Genomics and Epigenomics
A.Y. 2025/2026
Learning objectives
Students will learn to:
- Master the role of genomic and epigenomic mechanisms in cellular homeostasis and diseases
- Understand the scientific context of genomics and epigenomics technologies (what type of questions can be addressed)
- Design and execute state-of-the-art genomics and epigenomics analyses
- Understand the technological potential and limits of the genomics and epigenomics approaches
- Design genomics and epigenomics experiments based on the specific medical or biological questions
- Carry out trouble-shooting and development of genomics and epigenomics analyses
- Interpret and report results from various genomics and epigenomics technologies (data analyses)
- Learn the medical potential of epi-genomic analyses, in terms of diagnosis, patient stratification, and medical research
- Master the role of genomic and epigenomic mechanisms in cellular homeostasis and diseases
- Understand the scientific context of genomics and epigenomics technologies (what type of questions can be addressed)
- Design and execute state-of-the-art genomics and epigenomics analyses
- Understand the technological potential and limits of the genomics and epigenomics approaches
- Design genomics and epigenomics experiments based on the specific medical or biological questions
- Carry out trouble-shooting and development of genomics and epigenomics analyses
- Interpret and report results from various genomics and epigenomics technologies (data analyses)
- Learn the medical potential of epi-genomic analyses, in terms of diagnosis, patient stratification, and medical research
Expected learning outcomes
Students will gain theoretical knowledge and practical experience in genomics and epigenomics analyses related to fundamental research and clinical applications. Key competences will include the ability to design experiments, manage work flow, analyze and interpret data and devise new strategies for further development in genomics and epigenomics research and experimental approaches. Training activities will provide specific skills in genomics and epigenomics and the necessary tools for the interpretation of results.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Prerequisites for admission
Students must possess a basic knowledge of biology, biochemistry, and genetics, typically acquired through a Bachelor's degree (Laurea Triennale) in Biology, Biotechnology, Chemistry, Pharmaceutical Sciences, or an equivalent qualification. This foundational knowledge should include a general understanding of cellular and molecular biology, particularly mechanisms related to DNA and protein function, as well as the conservation and utilization of genetic material.
Assessment methods and Criteria
Students will be evaluated through a single comprehensive written examination, consisting of multiple-choice and open-ended questions. Specific details regarding the exam format and content will be communicated at the beginning of the course.
Genomics
Course syllabus
The course is divided into thematic modules, each comprising dedicated lectures that address key concepts and molecular mechanisms in genomics and epigenomics. The curriculum includes state-of-the-art technological approaches for studying genomic and epigenomic features, along with group work aimed at developing skills in experimental design to tackle specific scientific questions or problems.
Module 1: Genetic and Epigenetic Evolutionary Perspectives (4 lessons)
· Principles of Genetic Evolution
· Hallmarks of Cancer
· Cancer Epigenetics
Module 2: Epigenetic Molecular Mechanisms (8 lessons)
· Cell Identity and Gene Expression Control
· DNA Modifications
· Chromatin Modifications
· 3D Genome Organization
· Non-coding RNAs and the Dark Genome
· Metagenomics
· Molecular Analysis of Complex Systems at Single-Cell and Spatial Resolution
Module 3: Genetic Engineering (2 lessons)
· Genetic Manipulation in Cell Culture and In Vivo
· Transgenes
· Recombinase-Based Manipulation
· CRISPR-Cas Editing
Module 4: Cancer Genetics (2 lessons)
· Understanding the Human Genome and Its Mutations
· Use of Genomic Information for Patient Diagnosis and Treatment
Module 5: Genomic and Epigenomic Technological Approaches (8 lessons)
· High-Throughput Next-Generation Sequencing
· Whole Genome and Whole Exome Sequencing
· Liquid Biopsies
· RNA Sequencing
· Chromatin Localization Analyses
· 3D Epigenomic Analyses
· Nanopore-Based Direct Sequencing
· Single-Cell Analyses
Module 6: Epigenetic Mechanisms in Human Diseases (8 lessons)
· Patient-Specific Genome and Epigenome Models
· Role of DNA Methylation in Development and Disease
· Epigenomic Architecture of Cancer
· Epigenomic Architecture of Neurological and Neuropsychiatric Disorders
· Multi-Omic Architecture of Viral Infections
Module 7: Experimental Design (Group Work)
· Approaching a Scientific Problem or Question
· Designing an Experimental Plan
· Development and Presentation of a Project Proposal
Module 1: Genetic and Epigenetic Evolutionary Perspectives (4 lessons)
· Principles of Genetic Evolution
· Hallmarks of Cancer
· Cancer Epigenetics
Module 2: Epigenetic Molecular Mechanisms (8 lessons)
· Cell Identity and Gene Expression Control
· DNA Modifications
· Chromatin Modifications
· 3D Genome Organization
· Non-coding RNAs and the Dark Genome
· Metagenomics
· Molecular Analysis of Complex Systems at Single-Cell and Spatial Resolution
Module 3: Genetic Engineering (2 lessons)
· Genetic Manipulation in Cell Culture and In Vivo
· Transgenes
· Recombinase-Based Manipulation
· CRISPR-Cas Editing
Module 4: Cancer Genetics (2 lessons)
· Understanding the Human Genome and Its Mutations
· Use of Genomic Information for Patient Diagnosis and Treatment
Module 5: Genomic and Epigenomic Technological Approaches (8 lessons)
· High-Throughput Next-Generation Sequencing
· Whole Genome and Whole Exome Sequencing
· Liquid Biopsies
· RNA Sequencing
· Chromatin Localization Analyses
· 3D Epigenomic Analyses
· Nanopore-Based Direct Sequencing
· Single-Cell Analyses
Module 6: Epigenetic Mechanisms in Human Diseases (8 lessons)
· Patient-Specific Genome and Epigenome Models
· Role of DNA Methylation in Development and Disease
· Epigenomic Architecture of Cancer
· Epigenomic Architecture of Neurological and Neuropsychiatric Disorders
· Multi-Omic Architecture of Viral Infections
Module 7: Experimental Design (Group Work)
· Approaching a Scientific Problem or Question
· Designing an Experimental Plan
· Development and Presentation of a Project Proposal
Teaching methods
The course will include:
i) Lectures delivered by master-class professors, providing students with foundational knowledge of genomic and epigenomic molecular concepts and their pathological implications;
ii) Technological lectures delivered by adjunct professors, offering students insight into state-of-the-art technologies used to study various aspects of the genome and epigenome;
iii) An interactive project design activity, where students will apply the knowledge acquired during the course to develop experimental plans aimed at addressing specific scientific questions or problems.
i) Lectures delivered by master-class professors, providing students with foundational knowledge of genomic and epigenomic molecular concepts and their pathological implications;
ii) Technological lectures delivered by adjunct professors, offering students insight into state-of-the-art technologies used to study various aspects of the genome and epigenome;
iii) An interactive project design activity, where students will apply the knowledge acquired during the course to develop experimental plans aimed at addressing specific scientific questions or problems.
Teaching Resources
There are currently no specific textbooks dedicated solely to the content of the course. Students are encouraged to use any molecular biology textbooks for general mechanistic knowledge.
The following books are suggested as reference materials:
· Molecular Biology of the Cell - ISBN-13: 9780815344322
· The Cell - ISBN-13: 9781605358635
·
Students may also benefit from textbooks covering specific areas and topics discussed during the course to deepen their understanding. Suggested titles include:
· Genomes 4 - ISBN: 9781315226828 (free electronic version available)
· Epigenetics, Second Edition - ISBN: 978-1-936113-59-0
· Next-Generation Sequencing in Medicine - ISBN: 978-1-621821-13-7
· Handbook of Epigenetics, 2nd Edition: The New Molecular and Medical Genetics - ISBN: 9780128053881 (free electronic version available).
In addition, teaching materials will be distributed electronically by all instructors. These will include PDF slides of all lectures, along with journal articles and reviews related to the course topics. Web-based handbooks on specific topics will also be made available to students.
The following books are suggested as reference materials:
· Molecular Biology of the Cell - ISBN-13: 9780815344322
· The Cell - ISBN-13: 9781605358635
·
Students may also benefit from textbooks covering specific areas and topics discussed during the course to deepen their understanding. Suggested titles include:
· Genomes 4 - ISBN: 9781315226828 (free electronic version available)
· Epigenetics, Second Edition - ISBN: 978-1-936113-59-0
· Next-Generation Sequencing in Medicine - ISBN: 978-1-621821-13-7
· Handbook of Epigenetics, 2nd Edition: The New Molecular and Medical Genetics - ISBN: 9780128053881 (free electronic version available).
In addition, teaching materials will be distributed electronically by all instructors. These will include PDF slides of all lectures, along with journal articles and reviews related to the course topics. Web-based handbooks on specific topics will also be made available to students.
Epigenomics
Course syllabus
The course is divided into thematic modules, each comprising dedicated lectures that address key concepts and molecular mechanisms in genomics and epigenomics. The curriculum includes state-of-the-art technological approaches for studying genomic and epigenomic features, along with group work aimed at developing skills in experimental design to tackle specific scientific questions or problems.
Module 1: Genetic and Epigenetic Evolutionary Perspectives (4 lessons)
· Principles of Genetic Evolution
· Hallmarks of Cancer
· Cancer Epigenetics
Module 2: Epigenetic Molecular Mechanisms (8 lessons)
· Cell Identity and Gene Expression Control
· DNA Modifications
· Chromatin Modifications
· 3D Genome Organization
· Non-coding RNAs and the Dark Genome
· Metagenomics
· Molecular Analysis of Complex Systems at Single-Cell and Spatial Resolution
Module 3: Genetic Engineering (2 lessons)
· Genetic Manipulation in Cell Culture and In Vivo
· Transgenes
· Recombinase-Based Manipulation
· CRISPR-Cas Editing
Module 4: Cancer Genetics (2 lessons)
· Understanding the Human Genome and Its Mutations
· Use of Genomic Information for Patient Diagnosis and Treatment
Module 5: Genomic and Epigenomic Technological Approaches (8 lessons)
· High-Throughput Next-Generation Sequencing
· Whole Genome and Whole Exome Sequencing
· Liquid Biopsies
· RNA Sequencing
· Chromatin Localization Analyses
· 3D Epigenomic Analyses
· Nanopore-Based Direct Sequencing
· Single-Cell Analyses
Module 6: Epigenetic Mechanisms in Human Diseases (8 lessons)
· Patient-Specific Genome and Epigenome Models
· Role of DNA Methylation in Development and Disease
· Epigenomic Architecture of Cancer
· Epigenomic Architecture of Neurological and Neuropsychiatric Disorders
· Multi-Omic Architecture of Viral Infections
Module 7: Experimental Design (Group Work)
· Approaching a Scientific Problem or Question
· Designing an Experimental Plan
· Development and Presentation of a Project Proposal
Module 1: Genetic and Epigenetic Evolutionary Perspectives (4 lessons)
· Principles of Genetic Evolution
· Hallmarks of Cancer
· Cancer Epigenetics
Module 2: Epigenetic Molecular Mechanisms (8 lessons)
· Cell Identity and Gene Expression Control
· DNA Modifications
· Chromatin Modifications
· 3D Genome Organization
· Non-coding RNAs and the Dark Genome
· Metagenomics
· Molecular Analysis of Complex Systems at Single-Cell and Spatial Resolution
Module 3: Genetic Engineering (2 lessons)
· Genetic Manipulation in Cell Culture and In Vivo
· Transgenes
· Recombinase-Based Manipulation
· CRISPR-Cas Editing
Module 4: Cancer Genetics (2 lessons)
· Understanding the Human Genome and Its Mutations
· Use of Genomic Information for Patient Diagnosis and Treatment
Module 5: Genomic and Epigenomic Technological Approaches (8 lessons)
· High-Throughput Next-Generation Sequencing
· Whole Genome and Whole Exome Sequencing
· Liquid Biopsies
· RNA Sequencing
· Chromatin Localization Analyses
· 3D Epigenomic Analyses
· Nanopore-Based Direct Sequencing
· Single-Cell Analyses
Module 6: Epigenetic Mechanisms in Human Diseases (8 lessons)
· Patient-Specific Genome and Epigenome Models
· Role of DNA Methylation in Development and Disease
· Epigenomic Architecture of Cancer
· Epigenomic Architecture of Neurological and Neuropsychiatric Disorders
· Multi-Omic Architecture of Viral Infections
Module 7: Experimental Design (Group Work)
· Approaching a Scientific Problem or Question
· Designing an Experimental Plan
· Development and Presentation of a Project Proposal
Teaching methods
The course will include:
i) Lectures delivered by master-class professors, providing students with foundational knowledge of genomic and epigenomic molecular concepts and their pathological implications;
ii) Technological lectures delivered by adjunct professors, offering students insight into state-of-the-art technologies used to study various aspects of the genome and epigenome;
iii) An interactive project design activity, where students will apply the knowledge acquired during the course to develop experimental plans aimed at addressing specific scientific questions or problems.
i) Lectures delivered by master-class professors, providing students with foundational knowledge of genomic and epigenomic molecular concepts and their pathological implications;
ii) Technological lectures delivered by adjunct professors, offering students insight into state-of-the-art technologies used to study various aspects of the genome and epigenome;
iii) An interactive project design activity, where students will apply the knowledge acquired during the course to develop experimental plans aimed at addressing specific scientific questions or problems.
Teaching Resources
There are currently no specific textbooks dedicated solely to the content of the course. Students are encouraged to use any molecular biology textbooks for general mechanistic knowledge.
The following books are suggested as reference materials:
· Molecular Biology of the Cell - ISBN-13: 9780815344322
· The Cell - ISBN-13: 9781605358635
·
Students may also benefit from textbooks covering specific areas and topics discussed during the course to deepen their understanding. Suggested titles include:
· Genomes 4 - ISBN: 9781315226828 (free electronic version available)
· Epigenetics, Second Edition - ISBN: 978-1-936113-59-0
· Next-Generation Sequencing in Medicine - ISBN: 978-1-621821-13-7
· Handbook of Epigenetics, 2nd Edition: The New Molecular and Medical Genetics - ISBN: 9780128053881 (free electronic version available).
In addition, teaching materials will be distributed electronically by all instructors. These will include PDF slides of all lectures, along with journal articles and reviews related to the course topics. Web-based handbooks on specific topics will also be made available to students.
The following books are suggested as reference materials:
· Molecular Biology of the Cell - ISBN-13: 9780815344322
· The Cell - ISBN-13: 9781605358635
·
Students may also benefit from textbooks covering specific areas and topics discussed during the course to deepen their understanding. Suggested titles include:
· Genomes 4 - ISBN: 9781315226828 (free electronic version available)
· Epigenetics, Second Edition - ISBN: 978-1-936113-59-0
· Next-Generation Sequencing in Medicine - ISBN: 978-1-621821-13-7
· Handbook of Epigenetics, 2nd Edition: The New Molecular and Medical Genetics - ISBN: 9780128053881 (free electronic version available).
In addition, teaching materials will be distributed electronically by all instructors. These will include PDF slides of all lectures, along with journal articles and reviews related to the course topics. Web-based handbooks on specific topics will also be made available to students.
Modules or teaching units
Epigenomics
BIO/10 - BIOCHEMISTRY - University credits: 1
BIO/11 - MOLECULAR BIOLOGY - University credits: 4
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY - University credits: 1
BIO/11 - MOLECULAR BIOLOGY - University credits: 4
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY - University credits: 1
Lessons: 48 hours
Genomics
BIO/10 - BIOCHEMISTRY - University credits: 1
BIO/11 - MOLECULAR BIOLOGY - University credits: 1
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY - University credits: 4
BIO/11 - MOLECULAR BIOLOGY - University credits: 1
MED/04 - EXPERIMENTAL MEDICINE AND PATHOPHYSIOLOGY - University credits: 4
Practicals: 32 hours
Lessons: 32 hours
Lessons: 32 hours