Molecular bioinformatics
A.A. 2024/2025
Obiettivi formativi
The development of several high-throughput analytical approaches in molecular biology has revolutionized genomics. In particular, Next Generation Sequencing has wide applications in many functional genomics settings. This course will introduce a range of these applications, focusing on the nature of data generated, its strengths and limitations as well as computational and statistical approaches used to analyze genomic and transcriptomic datasets in various contexts.
Risultati apprendimento attesi
At the end of the course, students will acquire:
- A knowledge of the scope of bioinformatics in genomics and functional genomics.
- A detailed appreciation of the nature of Next Generation Sequencing data from different platforms, their characteristics, advantages and weaknesses.
- An understanding of fundamental aspects of experimental design in genomics and transcriptomics.
- An understanding of data quality checking and filtering approaches.
- An appreciation of theoretical considerations underlying data analytical approaches in genomics and transcriptomics (genome assembly and annotation, variant detection, gene annotation, quantitative analysis of gene expression, analysis of small non-coding RNAs).
- The ability to critically interpret results of genome wide studies.
- Experience in the evaluation and synthesis of results of genomics experiments through the preparation and presentation of a scientific poster.
- A knowledge of the scope of bioinformatics in genomics and functional genomics.
- A detailed appreciation of the nature of Next Generation Sequencing data from different platforms, their characteristics, advantages and weaknesses.
- An understanding of fundamental aspects of experimental design in genomics and transcriptomics.
- An understanding of data quality checking and filtering approaches.
- An appreciation of theoretical considerations underlying data analytical approaches in genomics and transcriptomics (genome assembly and annotation, variant detection, gene annotation, quantitative analysis of gene expression, analysis of small non-coding RNAs).
- The ability to critically interpret results of genome wide studies.
- Experience in the evaluation and synthesis of results of genomics experiments through the preparation and presentation of a scientific poster.
Periodo: Primo semestre
Modalità di valutazione: Esame
Giudizio di valutazione: voto verbalizzato in trentesimi
Corso singolo
Questo insegnamento può essere seguito come corso singolo.
Programma e organizzazione didattica
Edizione unica
Responsabile
Periodo
Primo semestre
Programma
Over the last 15-20 years, a series of high throughput analytical methods have revolutionized biological and biomedical research. Among these "big data" approaches, "Next Generation Sequencing" (NGS) methods have proved to be particularly powerful and transversal in their application. The course will focus on the strengths and limitations of NGS for various applications, as well as the nature of the data produced and their computational processing, as well as the integration of various types of "big data" in current biological and biomedical research.
1) Historical perspectives and the role of bioinformatics in genomics
2) NGS technologies, read lengths, error profiles, base quality scores, data formats, data quality control.
3) Preparation of sequencing libraries, coverage biases and the impact of PCR, targeted resequencing, indexed libraries.
4) Variant discovery and structural variation between genomes
5) Di novo genome assembly
6) Annotation of genes, transcripts and alternative splicing
7) Quantitative transcriptomics
8) Analysis of small non-coding RNAs
9) Analysis of ChIP-Seq data
10) In silico promoter analysis
11) Innovative applications of NGS in genomics
12) Poster presentation sessions
13) Integration of "Big Data" resources
1) Historical perspectives and the role of bioinformatics in genomics
2) NGS technologies, read lengths, error profiles, base quality scores, data formats, data quality control.
3) Preparation of sequencing libraries, coverage biases and the impact of PCR, targeted resequencing, indexed libraries.
4) Variant discovery and structural variation between genomes
5) Di novo genome assembly
6) Annotation of genes, transcripts and alternative splicing
7) Quantitative transcriptomics
8) Analysis of small non-coding RNAs
9) Analysis of ChIP-Seq data
10) In silico promoter analysis
11) Innovative applications of NGS in genomics
12) Poster presentation sessions
13) Integration of "Big Data" resources
Prerequisiti
Base solida di Biologia molecolare (DNA replication, transcription, translation)
Metodi didattici
Frontal teaching with a high level of teacher interaction, supported by projected teaching materials, which will be made available on the course Ariel website. Extensive discussions will be carried out to allow development of critical thinking and to encourage constructive individual involvement in the teaching/learning process. Lecture attendance is highly encouraged. During the course the studentes are encouraged to prepare scientific posters on specific arguments under the guidance of the teacher.
Materiale di riferimento
il materiale di riferimento non subira variazioni.
Next-Generation Sequencing Data Analysis By Xinkun Wang ISBN 9781482217889
Essential Bioinformatics By Jin Xiong ISBN 978-0521600828
Scientific articles will be selected and provided by the teacher via the course Ariel and Teams websites.
Next-Generation Sequencing Data Analysis By Xinkun Wang ISBN 9781482217889
Essential Bioinformatics By Jin Xiong ISBN 978-0521600828
Scientific articles will be selected and provided by the teacher via the course Ariel and Teams websites.
Modalità di verifica dell’apprendimento e criteri di valutazione
La valutazione consiste di 2 parte (con pesi uaguali), la preparazione e presentazione di un poster basato su un articolo di ricerca ed un esame scritto (1 ora, domande "crocette" (15-18 domande) ed aperte (3-4 domande)
Gli esami scritti sono in presenza
L'esame, in particolare, sarà volto a:
- accertare il raggiungimento degli obiettivi del corso in termini di conoscenza e capacità di comprensione;
- accertare la capacità di applicare conoscenza e comprensione e verificare l'autonomia di giudizio attraverso la discussione degli argomenti oggetto delle lezioni;
- accertare la padronanza del linguaggio specifico che attiene all'ambito della genetica e la capacità di esporre gli argomenti in modo chiaro e logico, con i dovuti collegamenti al contenuto di altri corsi di insegnamento del Corso di laurea.
Poster presentations by groups of students will take place, where possible, during synchronous programmed lecture hours.
Gli esami scritti sono in presenza
L'esame, in particolare, sarà volto a:
- accertare il raggiungimento degli obiettivi del corso in termini di conoscenza e capacità di comprensione;
- accertare la capacità di applicare conoscenza e comprensione e verificare l'autonomia di giudizio attraverso la discussione degli argomenti oggetto delle lezioni;
- accertare la padronanza del linguaggio specifico che attiene all'ambito della genetica e la capacità di esporre gli argomenti in modo chiaro e logico, con i dovuti collegamenti al contenuto di altri corsi di insegnamento del Corso di laurea.
Poster presentations by groups of students will take place, where possible, during synchronous programmed lecture hours.
Siti didattici
Docente/i
Ricevimento:
Giovedi 14.00 - 17.00
Via Celoria 26, Torre B, Piano 2