General Bioinformatics and Computational Methods in Environmental Microbiology
A.Y. 2026/2027
Learning objectives
Undefined
Expected learning outcomes
Undefined
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
Responsible
Course syllabus
First, the courses will introduce students to the principles, concepts, and statistical methods commonly used for analyzing and interpreting large-scale biological data:
Introduction to bioinformatics methods for studying microbial communities
- 16S rRNA amplicon sequencing
- Shotgun metagenomics
- Beta-diversity
- Alpha-diversity
- A primer on phylogeny
Introduction to the R environment for analyzing biological data:
- Importing data into R
- Basic data structures, data frames, vectors, matrices
- Installing and managing software packages
- Introduction to Rstudio
- Introduction to the basic principles of statistics
- Introduction to statistical analysis using R
- Data representation techniques, including PCA, boxplots, histograms, and heatmaps
Presentation of data and results
- Introduction to preparing a scientific presentation/report
Introduction to bioinformatics methods for studying microbial communities
- 16S rRNA amplicon sequencing
- Shotgun metagenomics
- Beta-diversity
- Alpha-diversity
- A primer on phylogeny
Introduction to the R environment for analyzing biological data:
- Importing data into R
- Basic data structures, data frames, vectors, matrices
- Installing and managing software packages
- Introduction to Rstudio
- Introduction to the basic principles of statistics
- Introduction to statistical analysis using R
- Data representation techniques, including PCA, boxplots, histograms, and heatmaps
Presentation of data and results
- Introduction to preparing a scientific presentation/report
Prerequisites for admission
A knowledge of basic molecular biology topics is strongly recommended for attending the course, with particular emphasis on nucleic acid sequencing and the structure of genes and the genomes of prokaryotic and eukaryotic organisms.
Teaching methods
Teaching methodology: Lectures complemented by exercises. Instructors assign exercises at the end of most lectures to help consolidate concepts between lectures. Attendance is highly recommended. A journal club (not mandatory) will be organized to explore the methods related to the study of environmental microbiology. For educational purposes only and not for assessment, self-evaluation activities may be conducted during the course through anonymous multiple-choice tests. These tools will be used to identify topics that students find less clear, thereby enabling further discussion and additional explanation of those topics.
Teaching Resources
Copies of the slides shown during lectures, as well as additional materials and datasets, will be made available through the course website on the ARIEL platform of the University of Milan. This material is intended to support lectures and its study cannot be considered a complete alternative to regular attendance. The material is made available only to students enrolled in the course and must not be distributed to others without the express consent of the instructors.
Assessment methods and Criteria
Individual Project + Oral Exam
Students will be asked to complete a small project consisting of the analysis of real data, using the techniques and methods learned during the course. Students will produce and present a report describing their findings to their instructors.
The report is due at least 48 hours before the chosen exam session.
The exam includes a critical discussion with the instructors of the main results and techniques used. A score of 18/30 or higher will be considered a pass.
Students will be asked to complete a small project consisting of the analysis of real data, using the techniques and methods learned during the course. Students will produce and present a report describing their findings to their instructors.
The report is due at least 48 hours before the chosen exam session.
The exam includes a critical discussion with the instructors of the main results and techniques used. A score of 18/30 or higher will be considered a pass.
BIOS-08/A - Molecular Biology - University credits: 3
BIOS-15/A - Microbiology - University credits: 3
BIOS-15/A - Microbiology - University credits: 3
Lessons: 48 hours
Professor:
Comandatore Francesco
Professor(s)
Reception:
Every Monday at 15:00, available online or in person upon request.
Milan – Via G. B. Grassi 74, Sacco Hospital, Building 62, first floor