People

Nunzio D'Agostino (PI)

Since December 2021, I have served as an Associate Professor of Bioinformatics and Genomics (sector E5/02 - Molecular Biology) in the Department of Agricultural Sciences at the University of Naples Federico II.

Academic Background

2008: Defended my PhD thesis in "Agrobiology and Agrochemistry: Genetic Improvement and Horticulture" at the University of Naples Federico II.
2003: Earned a Master's certificate in Bioinformatics from the University of Sannio.
2002: Graduated with full marks in Biological Sciences from the University of Siena.

Professional Experience

December 2018 - November 2021: Assistant Professor of Bioinformatics and Genomics at the Department of Agricultural Sciences, University of Naples Federico II.
February-August 2012: Visiting scientist at the Department of Molecular Plant Physiology, Radboud University, Nijmegen, Netherlands.
2010-2018: Permanent researcher at CREA Research Centre for Vegetable and Ornamental Crops (Pontecagnano Faiano, Salerno), focusing on agricultural genetics and molecular biology. I led the Bioinformatics lab.

Current Roles

Teaching:
- Core Course: Bioinformatics (6 credits)
- Elective Courses: Basics on the Bioinformatics Analysis of Genomes (6 credits); Basics on Linux (6 credits)
Supervision:
- Supervisor/co-supervisor for several master’s degree theses in Molecular Biology.
- Supervised a PhD dissertation in Biotechnology.
- Tutor for various trainees in post-graduate training courses.
PhD Program: Member of the teaching body for the PhD in Computational and Quantitative Biology (CQB) at the University of Naples Federico II.

Scholarly Contributions

Speaker at national and international conferences.
Invited seminar speaker at various Italian universities and research institutes.
Reviewer for several international scientific journals.
Editorial Board member for:
- Frontiers in Genetics section Computational Genomics
- Scientific Reports
- Frontiers in Plant Science section Plant Bioinformatics

Affiliations

Since December 20, 2022: Associate member of the Georgofili Academy.
Since 2005: Member of the Italian Society of Agricultural Genetics (SIGA).

Gaetano Aufiero (PhD student)

I graduated in Plant, Environmental and Food Biotechnologies at the University of Naples Federico II with full marks. At present, I’m a PhD student in Sustainable Agricultural and Forestry Systems and Food Security working on "Dual RNA-sequencing to characterize non-coding RNAs as critical regulators in the interaction between the parasitic weed Phelipanche ramosa and tomato". My PhD project is in the frame of the TOMORROv project.

XXXVIII cycle, AY 2022/2023

Davide D'Angelo (PhD student)

I graduated in Plant, Environmental and Food Biotechnologies at the University of Naples Federico II with full marks. At present, I’m a PhD student in Computational and Quantitative Biology working on "Multi-omics profiling of tanscriptomic and epigenetic signatures in Parkinson’s Disease: unravelling lncRNA patterns as potential biomarkers". My PhD project is in collaboration with prof. Alfonso De Simone , Department of Pharmacy, University of Naples Federico II.

XXXIX cycle, AY 2023/2024

Irene Antonietta Coppola (Graduating student)

I hold a Bachelor's degree in Food Technologies from the University of Naples Federico II, where I graduated with full marks. Currently, I am pursuing a Master's degree in Plant, Environmental, and Food Biotechnologies.

As part of my thesis work, I am engaged in a research project entitled "From transcriptomics to regulatory networks: inference of gene regulatory networks in tomato under abiotic stress." This research is being conducted at CNR-IBBR, under the supervision of Dr. Giorgia Batelli and Dr. Salvatore Esposito.

Chiara Ascione (Graduating student)

I hold a Bachelor's degree in Agricultural, Forestry, and Environmental Sciences from the University of Naples Federico II, where I graduated with top honors.

Currently, I am pursuing a Master's degree in Plant, Environmental and Food Biotechnologies.

For my thesis research, I am working on a project titled "Isolation and characterization of autochthonous root-associated bacteria from desert environments contributing to crop resistance to salt and drought stress". This research is being conducted at the CNR-IBBR, under the supervision of Dr. Alessandra Ruggiero.

Enzo Satiro (Graduating student)

I hold a Bachelor's degree in Agricultural, Forestry, and Environmental Sciences from the University of Naples Federico II. I am currently pursuing a Master's degree in Agro-Environmental and Food Biotechnology.

My thesis project focuses on the management and analysis of omics big data generated by next-generation sequencing (NGS) technologies.

Nicola Iurillo (Graduating student)

I hold a Bachelor's degree in Agricultural, Forestry, and Environmental Sciences from the University of Naples Federico II, where I am currently pursuing a Master's degree in Plant, Environmental, and Food Biotechnologies. in Plant, Environmental and Food Biotechnologies.

My thesis project focuses on the in silico identification of the nuclear partner of orf125 involved in cytoplasmic male sterility in interspecific potato cybrids. This research is being conducted at the CNR-IBBR, under the supervision of Dr. Salvatore Esposito.

Former members

Post-Doc:

Silvana Francesca. Project title: Genome editing to improve the nutritional and technological quality of tomato fruits. Duration of the contract: 01/12/2021 - 30/09/2022

PhD students:

Carmine Fruggiero. Thesis title: Dual RNA-Sequencing assessment and implementation to study transcriptome alteration of Solanum lycopersicum during the interaction with Orobanchaceae spp. Phd program in Computational and Quantitative Biology, XXXVII cycle.

Visiting PhD students:

Concetta Simona Taranto (visiting PhD student from The University of Catania). Project title: The healthy colour of blood oranges: a genetic and epigenetic analysis of anthocyanin production and accumulation. Duration of stay: from 03/06/2025 to 31/07/2025
Rahma Zarkouna ( University of Tunis El Manar). Project title: Genome assembly, annotation, and comparative analysis for identifying SNPs in genes associated with fruit quality and ripening mechanisms in the Deglet Nour date palm cultivar. Duration of stay: from 17/09/2024 to 14/11/2024
Lucas Beltrame (University of Bari "Aldo Moro"). Project title: RNA-seq transcriptome profiling of Olea europaea in response to Xylella fastidiosa subsp. pauca". Duration of stay: from 14/11/2022 to 25/11/2022
Diletta Bagnoli (University of Molise). Project title: Metagenomic characterization of microbial communities in different food samples. Duration of stay: from 01/03/2022 to 31/07/2022
Giulia Frascarelli (Marche Polytechnic University). Project title: The evolutionary history of Phaseolus vulgaris as revealed by chloroplast genomes. Duration of stay: from 03/2019 to 07/2019

Early stage researchers:

Olga Cannavacciuolo. Project title: Development of a hairy root assay in tomato plants to study the Phelipanche ramosa infection process. Duration of the contract: 01/12/2022 - 30/11/2023
Davide D'Angelo. Project title: Characterization of Orobanchaceae resistance in different tomato lines by RNA-Seq data analysis. Duration of the contract: 01/02/2023 - 31/10/2024
Gaetano Aufiero. Project title: Ex ante and ex post bioinformatics to support genome editing experiments. Duration of the contract: 01/12/2021 - 31/05/2022

Research fellow:

Ivan Fruggiero. Project title: Design and development of a database for cataloguing chestnut genetic fingerprints. Duration of the contract: 15/06/2024 - 15/06/2025
Alessandro Maisto. Project title: Design and development of a database for cataloguing chestnut genetic fingerprints. Duration of the contract: 15/06/2024 - 15/06/2025

Volunteers:

Teresa Rosa Galise. Project title: Assembly and analysis of wild bean chloroplast genomes. Duration of stay: from 03/2019 to 08/2019
Gaetano Aufiero. Project title: Development of a pipeline for the identification and characterization of non-coding RNAs starting from RNA-seq data. Duration of stay: from 01/06/2022 to 31/10/2022

Graduate students:

Marco Porcelli. Thesis title: Selection of potato (Solanum tuberosum L.) genotypes tolerant to water stress and analysis of gene expression profiles in response to drought. Degree course in Plant, Environmental and Food Biotechnologies. AY 2023-2024.

The thesis work was carried out at CNR-IBBR under the supervision of Dr. Nunzia Scotti.

Francesca Bencivenga. Thesis title: Analysis of nucleotide diversity in the plastid genomes of Olea europaea L. Degree course in Plant, Environmental and Food Biotechnologies. AY 2023-2024.
Federica Palmaccio. Thesis title: Production of single-chain monellin mutants in transplastomic tobacco plants. Degree course in Plant, Environmental and Food Biotechnologies. AY 2023-2024.

The thesis work was carried out at CNR-IBBR under the supervision of Dr. Nunzia Scotti.

Amalia Chiariello. Thesis title: Genetic diversity analysis in an olive germplasm collection using genotyping by sequencing: conservation and genetic improvement implications. Degree course in Plant, Environmental and Food Biotechnologies. AY 2023-2024.
Enrico Maria Milito. Thesis title: Characterization of tomato mutant lines for genes coding for canonical and putative strigolactone transporters. Degree course in Plant, Environmental and Food Biotechnologies. AY 2023-2024.

The thesis work was carried out at CREA-OF under the supervison of Dr. Alessandro Nicolia.

Ivan Fruggiero. Thesis title: Counting and classification of Phelipanche ramosa seeds based on machine learning. Degree course in Plant, Environmental and Food Biotechnologies. AY 2022-2023.
Sara Solimeno. Thesis title: Hairy roots: an innovative platform for phytoremediation and the production of recombinant proteins of cosmetic interest. Degree course in Plant, Environmental and Food Biotechnologies. AY 2022-2023.

The thesis work was carried out at ArterraBioscience spa.

Davide D'Angelo. Thesis title: Analysis of the ascorbate oxidase gene family in tomato and functional study of some members by CRISPR/Cas9 mediated mutagenesis. Degree course in Plant, Environmental and Food Biotechnologies. AY 2021-2022.
Ermanno Di Serio. Thesis title: Analysis of genetic diversity between and within populations of Sicilian durum wheat landraces. Degree course in Plant, Environmental and Food Biotechnologies. AY 2020-2021.
Gaetano Aufiero. Thesis title: Analysis of potato mitochondrial genomes for the study of cytoplasmic male sterility. Degree course in Plant, Environmental and Food Biotechnologies. AY 2020-2021.

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