular Biotechnology Center in Torino. He is the co-founder of the Reproducible Bioinformatics Project, a community of scientists devoted to the development of reproducible bioinformatics workflows in the area of genomics. The actual main research focus of Prof. Calogero is reproducibility in single-cell data analysis. Spatial transcriptomics and single-cell multiOMICs workflow development.
SELECTED PUBLICATIONS
1: Alessandri S, Ratto ML, Rabellino S, Piacenti G, Contaldo SG, Pernice S,Beccuti M, Calogero RA, Alessandri L. CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. BMC Bioinformatics. 2024 Mar 12;25(1):110. doi: 10.1186/s12859-024-05695-9. PMID:38475691; PMCID: PMC10935966.
2: Arigoni M, Ratto ML, Riccardo F, Balmas E, Calogero L, Cordero F, Beccuti M, Calogero RA, Alessandri L. A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity. Sci Data. 2024 Feb 2;11(1):159. doi:10.1038/s41597-024-03002-y. PMID: 38307867; PMCID: PMC10837414.
3: Devan J, Nosi V, Spagnuolo J, Chancellor A, Beshirova A, Loureiro JP,Vacchini A, Hendrik Niess J, Calogero R, Mori L, De Libero G, Hruz P. Surface protein and functional analyses identify CD4+CD39+ TCR αβ+ and activated TCR Vδ1+ cells with distinct pro-inflammatory functions in Crohn's disease lesions. Clin Exp Immunol. 2024 Jan 9;215(1):79-93. doi: 10.1093/cei/uxad098. PMID: 37586415; PMCID: PMC10776239.
4: Chancellor A, Alan Simmons R, Khanolkar RC, Nosi V, Beshirova A, Berloffa G, Colombo R, Karuppiah V, Pentier JM, Tubb V, Ghadbane H, Suckling RJ, Page K, Crean RM, Vacchini A, De Gregorio C, Schaefer V, Constantin D, Gligoris T, Lloyd A, Hock M, Srikannathasan V, Robinson RA, Besra GS, van der Kamp MW, Mori L, Calogero R, Cole DK, De Libero G, Lepore M. Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses. J Exp Med. 2023 Sep 4;220(9):e20221939. doi: 10.1084/jem.20221939. Epub 2023 Jun 29. PMID: 37382893; PMCID: PMC10309188.
5: Mastini C, Campisi M, Patrucco E, Mura G, Ferreira A, Costa C, Ambrogio C,Germena G, Martinengo C, Peola S, Mota I, Vissio E, Molinaro L, Arigoni M, Olivero M, Calogero R, Prokoph N, Tabbò F, Shoji B, Brugieres L, Geoerger B, Turner SD, Cuesta-Mateos C, D'Aliberti D, Mologni L, Piazza R, Gambacorti-Passerini C, Inghirami GG, Chiono V, Kamm RD, Hirsch E, Koch R, Weinstock DM, Aster JC, Voena C, Chiarle R. Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma. Sci Transl Med. 2023 Jun 28;15(702):eabo3826. doi: 10.1126/scitranslmed.abo3826. Epub 2023 Jun 28. PMID: 37379367; PMCID: PMC10804420.
6: Salemme V, Vedelago M, Sarcinella A, Moietta F, Piccolantonio A, Moiso E, Centonze G, Manco M, Guala A, Lamolinara A, Angelini C, Morellato A, Natalini D, Calogero R, Incarnato D, Oliviero S, Conti L, Iezzi M, Tosoni D, Bertalot G, Freddi S, Tucci FA, De Sanctis F, Frusteri C, Ugel S, Bronte V, Cavallo F, Provero P, Gai M, Taverna D, Turco E, Pece S, Defilippi P. p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response. Nat Commun. 2023 May 11;14(1):2350. doi: 10.1038/s41467-023-37824-y. PMID: 37169737; PMCID: PMC10175288.
7: Pernice S, Sirovich R, Grassi E, Viviani M, Ferri M, Sassi F, Alessandrì L, Tortarolo D, Calogero RA, Trusolino L, Bertotti A, Beccuti M, Olivero M, Cordero F. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinformatics. 2023 May 4;39(5):btad201. doi: 10.1093/bioinformatics/btad201. PMID: 37079732; PMCID: PMC10159654.
2: Arigoni M, Ratto ML, Riccardo F, Balmas E, Calogero L, Cordero F, Beccuti M, Calogero RA, Alessandri L. A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity. Sci Data. 2024 Feb 2;11(1):159. doi:10.1038/s41597-024-03002-y. PMID: 38307867; PMCID: PMC10837414.
3: Devan J, Nosi V, Spagnuolo J, Chancellor A, Beshirova A, Loureiro JP,Vacchini A, Hendrik Niess J, Calogero R, Mori L, De Libero G, Hruz P. Surface protein and functional analyses identify CD4+CD39+ TCR αβ+ and activated TCR Vδ1+ cells with distinct pro-inflammatory functions in Crohn's disease lesions. Clin Exp Immunol. 2024 Jan 9;215(1):79-93. doi: 10.1093/cei/uxad098. PMID: 37586415; PMCID: PMC10776239.
4: Chancellor A, Alan Simmons R, Khanolkar RC, Nosi V, Beshirova A, Berloffa G, Colombo R, Karuppiah V, Pentier JM, Tubb V, Ghadbane H, Suckling RJ, Page K, Crean RM, Vacchini A, De Gregorio C, Schaefer V, Constantin D, Gligoris T, Lloyd A, Hock M, Srikannathasan V, Robinson RA, Besra GS, van der Kamp MW, Mori L, Calogero R, Cole DK, De Libero G, Lepore M. Promiscuous recognition of MR1 drives self-reactive mucosal-associated invariant T cell responses. J Exp Med. 2023 Sep 4;220(9):e20221939. doi: 10.1084/jem.20221939. Epub 2023 Jun 29. PMID: 37382893; PMCID: PMC10309188.
5: Mastini C, Campisi M, Patrucco E, Mura G, Ferreira A, Costa C, Ambrogio C,Germena G, Martinengo C, Peola S, Mota I, Vissio E, Molinaro L, Arigoni M, Olivero M, Calogero R, Prokoph N, Tabbò F, Shoji B, Brugieres L, Geoerger B, Turner SD, Cuesta-Mateos C, D'Aliberti D, Mologni L, Piazza R, Gambacorti-Passerini C, Inghirami GG, Chiono V, Kamm RD, Hirsch E, Koch R, Weinstock DM, Aster JC, Voena C, Chiarle R. Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma. Sci Transl Med. 2023 Jun 28;15(702):eabo3826. doi: 10.1126/scitranslmed.abo3826. Epub 2023 Jun 28. PMID: 37379367; PMCID: PMC10804420.
6: Salemme V, Vedelago M, Sarcinella A, Moietta F, Piccolantonio A, Moiso E, Centonze G, Manco M, Guala A, Lamolinara A, Angelini C, Morellato A, Natalini D, Calogero R, Incarnato D, Oliviero S, Conti L, Iezzi M, Tosoni D, Bertalot G, Freddi S, Tucci FA, De Sanctis F, Frusteri C, Ugel S, Bronte V, Cavallo F, Provero P, Gai M, Taverna D, Turco E, Pece S, Defilippi P. p140Cap inhibits β-Catenin in the breast cancer stem cell compartment instructing a protective anti-tumor immune response. Nat Commun. 2023 May 11;14(1):2350. doi: 10.1038/s41467-023-37824-y. PMID: 37169737; PMCID: PMC10175288.
7: Pernice S, Sirovich R, Grassi E, Viviani M, Ferri M, Sassi F, Alessandrì L, Tortarolo D, Calogero RA, Trusolino L, Bertotti A, Beccuti M, Olivero M, Cordero F. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system. Bioinformatics. 2023 May 4;39(5):btad201. doi: 10.1093/bioinformatics/btad201. PMID: 37079732; PMCID: PMC10159654.
OTHER MEMBERSHIPS
ISCB
SIBBM
ASCO
AACR
SIBBM
ASCO
AACR
EDITORIAL BOARDS
BMC Bioinformatics Associated Editor
MAIN TEACHINGS
Biologia Molecolare (Medicina e Chirurgia, Università di Torino)
Fisica e Informatica (Biotecnologie triennale, Università di Torino)
DATA ANALYSIS (Biotecnologie Molecolari, Università di Torino)
Bioinformatica (Biotecnologie Mediche, Università di Torino)
BIOLOGIA MOLECOLARE (Fisica, Università di Torino)
Fisica e Informatica (Biotecnologie triennale, Università di Torino)
DATA ANALYSIS (Biotecnologie Molecolari, Università di Torino)
Bioinformatica (Biotecnologie Mediche, Università di Torino)
BIOLOGIA MOLECOLARE (Fisica, Università di Torino)
OTHER TEACHINGS
Whole Transcriptome Analysis EMBL - Heidelberg
Analysis and integration of transcriptome and proteome data
RNAseq/ChIPseq course DUKE-NUS Singapore
Analysis and integration of transcriptome and proteome data
RNAseq/ChIPseq course DUKE-NUS Singapore
