Gerardo Pepe

Gerardo Pepe

Bioinformatico / Biostatistico 

         Articoli pubblicati: 8 / Scopus h-index: 4 / # Citazioni: 67

                     via Giulio Tesauro, 67 Salerno (SA)

                     +39 3881604796

        gerardopepe0@gmail.com /gerardo.pepe@uniroma2.it

        07/12/1988

                                    Formazione

2017 - 2020                   PhD in Biologia Cellulare e Molecolare (BCM)

Titolo: Identification of genomics signatures of drug response and tumorigenesis.

Università di Roma Tor Vergata

2015 - 2017                   Laurea Magistrale in Bioinformatica (LM6) 

110/110 cum laude

Titolo: Systematic identification of informative genes for an improved prediction and interpretation of drug response mechanisms in cancer cell lines.

                                               Università di Roma Tor Vergata

2015                             Laurea Triennale in Scienze Biologiche (L13)   

                                    Titolo: RT-PCR validation of putative sex-specific transcripts in 

                                               Phlebotomus pernicious adult stage.

                                               Università di Naploli, Federico II 

                                    Posizioni ricoperte 

dal 2023                       Ricercatore, RTDa

Methods for comparison and integrative analysis of healthy and control patients to develop targeted RNA based therapies.  

Università di Roma Tor Vergata

dal 2021                       Review Editor: Frontiers in Molecular Biosciences - Protein and RNA Networks. 

dal 2020 al 2023            Post-doc, lab prof. Manuela Helmer-Citterich 

Discovery and perturbation of pathogenic variations in the kinase network regulating cancer-associated super-enhancers.

Università di Roma Tor Vergata

                                    Premi

2022                             Contributo premiale per ricercatori ed assegnisti di ricerca

                                               Regione Lazio

tutto quanto corrisponde a verità, ai sensi degli articoli 46 e 47 del D.P.R. 445 del 2000

                                    Insegnamento

dal 2022                       Modulo di Bioinformatica nel CI Bioinformatica e Genetica Medica – 6 CFU, corso fondamentale 

Laurea triennale in Scienze Biologiche

                                                                       Università di Roma Tor Vergata

dal 2021                       Corso Biological Networks – 2 CFU, AAS

Laurea magistrale in Bioinformatica

                                               Università di Roma Tor Vergata

dal 2019                       Relatore di 3 tesi Magistrali in Bioinformatica.

dal 2018                        Co-relatore di 7 tesi Magistrali in Bioinformatica.

dal 2017                       Co-relatore di 14 tesi Triennali in Scienze Biologiche e Biotecnologie.

dal 2017                       Tutor e membro di Commissione d’esame per il Corso di Biologia Molecolare per la laurea triennale in Scienze Biologiche.

                                   Università di Roma Tor Vergata

dal 2017                        Tutor e membro di Commissione d’esame per il Corso di Bioinformatica per la laurea triennale in Scienze Biologiche.

                                   Università di Roma Tor Vergata

                                    Background accademico / Esperienze                

2021                             GTN Smörgåsbord: A Global Galaxy Course – Corso online

2021                            Winter school 2021: ‘Bioinformatics for discovery in structural and functional biology’ – Corso online

                                               Dipartimento di Farmacia e Biotecnologia dell’Università di Bologna

2021                            Advanced Training Course in ‘Data mining in Aquaculture and Biomedicine’ – Corso online

                                               Dipartimento di Biologia dell’Università di Roma Tor Vergata

2019                            2nd International Workshop in cancer genomics

                                               IRE, Regina Elena, Roma

2019                            2nd U-PGx personalized medicine (Pharmacogenomics into the clinic, cancer genomics)

                                    Università di Roma Tor Vergata

2019                             DeepLearn 2019 (data clustering, deep learning in medicine, feature extraction, big data and statistical inference, knowledge discovery from complex data)

                                   Varsavia, Global Expo

2016                             RNA-seq data analysis workshop (NGS data processing, de novo transcriptome assembly and analysis)

                                   Università di Napoli, Federico II 

                                    Lingue

Inglese                          Avanzato (B2)

Italiano                         Madrelingua

tutto quanto corrisponde a verità, ai sensi degli articoli 46 e 47 del D.P.R. 445 del 2000

                                    Abilità tecniche

Linguaggi di programmazione: Python, Pandas, Sklearn, Seaborn (Clustermap, Heatmap), Bash, R, C, Ruby, MySQL, HTML, CSS, PHP. 

Conoscenze computazionali: 

HPC (High performance cluster), Galaxy, Big data manipulation and analysis, Feature selection, Machine learning (Elastic Net, Random Forest, SVR), Deep learning, NGS analysis, RNA-seq data analysis, Variant calling, Chip-seq analysis, biological networks analysis and comparison, R/Bioconductor 

Esperienze sperimentali: 

PCR, RT-PCR, PCR real-time, DNA and RNA extraction, DNA cloning, Electrophoretic mobility shift assay, DNA sequencing, Plasmid miniprep 

Sistemi operativi: 

Linux, Windows, macOS

Altro:

Sviluppatore di applicazioni web per la bioinformatica

                                    Conferenze 

2022                            3D-BioInfo Annual General Meeting

Selected Talk: Identification of RNA modules in human lncRNAs

                                               Wellcome Genome Campus, Hinxton, Regno Unito

2022                            Annual conference of the Bioinformatics Italian Society (BITS) 2022

Selected Talk: Identification of RNA modules in human lncRNAs 

Polo Santa Marta, Verona

2022                             BEST HACKATHON 2022 – Invited Speaker

                                   DNA, Big Data & Informatics

Macroarea di Ingegneria - Università di Roma Tor Vergata

2021                            3D-Bioinfo Annual General meeting

Selected Talk: “Interactions RNA-RNA binding proteins”

Conferenza online

2021                             Annual conference of the Bioinformatics Italian Society (BITS) 2021

Selected Talk: “Variation in the co-expression profile highlights the loss of miRNA-mRNA regulation in several cancers”

Conferenza online

2018                                     Annual conference of the Bioinformatics Italian Society (BITS) 2018

Abstract: “Systematic identification of informative genes for an improved prediction and interpretation of drug response mechanisms in cancer cell lines”

                                    Università di Torino

tutto quanto corrisponde a verità, ai sensi degli articoli 46 e 47 del D.P.R. 445 del 2000

                                    Publicazioni

1.     Pepe, G., Appierdo, R., Carrino, C., Ballesio, F., Helmer-Citterich, M. and Gherardini, P.F. (2022) Artificial intelligence methods enhance the discovery of RNA interactions. Frontiers in Molecular Biosciences, 1113.

Scopus Citations: - / Journal Impact Factor: 6.113  

2.     Pepe, G., Carrino, C., Parca, L. and Helmer-Citterich, M. (2022)

Dissecting the genome for drug response prediction. Methods in molecular biology. 

Data Mining Thecniques for the Life Sciences, 187-196.

Scopus Citations: - / Journal Impact Factor: 1.37

3.     Pepe, G., Parca, L., Viviani, L., Ausiello, G., and Helmer-Citterich, M. (2022a). Variation in the co-expression profile highlights a loss of miRNA-mRNA regulation in multiple cancer types. Non-Coding RNA Research 7, 98–105.

Scopus Citations: 1 / Journal Impact Factor: 5.978  

4.     Pepe, G., Guarracino, A., Ballesio, F., Parca, L., Ausiello, G., and Helmer-Citterich, M. (2022). Evaluation of potential miRNA sponge effects of SARS genomes in human. Non-Coding RNA Research 7, 48–53.

Scopus Citations: 4 / Journal Impact Factor: 5.978  

5.     PDBe-KB consortium (2022). PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50, D534–D542.

Scopus Citations: 16 / Journal Impact Factor: 19.160  

6.     Novelli, G., Liu, J., Biancolella, M., Alonzi, T., Novelli, A., Patten, J.J., Cocciadiferro, D., Agolini, E., Colona, V.L., Rizzacasa, B., et al. (2021). Inhibition of HECT E3 ligases as potential therapy for COVID-19. Cell Death Dis. 12, 310.

Scopus Citations: 20 / Journal Impact Factor: 9.685  

7.     Guarracino A., Pepe* G., Ballesio F., Adinolfi M., Pietrosanto M., Sangiovanni E., Vitale I., Ausiello G., Helmer-Citterich M. BRIO: a web server for RNA sequence and structure motif scan. Nucleic Acids Res.2021; 49: W67–W71.

Scopus Citations: 3 / Journal Impact Factor: 19.160  

8.     Parca, L., Pepe*, G., Pietrosanto, M., Galvan, G., Galli, L., Palmeri, A., Sciandrone, M., Ferrè, F., Ausiello, G., and Helmer-Citterich, M. (2019). Modeling cancer drug response through drug-specific informative genes. Sci. Rep. 9, 15222.

Scopus Citations: 23 / Journal Impact Factor: 4.996

*co-primo autore

                                    Altre info ed interessi

Interessi                        Programmazione, Statistica, Data analysis, NGS, articoli scientifici, viaggiare, cucinare, cinema, e letteratura.                       

Patente di guida                 A, B 

                                    Privacy

Autorizzo al trattamento dei miei dati personali ai sensi del Decreto Legislativo Italiano n. 196/2003 Regolazione (EU) GDPR n.679/2016.   

tutto quanto corrisponde a verità, ai sensi degli articoli 46 e 47 del D.P.R. 445 del 2000