Raffaele Calogero
Socio Ordinario
Professore associato
Università di Torino
Contact Information
phone
++390116706454
mobile
3333827080
fax
++390112366457
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: Nosi V, Luca A, Milan M, Arigoni M, Benvenuti S, Cacchiarelli D, Cesana M,
Riccardo S, Di Filippo L, Cordero F, Beccuti M, Comoglio PM, Calogero RA. MET
Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer
Driver Genes by Deep Learning. Int J Mol Sci. 2021 Apr 19;22(8):4217. doi:
10.3390/ijms22084217. PMID: 33921709; PMCID: PMC8072630.
2: Alessandri L, Cordero F, Beccuti M, Licheri N, Arigoni M, Olivero M, Di Renzo
MF, Sapino A, Calogero R. Sparsely-connected autoencoder (SCA) for single cell
RNAseq data mining. NPJ Syst Biol Appl. 2021 Jan 5;7(1):1. doi:
10.1038/s41540-020-00162-6. PMID: 33402683; PMCID: PMC7785742.
3: Alessandrì L, Cordero F, Beccuti M, Arigoni M, Calogero RA. Computational
Analysis of Single-Cell RNA-Seq Data. Methods Mol Biol. 2021;2284:289-301. doi:
10.1007/978-1-0716-1307-8_16. PMID: 33835449.
4: Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R,
Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S,
Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD.
Live-animal imaging of native haematopoietic stem and progenitor cells. Nature.
2020 Feb;578(7794):278-283. doi: 10.1038/s41586-020-1971-z. Epub 2020 Feb 5.
PMID: 32025033; PMCID: PMC7021587.
5: Alessandrì L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino
S, Licheri N, De Libero G, Pace L, Calogero RA. rCASC: reproducible
classification analysis of single-cell sequencing data. Gigascience. 2019 Sep
1;8(9):giz105. doi: 10.1093/gigascience/giz105. PMID: 31494672; PMCID:
PMC6732171.
6: Ordoñez-Rueda D, Baying B, Pavlinic D, Alessandri L, Yeboah Y, Landry JJM,
Calogero R, Benes V, Paulsen M. Apoptotic Cell Exclusion and Bias-Free Single-
Cell Selection Are Important Quality Control Requirements for Successful Single-
Cell Sequencing Applications. Cytometry A. 2020 Feb;97(2):156-167. doi:
10.1002/cyto.a.23898. Epub 2019 Oct 11. PMID: 31603610.
7: Alessandrì L, Arigoni M, Calogero R. Differential Expression Analysis in
Single-Cell Transcriptomics. Methods Mol Biol. 2019;1979:425-432. doi:
10.1007/978-1-4939-9240-9_25. PMID: 31028652.
8: Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero
F, Beccuti M, Calogero RA. Reproducible bioinformatics project: a community for
reproducible bioinformatics analysis pipelines. BMC Bioinformatics. 2018 Oct
15;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x. PMID: 30367595; PMCID:
PMC6191970.
9: Beccuti M, Cordero F, Arigoni M, Panero R, Amparore EG, Donatelli S, Calogero
RA. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.
Bioinformatics. 2018 Mar 1;34(5):871-872. doi: 10.1093/bioinformatics/btx674.
PMID: 29069297; PMCID: PMC6030956.
10: Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic
M, Sun J, Calogero RA, Klein AM, Camargo FD. Clonal analysis of lineage fate in
native haematopoiesis. Nature. 2018 Jan 11;553(7687):212-216. doi:
10.1038/nature25168. Epub 2018 Jan 3. PMID: 29323290; PMCID: PMC5884107.
Riccardo S, Di Filippo L, Cordero F, Beccuti M, Comoglio PM, Calogero RA. MET
Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer
Driver Genes by Deep Learning. Int J Mol Sci. 2021 Apr 19;22(8):4217. doi:
10.3390/ijms22084217. PMID: 33921709; PMCID: PMC8072630.
2: Alessandri L, Cordero F, Beccuti M, Licheri N, Arigoni M, Olivero M, Di Renzo
MF, Sapino A, Calogero R. Sparsely-connected autoencoder (SCA) for single cell
RNAseq data mining. NPJ Syst Biol Appl. 2021 Jan 5;7(1):1. doi:
10.1038/s41540-020-00162-6. PMID: 33402683; PMCID: PMC7785742.
3: Alessandrì L, Cordero F, Beccuti M, Arigoni M, Calogero RA. Computational
Analysis of Single-Cell RNA-Seq Data. Methods Mol Biol. 2021;2284:289-301. doi:
10.1007/978-1-0716-1307-8_16. PMID: 33835449.
4: Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R,
Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S,
Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD.
Live-animal imaging of native haematopoietic stem and progenitor cells. Nature.
2020 Feb;578(7794):278-283. doi: 10.1038/s41586-020-1971-z. Epub 2020 Feb 5.
PMID: 32025033; PMCID: PMC7021587.
5: Alessandrì L, Cordero F, Beccuti M, Arigoni M, Olivero M, Romano G, Rabellino
S, Licheri N, De Libero G, Pace L, Calogero RA. rCASC: reproducible
classification analysis of single-cell sequencing data. Gigascience. 2019 Sep
1;8(9):giz105. doi: 10.1093/gigascience/giz105. PMID: 31494672; PMCID:
PMC6732171.
6: Ordoñez-Rueda D, Baying B, Pavlinic D, Alessandri L, Yeboah Y, Landry JJM,
Calogero R, Benes V, Paulsen M. Apoptotic Cell Exclusion and Bias-Free Single-
Cell Selection Are Important Quality Control Requirements for Successful Single-
Cell Sequencing Applications. Cytometry A. 2020 Feb;97(2):156-167. doi:
10.1002/cyto.a.23898. Epub 2019 Oct 11. PMID: 31603610.
7: Alessandrì L, Arigoni M, Calogero R. Differential Expression Analysis in
Single-Cell Transcriptomics. Methods Mol Biol. 2019;1979:425-432. doi:
10.1007/978-1-4939-9240-9_25. PMID: 31028652.
8: Kulkarni N, Alessandrì L, Panero R, Arigoni M, Olivero M, Ferrero G, Cordero
F, Beccuti M, Calogero RA. Reproducible bioinformatics project: a community for
reproducible bioinformatics analysis pipelines. BMC Bioinformatics. 2018 Oct
15;19(Suppl 10):349. doi: 10.1186/s12859-018-2296-x. PMID: 30367595; PMCID:
PMC6191970.
9: Beccuti M, Cordero F, Arigoni M, Panero R, Amparore EG, Donatelli S, Calogero
RA. SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.
Bioinformatics. 2018 Mar 1;34(5):871-872. doi: 10.1093/bioinformatics/btx674.
PMID: 29069297; PMCID: PMC6030956.
10: Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic
M, Sun J, Calogero RA, Klein AM, Camargo FD. Clonal analysis of lineage fate in
native haematopoiesis. Nature. 2018 Jan 11;553(7687):212-216. doi:
10.1038/nature25168. Epub 2018 Jan 3. PMID: 29323290; PMCID: PMC5884107.
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
RNAseq/ChIPseq course DUKE-NUS Singapore
RNAseq/ChIPseq course DUKE-NUS Singapore
