BOLOGNA SUMMER SCHOOL OF GENOME REGULATION

An intensive workshop on bioinformatics
Bologna 14-18 July 2025

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The Bologna Summer School of Genome Regulation, organized by G-Lab S.r.l. Impresa Sociale, in collaboration with Fondazione Golinelli and under the scientific direction of Alessandro Gardini, Associate Professor of Genome Regulation and Cell Signaling at The Wistar Institute (Philadelphia) and Giovanni Perini, Professor of Genetics at the University of Bologna, will feature a 5-day bioinformatics dry lab, theoretical classes on cutting-edge genomic techniques, seminars from international leaders in genome biology from the 14th to the 18th of July 2025.

The program will cover high-throughput DNA and RNA sequencing technologies, principles of epigenomics and transcriptomics, and 3D genome organization.

Aims and Structure of the School

The regulation of protein coding and noncoding gene expression is paramount to all developmental processes and is critical to maintain tissue and cell homeostasis. Malfunction of gene regulatory mechanisms is a hallmark of most inheritable and sporadic diseases, from cancer to neurodevelopmental disorders. While probing gene expression and regulation at the genome-wide scale is now accessible to all biomedical scientists, the analysis of genomic/epigenomic/transcriptomic datasets remains a bottleneck for most.

The Summer School of Genome Regulation is an intensive workshop for junior biomedical scientists interested in hands-on training on the bioinformatics analysis of a broad array of genomic datasets (i.e. ChIP-seq, CUT&TAG, ATAC-seq, single cell and bulk RNA sequencing, Hi-C). Students will also learn about the molecular foundations of coding and noncoding transcription, epigenetics, and nuclear organization through daily seminars and classes.

Eligibility

The school is open to graduate students (currently enrolled in a PhD program in the biological and biomedical sciences), postdoctoral fellows, and senior scientists. A bachelor’s degree is a minimum requirement, master-level education is preferred.

Prospective students must have background knowledge of biochemistry, genetics, molecular biology, and basic principles of biostatistics.

The course is delivered in English and designed for trainees with basic computer skills. While prior knowledge of computational biology is not required, some familiarity with the Linux shell and the R environment is appreciated.

How does it work?

Registration is open from March 21st until max attendance is reached ( and no later than May 31st 2025).
Participation is capped at 40. The school will be activated with a minimum of 25 participants.
Upon review of your application and acceptance into the school, you will receive instructions for payment.
Registration fee: 700 euros (excluding accommodations).
The registration includes: attendance of the 5-day program including courses, seminars, and dry lab. All lunches, coffee breaks, and the farewell reception are also included. Students must arrange their own travel.
While accommodation costs are not included, Fondazione Golinelli has negotiated special rates with hotels within walking distance from the school venue (information will be provided at the time of registration). Please note that Bologna is a busy travel destination in Northern Italy and also offers many other accommodation types (hostels, airbnb, etc.).
Students will be provided with cloud computing access for the duration of the course and are encouraged to use their own laptop. If needed, the school will provide a laptop (must be indicated at time of registration).

Programme

The summer school activities will begin on Monday, July 14 at 9am and run through Friday July 18, at 6pm.

School days will be structured as follows:

9:30am - Theoretical class

11:00am - Coffee break

11:30am - Seminar (invited speakers)

1:00pm- Lunch

2:00pm- Bioinformatics lab

6:00pm Discussion

Main scientific topics:

Epigenome regulation
Transcription & RNA processing
The 3D genome
Single Cell Omics

What the bioinformatics lab will cover:

Mapping, annotation and statistical analysis of histone marks, DNA methylation and transcription factors ( CUT&TAG, CUT&RUN, ChIP-seq)
Analysis of bulk RNA-seq datasets: from differential gene expression to correlation with the epigenome states
Pathway analysis and GSEA
Mapping and annotation of Hi-C datasets
Analysis of enhancer-promoter loops in mammalian cells
Principles of scRNAseq: clustering and pseudotime analysis

Scientific Organizers

Alessandro Gardini, PhD

Associate Professor of Genome Regulation and Cell Signaling
Scientific Director, Genomics Shared Resource
The Wistar Institute, Philadelphia

Giovanni Perini, PhD

Professor of Genetics
Department of Pharmacy and Biotechnology (Fabit)
University of Bologna

Scientific Instructors

Sandra Deliard, PhD

Associate Scientist
The Wistar Institute
Sandra is a bioinformatician in the Gardini lab at the Wistar Institute. She received her PhD in Biomedical Sciences from Temple University in 2019. Her main research interests are 3D genome regulation and enhancer dynamics during cell development.

Phillip Wulfridge, PhD

Postdoctoral Fellow
The Wistar Institute
Phillip is a bioinformatician in the Sarma lab at the Wistar Institute. He obtained his PhD in Cellular and Molecular Medicine from Johns Hopkins University in 2018. His research focuses on R-loops formation and regulation of DNA methylation in cancer.

Paolo Manzi

Biotech specialist and lab technician
G-Lab S.r.l. Impresa Sociale
Pharmaceutical chemist with experience as a research and development laboratory technician in the chemical-analytical field. Scientific tutor and trainer of Fondazione Golinelli.

Invited Speakers

Ari M. Melnick, MD

Gebroe Family Professor of Hematology/Oncology
Director, Sackler Center for Biomedical and Physical Sciences
Departments of Medicine and Pharmacology
Weill Cornell Medical College - New York City, US