Francesco Cecere

Francesco Cecere

Biologist & Bioinformatician

Location
Santa Maria Capua Vetere, Italy

About Me

Date of Birth
22/09/1995
Nationality
Italian

I am Francesco Cecere, a Biologist with a deep-rooted interest in Genomics and Bioinformatics.

With experience in both rare genetic syndromes (Beckwith-Wiedemann and Silver-Russell syndromes) and pediatric cancer (Wilms tumor), I have developed a strong foundation in translational research.

My work primarily focuses on the intricate world of gene regulatory networks, where I leverage advanced Bioinformatics techniques to analyze Genomics data.

This blend of biology and informatics is not just my profession but my passion.

This passion drives my dedication to scientific innovation, particularly in Bioinformatics, and my commitment to applying this expertise for the advancement of health and science.

Work Experience

Researcher, Clinical and Translational Research Unit, Santobono-Pausilipon Children’s Hospital
01/12/2025 – Present | Napoli, Italy Deliberazione n. 761 prot. 23429 del 31/10/2025

Project: "Progetto PNC-E3-2022-23683269 Hub Life Science-Terapia Avanzata (HLS-TA)"

Title: Set-up delle pipeline di analisi omiche e multi-omiche per la caratterizzazione dei campioni a supporto degli studi clinici.

Codice univoco investimento: PNC-E.3 - CUP:H63C22000650001 - WBS: HPNR0004

Researcher III, Insitute of Genetics and Biofisics "Adriano Buzzati-Traverso" (IGB) - CNR
26/08/2024 – 25/08/2025 | Napoli, Italy Bando n. 400.5 IGB PNRR prot. 401541 del 15/12/2023

Project: "National Centre for HPC, Big Data and Quantum Computing"

Title: Development and testing of algorithms for the reconstruction of gene regulatory networks from single-cell transcriptomic data.

European Union – Next Generation EU – CN00000013 - CUP: B93C22000620006

Visiting Postdoc, Josep Carreras Leukaemia Research Institute
May 2023 – Jul 2023 | Badalona, Spain

Integrated clinical, genetic, and epigenetic data for Wilms tumor stratification. Tools: EPIC methylation arrays, RNA-seq, Exome-seq.

Postdoc, University of Campania “Luigi Vanvitelli”
Feb 2023 – Aug 2024 | Caserta, Italy

D.R. n. 1018 del 21/11/2022 durata n. 36 mesi

Project: AIRC IG 2020 - ID 24405

Title: Causes and mechanisms of genomic imprinting disturbances in Beckwith-Wiedemann syndrome and Wilms Tumor

Visiting Student, Babraham Institute
Jul 2022 | Cambridge, UK

Analyzed BS-seq & scRNA-seq of germ cells with Dr. Kelsey & Andrews.

Education

PhD in Molecular Life Sciecies (SSD:BIO/18), Università degli Studi della Campania "Luigi Vanvitelli"
01/11/2019 – 31/01/2023 | Caserta, Italy Decreto prot. n. 76400 repertorio DRR n. 478/2019

Thesis Title: Investigating the causes of DNA methylation disturbances in Imprinting Disorders.

Evaluation: Excellent

Master Degree in Molecular Biology, Università degli Studi della Campania "Luigi Vanvitelli"
2017 – 24/07/2019 | Caserta, Italy

Title: Identificazione di nuovi fattori trascrizionali che legano le regioni di controllo dell'imprinting.

Final grade: 110/110 cum laude

Benchelor Degree in Biological Sciences, Università degli Studi della Campania "Luigi Vanvitelli"
September 2014 – 27/10/2017 | Caserta, Italy

Title: Effetti neuropatologici dell'abuso di alcol associati a carenza di Tiamina.

Final grade: 110/110 cum laude

Publications

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Memberships

Activities

Professional Courses

scRNA-seq hands-on course
26/09/2023 – 29/09/2023

Università degli studi di Torino, Dip. di Biotecnologie e Scienze per la Salute

10x single cell RNA Seq Analysis
01/12/2021

Babraham Institute

Data Science: Machine Learning and its Application in Cancer Genomics
06/09/2021 – 17/09/2021

The Intensive School for Advanced Graduate Studies (ISAGS)

Analisi dei dati NGS ed applicazioni in ambito diagnostico
08/03/2021 – 11/03/2021

Università di Pavia

Poster

H19 overexpression drives an inflammatory response in mice
Del Prete R, Cecere F, Sparago A, Pignata L, Cerrato F, Riccio A.
Genomic Imprinting – from Biology to Disease, Virtual Conference, 28/09/2020 – 01/10/2020
Novel pathogenic variants associated with the imprinting disorders Beckwith-Wiedemann syndrome and Silver-Russell syndrome
Pignata L, Verma A, Cecere F, Giaccari C, Hay Mele B, Acurzio B, Saadat A, Angelini C, Sparago A, Cerrato F, Cubellis MV, Riccio A.
XXIV Congresso Nazionale SIGU 2021, Virtual Edition, 2021
Recent advances in the genetics of multi-locus methylation disturbances in the Beckwith-Wiedemann syndrome
Riccio A, Pignata L, Cecere F, Verma A, Hay Mele B, Monticelli M, Acurzio B, Giaccari C, Sparago A, Palumbo O, Carella M, Prontera P, Piscopo C, Accadia M, Cubellis MV, Cerrato F.
XXV Congresso Nazionale SIGU 2022, Trieste, 2022
Prioritization and characterization of genetic variants in Beckwith-Wiedemann syndrome patients with multi-locus imprinting disturbances (MLID)
Cecere F, Hay Mele B, Pignata L, Patalan M, Lapunzina P, Mackay D, Cubellis MV, Cerrato F, Riccio A.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
Molecular analysis of a mouse line carrying a hypomorphic variant of the maternal-effect gene Padi6
Giaccari C, Cecere F, Argenziano L, Acampora D, Cecconi S, Rossi G, Galvao A, Andrews S, Kelsey G, Riccio A.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
Screening for genomic imprinting modifiers in humans reveals a role for several epigenetic regulator genes
Relator R, Verma A, McConkey H, Pignata L, D'Angelo E, Cecere F, Cuomo M, Chiariotti L, Scala I, Cerrato F, Sadikovic B, Riccio A.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
A new possible molecular mechanism involved in Silver-Russell Syndrome
Pignata L, D'Angelo E, Cecere F, Sparago A, Cerrato F, Riccio A.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
Distinct profiles of epigenetic alterations are associated with Chr11p15.5 molecular defects in Wilms tumor
Saadat A, Cecere F, Pignata L, Hay Mele B, De Alava E, Roma J, Verde G, Cerrato F, Riccio A, Sparago A.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
Co-occurrence of Beckwith-Wiedemann Syndrome and early-onset colorectal cancer
Cecere F, Pignata L, Saadat A, D'Angelo E, Hay Mele B, Palumbo O, Palumbo P, Carella M, Scarano G, Rossi GB, Angelini C, Sparago A, Riccio A, Cerrato F.
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 22/03/2023 – 24/03/2023
GIMP - A Comprehensive R package for exploring Genomic Imprinting Methylation Patterns in Imprinting Disorders
Francesco Cecere, Abu Saadat, Andrea Riccio, Claudia Angelini
BBCC 2024, 27–29 November 2024
🏆 Best Poster Award
Screening for modifiers of genomic imprinting in human blood reveals a role for several genetic and non-genetic factors
Genomic Imprinting – From Biology to Disease, Wellcome Genome Campus, UK, 10/03/2025 – 12/03/2025

Talk

scGraphVerse: A Unified Framework for Network Inference, Evaluation, and Visualization from Single-Cell Gene Expression Data
Bioinformatics Italian Society (BITS 2025), 11/06/2025 – 13/06/2025
scGraphVerse: An R package for Inferring and Integrating Single-Cell Gene Regulatory Networks
Bioinformatics and Computational Biology Conference (BBCC 2025)

Workshop

From raw matrices to differential expression/methylation patterns: a functional genomics approach to detect molecular insights
25/11/2024

Instructors and Organizers: Dr. Luca Ambrosino and Dr. Francesco Cecere

Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", Consiglio Nazionale delle Ricerche, Naples, Italy

R frameworks for single cell data analysis
07/12/2023

BBCC Tutorial – scRNA-seq data analysis using R, from raw counts to cell clustering.

Instructors: Prof. Annamaria Carissimo (IAC/CNR), Dr. Dario Righelli (Univ. Padova), Dr. Valeria Policastro (Univ. Federico II Naples), Dr. Francesco Cecere (DiSTABiF, Univ. Campania "Luigi Vanvitelli")

NGS - DNA methylation analysis
16/12/2022 – 25/12/2022

Virtual Workshop

Teaching, Awards & Packages

Teaching

Contract Professor in Bioinformatics (BIO/18)
20/10/2025 – Present

Prot. N. 162103 del 15/09/2025 – Repertorio DDMF N. 173/2025

Lecturer – Molecular Biology for Master's students in "Statistical Sciences for Decision Making"
19/09/2025 | Università Federico II, Naples

4 hours

Lecturer – Bioinformatics (Molecular Genetics course, Master's degree in Biologia)
05/12/2024 – 11/12/2024 | Università degli Studi della Campania "Luigi Vanvitelli", Caserta

Two lectures, 5 hours total

Lecturer – Molecular Biology for Master's students in "Statistical Sciences for Decision Making"
26/09/2024 – 30/09/2024 | Università Federico II, Naples

4 hours

Tutor in Genetics
2022

D.D n. 242/2022 prot. n. 81546 del 1/06/22 – CdL Biotecnologie

Tutor in Genetics for students with disabilities
2022

D.D n. 280 del 23/06/22 – CdL Scienze Ambientali

Awards

BBCC 2024 – Best Poster Presentation

GIMP - A Comprehensive R package for exploring Genomic Imprinting Methylation Patterns in Imprinting Disorders

Packages

GIMP

Genomic Imprinting Methylation Patterns

An R package for exploring genomic imprinting methylation patterns in imprinting disorders, providing comprehensive tools for analysis and visualization.

View on GitHub
scGraphVerse

Single-Cell Gene Regulatory Network Analysis

A comprehensive R package for inferring, evaluating, and visualizing gene regulatory networks (GRNs) from single-cell RNA sequencing data, with multiple inference algorithms, consensus construction, and rich visualizations.