Courses

Courses The training activities are held both in Milan and Naples. Check out the corresponding schedules:

Organizers: Ylli Doksani & Marina Mapelli - Dates: 8-10 July 2024

Location: IEO Campus, Via Adamello 16, Milan

The course aims at providing theoretical knowledge and practical principles on the main forefront strategies used for genome editing and biochemistry.

Timetable
9.30-10.30
Lesson Argument

Expression of coding and non-coding genes in mammalian genome

Teachers

Francesco Nicassio,

Affiliations

IIT

Lesson Location
IEO Silver Room
Timetable
10.30-11.30
Lesson Argument

Challenges in measuring RNA expression

Teachers

Matteo Marzi,

Affiliations

IIT

Lesson Location
IEO Silver Room
Timetable
11.30-12.30
Lesson Argument

Capturing specific protein–DNA interactions in biological systems by ChIP 

Teachers

Ivan Dellino,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
14.00-15.00
Lesson Argument

DNA Cloning strategies

Teachers

Chiara Bruckmann,

Affiliations

Thermo Fischer

Lesson Location
IEO Silver Room
Timetable
15.00-16.00
Lesson Argument

RNA-based therapies 

Teachers

Chiara Bruckmann,

Affiliations

Thermo Fischer

Lesson Location
IEO Silver Room
Timetable
16.00-17.00
Lesson Argument

Working with mammalian genomic DNA

Teachers

Ylli Doksani,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
9.30-10.30
Lesson Argument

CRISPR technology and its applications in drug discovery

Teachers

Danilo Maddalo,

Affiliations

Genentech

Lesson Location
IEO Silver Room
Timetable
10.30-11.30
Lesson Argument

Protein expression and purification

Teachers

Marina Mapelli,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
11.30-12.30
Lesson Argument

Biochemical and biophysical protein characterization

Teachers

Sebastiano Pasqualato,

Affiliations

Human Technopole

Lesson Location
IEO Silver Room
Timetable
14.00-15.00
Lesson Argument

Protein interactions in vitro

Teachers

Luigi Scietti,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
15.00-16.00
Lesson Argument

Measuring protein interactions in vivo 

Teachers

Sara Sigismund,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
16.00-17.00
Lesson Argument

Working with Antibodies

Teachers

Elena Maspero,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
9.30-10.30
Lesson Argument

Protein-DNA interactions involved in DNA repair and DNA replication

Teachers

Vincenzo Costanzo,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
10.30-11.30
Lesson Argument

Principles of enzymology 

Teachers

Loredano Pollegioni,

Affiliations

Università degli Studi dell'Insubria

Lesson Location
IEO Silver Room
Timetable
11.30-12.30
Lesson Argument

Liquid-liquid phase separation

Teachers

Philipp Erdmann,

Affiliations

Human Technopole

Lesson Location
IEO Silver Room
Timetable
14.00-15.00
Lesson Argument

Proteins on DNA – just look at the thing. What can we learn from using single molecule approach

Teachers

Joanna Jadwiga Andrecka,

Affiliations

Human Technopole

Lesson Location
IEO Silver Room
Timetable
15.15-17.30
Lesson Argument

Case Studies

Lesson Location
IEO Silver Room

Teacher: M. Cereda (IIGM & UNIMI) - Dates: 23-25 September 2024

Location: Silver & Platinum Room, IEO, Via Adamello 16, Milan

Theoretical lessons and practicals

 

Timetable
9.30-12.30
Lesson Argument

- Course Introduction
- Programming imprinting 
- Code writing

Lesson Location
IEO Silver Room
Timetable
14.00-16.00
Lesson Argument

R basics: language structure, data types, object-oriented programming

Lesson Location
IEO Silver Room
Timetable
9.30-12.30
Lesson Argument

- Data manipulation
- Performance testing

Lesson Location
IEO Platinum Room
Timetable
14.00-17.00
Lesson Argument

Writing R Extensions (by Uberto Pozzoli)

Lesson Location
IEO Platinum Room
Timetable
9.00-12.30
Lesson Argument

- Bioconductor & Data Visualization (by Fabio Iannelli)
- Memory Handling

Lesson Location
IEO Silver Room
Timetable
13.30-16.00
Lesson Argument

Data Communication + Build interactive web app: Shiny

Lesson Location
IEO Silver Room

Organizers: Emanuele Martini & Chiara Soriani

Dates: 1-2-3 October 2024

Venue: IFOM, Meeting Room 1-2

The aim of this course is to help students acquire new skills in the analysis of microscopy images using advanced image analysis tools. Through theoretical and practical lessons, the course will cover topics related to python/jython programming in Fiji and the application of machine learning and deep learning algorithms for the analysis of microscopy data.

Timetable
9.00-12.30
Lesson Argument

Introduction to Python/Jython programming languages:

  • From ImageJ macro language to Jython programming language in Fiji
  • Python basics: syntax, statements, expressions, list, loops, conditional statements, functions
  • From Python to Jython: object oriented programming
  • Jython main APIs and Classes for Fiji
  • Python vs Jython: Pros and cons

Hands-on: practice on a nuclei segmentation macro and comparison with Jython language

  • Implementation of nuclei segmentation
  • Focus on Regions Of Interest Manager
  • Creation of customized Results table
Teachers

Emanuele Martini, Fabrizio Orsenigo & Serena Magni,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-17.00
Lesson Argument

More complex image analysis and Analysis of Multiple Images

Hands-on: nuclei segmentation with spots count and intensity measurement

  • Bio-formats handling
  • User interaction
  • Multiple channel handling
  • Parent-children objects handling
  • Multiple Results Table management
  • Multiple images analysis
Teachers

Fabrizio Orsenigo & Serena Magni,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
9.00-12.30
Lesson Argument

Introduction to machine learning and deep learning in image analysis

  • Theoretical introduction about machine learning and deep learning
  • Machine learning as tool for semantic segmentation/pixel classification
  • Deep Learning as tool for image restoration and instance segmentation

Hands-on: Semantic segmentation/pixel classification with Labkit

Teachers

Damian Edward Dalle Nogare,

Affiliations

Human Technopole

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-17.00
Lesson Argument

Image restoration and instance segmentation using Deep Learning in Python

  • Introduction to Jupyter (Python) notebooks and their use in cloud with ZeroCostDL4Mic
  • Deep Learning algorithms for image restoration and instance

Hands-on: Image restoration and nuclear segmentation with Deep Learning algorithms

  • Image restoration using Noise2Void algorithm; model training and application using Jupiter notebooks in ZeroCostDL4Mic
  • Nuclear segmentation using 2D and 3D Stardist using Jupyter notebooks in ZeroCostDL4Mic
Teachers

Joran Deschamps,

Affiliations

Human Technopole

Lesson Location
IFOM - Meeting Room 1-2
Timetable
9.00-12.00
Lesson Argument

Segmentation in tissues using Stardist with QuPath software:

  • Introduction to QuPath for tissue sections analysis
  • Cell segmentation in tissues

Hands-on: Cell segmentation in tissues using Stardist and cell-type classification in different populations

Teachers

Chiara Soriani,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-17.00
Lesson Argument

Cell segmentation using Cellpose software in Python:

  • Introduction to conda environments and their utility for using local Jupyter (Python) notebooks
  • CellPose Deep Learning software for cell and nuclear segmentation

Hands-on: Segmentation of cells and nuclei using CellPose and evaluation of cytoplasmic signal using local Jupyter notebooks

Teachers

Mattia Marenda,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2

Teacher: Davide Mazzoni, UNIMI - Dates: 24 & 29 October, 5 November 2024

Location: Cascina Brandezzata, Via Ripamonti, Milan

Timetable
10.00-13.00
Lesson Argument

General principles of qualitative analysis

Lesson Location
Cascina Brandezzata
Timetable
14.00-16.00
Lesson Argument

Collecting and working with different qualitative data

Lesson Location
Cascina Brandezzata
Timetable
10.00-12.00
Lesson Argument

The main approaches to qualitative analysis

Lesson Location
Cascina Brandezzata
Timetable
10.00-12.00
Lesson Argument

The use of software and AI in qualitative research

Lesson Location
Cascina Brandezzata
Timetable
12.00-13.00
Lesson Argument

Applications of qualitative analysis in medical humanities (with Valeria Sebri)

Lesson Location
Cascina Brandezzata

Organizer: Anna Giulia Bottaccioli (UNIMI) - Dates: 11-12 February 2025

Format: in-person course

Location: IEO, Cascina Brandezzata, Milan

Timetable
10.00-13.00
Lesson Argument

The Philosophical and Scientific Basis for the Integration of Medicine and Psychology.

PsychoNeuroEndocrineImmunology: Integration of Psychology, Neurology, Endocrinology and Immunology. An overview (part I).

Lesson Location
Cascina Brandezzata - Aula Integrativa
Timetable
14.00-17.00
Lesson Argument

PsychoNeuroEndocrineImmunology: Integration of Psychology, Neurology, Endocrinology and Immunology. An overview (part II).

Epigenetics and fetal programming of adulthood.

Lesson Location
Cascina Brandezzata - Aula Integrativa
Timetable
9.00-13.00
Lesson Argument

Principles of gut-microbiota-brain axis in human physiology and pathology.

Lesson Location
Cascina Brandezzata - Aula Integrativa

Teacher: Sara Marceglia (UNIMI) - Dates: February/March 2025

Teacher: Arnaud Ceol (IEO). Dates: 19 February 2025

Location: IFOM & IEO Campus, Via Adamello 16

Aim of the course: the course will provide useful tools for researchers to respond to the new paradigm in handling and sharing research results. A variety of training methodologies will be used, such as plenary sessions, hands-on sessions, the completion of assignments and complementary e-learning materials.

Timetable
10.00-12.30
Lesson Argument
  • Aim of the Data management session
  • Introduction: The Data Management Plan (DMP)
  • Data management: who is involved?
  • Analysis of a DPM, focus and relevant sections
  • Open science & FAIR data
  • Data
Teachers

Arnaud Ceol,

Affiliations

IEO

Lesson Location
IFOM Conference Room
Timetable
14.00-17.30
Lesson Argument
  • Data storage
  • Data Security
  • Documenting your data
  • Data management good practices.
  • Research ethics and data protection,
  • Writing a Data Management Plan, Conclusions
Teachers

Arnaud Ceol,

Affiliations

IEO

Lesson Location
IEO Silver Room

Teacher: Rosella Visintin - Dates: 26-28 February 2025

Format: In-Person only course. Lectures and practical activities

Location: IEO Campus, Via Adamello 16, Milan

Aim of the course: The course aims to provide students with the necessary tools to approach scientific research in a conscious and responsible manner. The course is interactive and alternates between theoretical lectures and practical sessions. Students will learn to critically evaluate the scientific literature, design experiments starting from the formulation of the experimental hypothesis, analyze data rigorously, and identify the principles and responsibilities required of every researcher throughout the research process, from experiment planning to data publication. The course includes a dedicated module on research integrity, addressing questionable practices and misconduct through real-world examples and case studies.

 

Timetable
9.30-12.30
Lesson Argument

Critical reading of the literature:

  • How to read a scientific manuscript
  • How to prepare effective Journal Clubs
  • Practical
Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Platinum Room
Timetable
14.00-17.00
Lesson Argument

Experimental Design

  • From question to conclusions
  • Gender diversity in scientific experiments
Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Gold Room
Timetable
9.30-12.30
Lesson Argument

Research integrity:

  • Shared values in scientific research
  • Running and recording experiments
Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
14.00-17.00
Lesson Argument

Scientific integrity vs scientific misconduct:

  • Generating and manipulating data - Standard of conduct
  • Famous cases of alleged scientific misconduct
  • Time management
Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
9.30-12.30
Lesson Argument

Practical activity

Teachers

Rosella Visintin

Affiliations

IEO

Lesson Location
IEO Coral Room

Organizer: Nereo Kalebic (HT) - Dates: 3-5 March 2025

Venue: Human Technopole, Milan

Format: in-person only course

The course aims at providing a basic theoretical insight into the development and evolution of nervous systems, neuronal physiology, cancer neuroscience and brain pathologies. Through 4 different workshops, tutorials and demonstration, the students will become familiar with various in vitro, ex vivo and in vivo model systems employed in neurobiology as well as basic computational neurogenomic methods.

Timetable
9.00-9.30
Lesson Argument

Course introduction: Intro, aims, expectations

Teachers

Nereo Kalebic,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
9.30-11.00
Lesson Argument

Development and functions of neocortex

Teachers

Nereo Kalebic,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
11.30-12.30
Lesson Argument

Neuronal guidance and connectivity

Teachers

Dario Bonanomi,

Affiliations

Ospedale San Raffaele, Milan

Lesson Location
Mezzanine Training Room
Timetable
14.30-17.00
Lesson Argument

Practical sessions – Demonstration

Microinjection into organoids/mouse cortical slices (Elena Taverna, Elena Restelli)

Electrophysiology (Filippo Mirabella)

Timetable
9.00-10.00
Lesson Argument

Introduction into human PSC models and neuroimmunology

Teachers

Oliver Harschnitz,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
10.00-11.00
Lesson Argument

PSC models to study evolutionary neurobiology

Teachers

Elena Taverna,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
11.30-12.30
Lesson Argument

From neurodiversity to physiopathology: an introduction

Teachers

Giuseppe Testa,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
14.30-17.00
Lesson Argument

Workshop and tutorial stem cells, reprogramming and organoids

  • Reprogramming
  • Stem cell culture
  • Organoid automation
Teachers

Giovanni Fagà,

Affiliations

Human Technopole

Timetable
9.00-10.00
Lesson Argument

Neuroglial biology

Teachers

José Davila-Velderrain,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
10.30-12.30
Lesson Argument

Workshop and tutorial: Neurogenomics - Part I

Teachers

Cristina Cheroni,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
13.30-15.30
Lesson Argument

Workshop and tutorial: Neurogenomics - Part II

Teachers

Cristina Cheroni,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room
Timetable
16.00-17.00
Lesson Argument

Wrap-up & Discussion

Teachers

Nereo Kalebic,

Affiliations

Human Technopole

Lesson Location
Mezzanine Training Room

Teachers: Valeria Ranzani (INGM), Camilla Ugolini (IIT) - Dates: 10-13 March 2025

Location: INGM, Via F. Sforza 35, Milan

Timetable
10.00-17.30 with lunch break
Lesson Argument

Usable R fundamentals:

  • Introduction and history of R
  • IDEs, RStudio, packages and good practices
  • Anatomy of a command, standard output/error, batch & interactive mode
  • R data structures, basic operators, objects, classes
  • Reading data into R objects
  • The Tidy data
  • Important functions in R for Tidy Data
Timetable
10.00-17.30 with lunch break
Lesson Argument

The grammar of graphics with ggplot & data visualization:

  • Introductory rules of data visualisation
  • The generic R graphic devices, plot command, colours
  • Colours in R
  • The grammar of graphics
  • The ggplot2 levels and hierarchy
  • Different types of geoms for different types of data (histograms, bar plots, pie charts, density plots, scatter plots, box plots)
  • Piping summarized data into ggplot
  • Special purpose graphics: volcano, heatmap, bubble plot
Timetable
10.00-17.30 with lunch break
Lesson Argument

Fundamentals of descriptive statistics:

  • Different kind of data, how to distinguish them
  • Basic descriptive indices
  • How to evaluate data position, variability and symmetry.
  • How to interpret data position, variability and symmetry.
  • Correlation and covariance
Timetable
10.00-17.30 with lunch break
Lesson Argument

Bases of statistical inferences:

  • Research hypotheses and tests
  • Definition of null and alternative hypothesis
  • The p-value
  • One and two-sided tests
  • (optional) Type I and II errors and power of a test
  • Evaluating performances: Sensitivity and Precision
  • Differences between parametric and non-parametric tests
  • Choosing the most fitting test to answer a question
  • Differences between independent and paired tests
  • How to choose a test

Organizers: Dario Parazzoli (IFOM) - Dates: 7-9 April 2025

The course offers a comprehensive introduction to optical microscopy, focusing on fundamental principles, sample preparation, and advanced techniques. Designed for cancer research, it provides participants with the theoretical foundation to visualize cellular and subcellular structures, analyze tumor microenvironments, and apply imaging methods to study cancer biology

Organizers: R. Visintin - Dates: 14 April 2025

Format: In-person only course.

Location: IEO Campus, Via Adamello 16 - Milan

Teacher: Myriam Alcalay, IEO - Dates: 5,8,14 May 2025

Format: In person course

Location: IFOM, Via Adamello 16 - Milan

Teacher: Davide La Torre (UNIMI) - Dates: 19-21 May 2025

Format: In-person course

Location: IEO Campus, Via Adamello 16, Milan

Aim: This course introduces basic concepts of artificial intelligence and machine learning and their applications to the field of medicine. Students will explore various AI methods and technologies used for data analysis, medical diagnosis, treatment planning, and healthcare management. The course will introduce fundamental concepts, algorithms, and real-world applications.

Timetable
9.00-12.30
Lesson Argument
  • Introduction To Ai In Medicine
  • Overview Of Artificial Intelligence And Machine Learning
  • Introduction To The Application Of Ai In Medicine
  • Regulatory And Ethical Considerations. The Role Of Xai
Lesson Location
IEO Silver Room
Timetable
13.30-17.30
Lesson Argument
  • Machine Learning Fundamentals
  • Basic Concepts Of Supervised, Unsupervised, And Reinforcement Learning
  • Applications Of Machine Learning In Medicine: Diagnosis, Prognosis, Treatment Selection, Drug Discovery, Etc.
  • Evaluation Metrics For Machine Learning Models In Healthcare
Lesson Location
IEO Platinum Room
Timetable
11.00-13.00
Lesson Argument
  • Introduction To Python Programming Language And Its Applications In Data Analysis
  • Data Manipulation And Analysis Using Python Libraries Such As Numpy, Pandas, And Matplotlib
  • Hands-On Exercises And Coding Assignments Using Python For Data Preprocessing And Exploratory Data Analysis With Medical Datasets
Lesson Location
IEO Platinum Room
Timetable
14.00-18.00
Lesson Argument
  • Overview Of Orange Data Mining Software And Its Functionalities
  • Data Preprocessing, Feature Engineering, And Model Building Using Orange
  • Hands-On Tutorials And Case Studies Using Orange For Machine Learning Tasks With Medical Datasets
Lesson Location
IEO Platinum Room
Timetable
10.30-12.30
Lesson Argument
  • Overview Of Chatgpt And Its Applications In Natural Language Processing (Nlp)
  • Basics Of Text Preprocessing
Lesson Location
IEO Platinum Room
Timetable
13.30-17.30
Lesson Argument

Hands-On Workshop On Using Chatgpt And Medical Text Data

Lesson Location
IEO Platinum Room

Organizer: hfp consulting - Dates: 27-29 May 2025

Format: In-person course

Location: IFOM, Via Adamello 16, Milan

Organizers: Chiara Soriani (IEO) - Dates: 17-20 June 2025

Location: IFOM, Milan

The course aims at teaching the theoretical concepts of image analysis and providing practical tools, basic and advanced, for the analysis of microscopy images. Students will learn how to use ImageJ/FIJI, including macro language. It will also cover python/jython programming in Fiji and the application of machine learning and deep learning algorithms for the analysis of microscopy data.

Organizer: Maria Grazia Totaro (IFOM) - Dates: 23-24 June 2025

Location: IFOM, Via Adamello 16, Milan

The aim of course is to provide participants with a comprehensive understanding of the principles, techniques, and applications of flow cytometry. This course is designed for new PhD students who want to learn how to use this technology. By the end of the course, participants should be able to confidently design, execute, and analyse flow cytometry experiments.

Organizers: Chiara Segrè & Agnese Collino (FUV) - Dates: 1-3 July 2025

Format: In person course

Location: IFOM, Via Adamello 16, Milan

Organizer: Beatrice Bodega (INGM) - Dates: 15-16 July 2025

Location: INGM

The course offers an in-depth exploration of the mechanisms regulating cellular processes in complex organisms, both in health and disease. It highlights the roles of cell plasticity and adaptability in maintaining cellular homeostasis and responding to environmental cues. The genome is presented as the central input, with its structure and function ensuring cell identity and regulating transcription through a diverse array of interconnected epigenetic mechanisms. Key topics include genome integrity, transcriptional regulation, three-dimensional organization, and nuclear compartmentalization, all of which are dynamic, quantitative factors that operate at the single-cell level to govern tissue organization and specialization.

Organizer: B. Bodega (INGM) - Dates: September 2025

Location: INGM, Milan

The Immunology course, delivered as a series of seminars, would cover state-of-the art and hot topics in immunology important for human health.

Organizer: Pier Paolo Di Fiore (IEO) - Dates: 2-3, 6-8 October 2025

Basic and advanced lectures on cancer biology to provide a complete overview on the current knowledge about cancer

Organizer: M. Mapelli (IEO) & A. Casanal (HT) - Dates: 24-28 November  2025

Format: in-person only course

The course is meant to illustrate the basic principles of various techniques used in fore-front integrative structural biology approaches, including cryo-electron microscopy and tomography, crystallography, NMR, Mass-Spec Cross-Linking and Alpha-Fold. The topics will be introduced by lectures given by SEMM faculty members and external speakers, complemented with several hands-on tutorials in which the students will familiarize with software and instrumentation.