Personal information

transcriptomics, next generation sequence, single cell omics, reproducibility, Deep learning, Sparsely connected autoencoder

Biography

EDUCATION:
1984: Laurea in Biological Sciences summa cum laude from Naples University "Federico II" (Italy).
1984-1985: Post-laurea training at Institute of Genetics, General and Molecular Biology (Naples University "Federico II").
1985-1988: Fellowship at Max Plank Institute fuer Molekulare Genetik in Berlin (Germany).

PROFESSIONAL EXPERIENCES:
1989-1992: Researcher at SORIN Biomedica S.p.A. (I).
1992-1998: Associate Professor of Molecular Biology, at Naples University "Federico II".
1998-present: Associate Professor of Molecular Biology at University of Torino.

CONSULTANCY ACTIVITIES:
2004-2008: Consultant for the microarray program (AXXAM S.r.l, Milano, I)
2005-2009: Consultant for the microarray program (Nerviano Medical Sciences S.r.l, Nerviano, MI, I)
2010-2013: Consultant for Next generation sequencing application in QC (RBM SERONO, IVREA, I)
2016-2019: Consultant for Next generation sequencing application Galderma R&D, France.
2017: Consultant for Next generation sequencing application S. Raffaele Hospital (Milan,I).

RESPONSIBILITIES
2018-present: Reference person for University of Torino at Elixir Italy.
2019-present: Co-coordinator of Elixir IT single cell Omics community.
2021-present: Member of the management committee of Elixir IT node.
2021-present: Member of the scientific committee of CINI InfoLife lab.
2021-present: President of the Italian Society of Bioinformatics (BITS)
2022-present: PMember of the Elixir Single Cell Omics Community.


RESEARCH INTERESTS:
My research experience focuses on the development, optimization of bioinformatics analysis workflows and on mining transcription-based experiments, mainly in the oncology framework. An important aspect of my past and present work is the constant interest on new technologies (e.g. today single-cell omics and spatial transcriptomics) and their integration in bioinformatics analysis workflows.
In 1992, I got the position as associate professor of Molecular Biology at University “Federico II” of Napoli. After few years, dedicated to finish the projects related to my previous position at Sorin Biomedica SPA (Saluggia, VC, Italy), I shifted my interest to the newborn technology of microarrays with a specific attention to data analysis.
In 1998, I moved to University of Torino, where my professional journey in Bioinformatics begun. I established the Genomics and Bioinformatics unit (B&Gu), which is an interdisciplinary group devoted to the study of multifactorial diseases by mean of high throughput technologies - i.e. microarray, Next Generation Sequencing – and bioinformatics.
From 1998 to 2007 the research activity of my group was focused on the identification of oncology biomarkers.
From 2007 to 2010, my groups started to address the problem of characterizing the transcriptome of circulating extracellular vesicles, which represented the starting point of our interest in the use of circulating microvesicles as source of biomarkers.
From 2010 to 2014, we started the development of bioinformatics tools devoted to the use of RNAseq to depict functional molecules and biomarkers from oncological specimens.
From 2014 to 2020, we started a fruitful collaboration with Camargo’ lab at Children Hospital (Harvard, Boston, USA). As part of this collaboration, we performed most of the bioinformatic analysis in various projects. In this period, we also started the development of tools for the analysis of single cell. Exploiting these tools, we supported the Camargo lab in two high impact papers (Rodriguez-Fraticelli Nature. 2018, Christodoulou et al. Nature. 2020). In this period, we also point our attention to the “reproducibility crisis” that was affecting various areas of biology. We founded the Reproducible Bioinformatics Project (reproducible-bioinformatics.org), which is a community of developers focusing on the production of reproducible bioinformatics workflows.
Since 2020, we continue working in the field of single cell Omics. Specifically, we are developing a new type of autoencoder, sparsely connected autoencoder, which is particularly suitable to extract biological information from single cell omics data. INTEL granted our project on the use of neuromorphic computing infrastructure to develop a more efficient implementation of the sparsely connected autoencoders. Furthermore, we extended our deep learning studies to the development of a tool for the detection of MET exon 14 skipping events in oncological samples.
Since the beginning of my carrier, I published 183 peer-reviewed papers. Since 2007, I deposited on GEO repository (www.ncbi.nlm.nih.gov/geo) a total of 927 samples as part of 84 different experiments involving the use of microarrays and RNAseq.

Activities

Employment (5)

University of Turin: Torino, Piemonte, IT

2023-07-01 to present | Full Professor (Molecular Biotechnology and Health Science)
Employment
Source: Self-asserted source
Calogero Raffaele

Università degli Studi di Torino: Torino, Piemonte, IT

1998-11-01 to 2023-06-30 | Associate Professor (Dipartimento di Biotecnologie Molecolari e Scienze della Salute)
Employment
Source: Self-asserted source
Calogero Raffaele

Università degli Studi di Napoli Federico II: Napoli, Campania, IT

1992-11-01 to 1998-10-31 | Associate Professor (Dipartimento di Genetica e Biologia Molecolare)
Employment
Source: Self-asserted source
Calogero Raffaele

Gruppo SORIN: Milano, Lombardia, IT

1987-02-01 to 1992-11-01 | researcher
Employment
Source: Self-asserted source
Calogero Raffaele

Max Plank Institute fuer Mulekulare Genetik: Berlin, DE

1985-01-02 to 1987-01-31 | Fellow
Employment
Source: Self-asserted source
Calogero Raffaele

Funding (12)

PNRR HPC Spoke 8, In Silico Medicine and Omics Data

2022-09 to 2025-08 | Grant
Ministero dell'Università e della Ricerca (Rome, IT)
Source: Self-asserted source
Calogero Raffaele

Retrieving, handling and analyzing publicly available TCRseq data

2021-07 to 2021-09 | Contract
Matterhorn Biosciences AG (Basel, CH)
Source: Self-asserted source
Calogero Raffaele

Next Generation Sequencing platform for targeted Personalized Therapy of Leukemia

2013 to 2015 | Grant
European Commission (Brussel, BE)
GRANT_NUMBER:

306242

Source: Self-asserted source
Calogero Raffaele

EPIGEN Bioinformatics work package

2012 to 2018 | Grant
CNR (roma, IT)
GRANT_NUMBER: undefined id
Source: Self-asserted source
Calogero Raffaele

Oncoantigens and microenvironment perturbatins as a new antitumor vaccine strategy for inhibition of cancer

2008 to 2010 | Grant
Ministero dell’Istruzione, dell’Università e della Ricerca (roma, IT)
Source: Self-asserted source
Calogero Raffaele

Innovative approaches to anticipate the diagnosis and to target therapies of colorectal cancer

2006 to 2009 | Grant
Associazione Italiana per la Ricerca sul Cancro (Torino, IT)
Source: Self-asserted source
Calogero Raffaele

Pipeline for Rapid Evaluation and Scoring of Targets in Oncology

2006 to 2009 | Grant
regione piemonte (Torino, IT)
Source: Self-asserted source
Calogero Raffaele

An integrated Bioinformatics and Genomics approach for oncoantigens identification

2006 to 2008 | Grant
Ministero dell’Istruzione, dell’Università e della Ricerca (roma, IT)
Source: Self-asserted source
Calogero Raffaele

Identification of new targets for the immunoprevention of cancer

2004 to 2006 | Grant
Regione Piemonte (Torino, IT)
Source: Self-asserted source
Calogero Raffaele

Isolation and functional characterization of p63 ligands involved in Hay-Wells Syndrome (AEC).

2002 to 2003 | Grant
Ministero dell’Istruzione, dell’Università e della Ricerca (roma, IT)
Source: Self-asserted source
Calogero Raffaele

Design and construction of expression vectors based on the translational reinitiation process

2001 to 2003 | Grant
Consiglio Nazionale delle Ricerche (Roma, IT)
Source: Self-asserted source
Calogero Raffaele

Identification of p63 specific target genes by p63 isoforms-mediated transcriptional profiling

2001 to 2002 | Grant
Ministero dell’Istruzione, dell’Università e della Ricerca (roma, IT)
Source: Self-asserted source
Calogero Raffaele

Peer review (9 reviews for 3 publications/grants)

Review activity for GigaScience. (1)
Review activity for Nature communications (7)
Review activity for Wellcome open research. (1)