Courses

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

Teacher: Rosella Visintin - Dates: 14-15 & 22 March 2024

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

Location: IEO, Milan

Timetable
9.30-10.00
Lesson Argument

Introduction to the course

Lesson Location
IEO Silver Room
Timetable
10.00-11.00
Lesson Argument

Critical reading of the literature

Lesson Location
IEO Silver Room
Timetable
11.00-12.15
Lesson Argument

How to do a Journal club

Lesson Location
IEO Silver Room
Timetable
14.00-15.00
Lesson Argument

Experimental design - From hypothesis to conclusions

Lesson Location
IEO Silver Room
Timetable
15.00-16.00
Lesson Argument

Case Study

Lesson Location
IEO Silver Room
Timetable
16.00-17.00
Lesson Argument

Gender diversity in scientific experiments - Susanna Chiocca - IEO - Milan

Lesson Location
IEO Silver Room
Timetable
9.30-11.30
Lesson Argument

Research integrity module:

  • Shared values in scientific research;
  • Running and recording experiments (labnotebook);
  • Generating and manipulating data (scientific misconduct - falsification; fabrication and plagiarism);
  • Time management
Lesson Location
IEO Silver Room
Timetable
11.30-12.30
Lesson Argument

Famous cases of alleged scientific misconduct

Lesson Location
IEO Silver Room
Timetable
14.00-15.00
Lesson Argument

Seminar by William Teale, EMBO Editor

Lesson Location
IFOM - Conference Room
Timetable
9.30-11.30
Lesson Argument

Paper discussion

Lesson Location
IEO Silver Room

Organizer: M. Mapelli (IEO) & A. Casanal (HT) - Dates: 18-21 March 2024

Venue: Human Technopole, Milan

Format: in-person only course

The course will focus on how to analize the structures and on structural biology projects. There will be a day dedicated to Cryo-EM with practicals at the microscope.

Timetable
9.30-11.30
Lesson Argument

Crystallization theory and practical

Teachers

Sebastiano Pasqualato (HT) & Luigi Scietti (IEO)

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Basis of crystallography

Teachers

Marina Mapelli,

Affiliations

IEO

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-15.00
Lesson Argument

Structure based drug design

Teachers

Mario Milani,

Affiliations

UNIMI

Lesson Location
Human Technopole - Auditorium
Timetable
15.00-17.00
Lesson Argument

Pymol tutorial

Teachers

Sebastiano Pasqualato (HT) & Luigi Scietti (IEO)

Lesson Location
Egg Rooms, 4th floor, PITA
Timetable
9.30-10.20
Lesson Argument

Principles of Cryo-EM SPA

Teachers

Francesca Coscia,

Affiliations

Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
10.40-11.30
Lesson Argument

Anatomy of the microscopes and sample preparation

Teachers

Paolo Swuec,

Affiliations

Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Challenges of a SPA project “Structural Biology impact in drug discovery"

Teachers

Chiara Rapisarda,

Affiliations

Sanofi, Paris

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-14.30
Lesson Argument

Working with Cryo-EM microscopes

Teachers

Paolo Swuec,

Affiliations

Human Technopole

Lesson Location
Egg Rooms, 4th floor PITA
Timetable
14.30-15.00
Lesson Argument

Group 1: Visit to microscopes

Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial

Teachers

Simona Sorrentino & Malan Silva,

Affiliations

Human Technopole

Lesson Location
Egg rooms 4th floor PITA
Timetable
15.00-15.30
Lesson Argument

Group 1: Negative staining tutorial

Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial

Teachers

Paolo Swuec & Simona Sorrentino,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
15.30-17.00
Lesson Argument

Model building tutorial: Coot for model building and structure interpretation of cryoEM maps

Teachers

Martin Høgholm Jørgensen,

Affiliations

Aarhus University, Denmark

Lesson Location
Egg Rooms 4th floor PITA
Timetable
9.30-10.20
Lesson Argument

CLEM: correlative light and electron microscopy

Teachers

Malan Silva,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
10.40-11.30
Lesson Argument

Principles of Cryo-ET: sample prep and theory

Teachers

Philipp Erdmann,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
11.45-12.45
Lesson Argument

A Cryo-ET story: “TBD”

Teachers

Mirko Cortese,

Affiliations

TIGEM

Lesson Location
Egg Rooms 4th floor PITA
Timetable
14.00-17.00
Lesson Argument

Cryo-ET workshop and tutorial

Teachers

Philipp Erdmann,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
9.30-10.20
Lesson Argument

Principles of NMR

Teachers

Giovanna Musco,

Affiliations

San Raffaele Hospital

Lesson Location
Human Technopole - Auditorium
Timetable
10.40-11.30
Lesson Argument

Mass Spectrometry for Structural Biology: XL-MS

Teachers

Andrea Graziadei,

Affiliations

IEO & HT

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Principles of Alpha-fold

Teachers

Andrea Graziadei,

Affiliations

IEO & HT

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-15.30
Lesson Argument

Alpha-fold tutorial

Teachers

Helen Foster,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
15.30-17.00
Lesson Argument

Students’ presentation of articles

Teachers

Ana Casañal & Marina Mapelli

Lesson Location
Egg Rooms 4th floor PITA

Organizers: Dario Parazzoli and Nils Gauthier - Dates: 8-12 April 2024

The course will cover all basic microscopy techniques and provide an overview of a broad range of innovative imaging approaches. Each lecture will include an overview of the topic and a presentation of the lecturer’s specific field of interest.

Timetable
9.00-9.30
Lesson Argument

Introduction

Teachers

Dario Parazzoli - Nils Gauthier,

Affiliations

IFOM

Lesson Location
IFOM Red Room
Timetable
9.30-10.40
Lesson Argument

Fixed sample preparation and artifacts

Teachers

Sara Barozzi,

Affiliations

IFOM

Lesson Location
IFOM Red Room
Timetable
11.00-11.45
Lesson Argument

Flow cytometry basic

Teachers

Simona Ronzoni,

Affiliations

IEO

Lesson Location
IFOM Red Room
Timetable
11.45-12.30
Lesson Argument

Flow cytometry: sample preparation and applications

Teachers

Maria Grazia Totaro,

Affiliations

IFOM

Lesson Location
IFOM Red Room
Timetable
14.00-14.45
Lesson Argument

Moving forward: full spectrum flow cytometry

Teachers

Maria Grazia Totaro,

Affiliations

IFOM

Lesson Location
IFOM Red room
Timetable
15.00-15.30
Lesson Argument

Seminar by Achille Anselmo (HSR research, Ospedale San Raffaele)

Lesson Location
IFOM Red Room
Timetable
15.30-16.00
Lesson Argument

Seminar by Francesca Simoncello (IFOM)

Lesson Location
IFOM Red Room
Timetable
9.00-12.30
Lesson Argument

Widefield microscopy and optical sectioning

Teachers

Dario Parazzoli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-14.45
Lesson Argument

Colocalization

Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.45-15.30
Lesson Argument

Multiplexing

Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
15.45-16.15
Lesson Argument

Seminar by Grazisa Rossetti (IFOM)

Lesson Location
IFOM - Conference Room
Timetable
9.00-10.00
Lesson Argument

Introduction live cell imaging

Teachers

Sara Barozzi,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-11.30
Lesson Argument

Quantitative fluorescence microscopy techniques (F-techniques)

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
11.45-12.30
Lesson Argument

Scale your imaging up, from cells to tissues and beyond

Teachers

Fabrizio Orsenigo,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.00
Lesson Argument

Optical sectioning in 3D with light sheet microscopy

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
15.00-16.00
Lesson Argument

The “perfect” microscope utopia: a discussion on experiment design in optical microscopy

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
9.00-10.00
Lesson Argument

Electron microscopy 

Teachers

Alexander Mironov,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.30
Lesson Argument

Super resolution

Teachers

Nils Gauthier,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.00
Lesson Argument

Mechanobiology

Teachers

Nils Gauthier,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room

Organizer: Nereo Kalebic (HT) - Dates: 16-18 April 2024

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

Introduction to the course

Teachers

Nereo Kalebic,

Affiliations

Human Technopole 

Timetable
9.30-10.30
Lesson Argument

Development and function of neocortex

Teachers

Nereo Kalebic,

Affiliations

Human Technopole

Timetable
10.45-11.45
Lesson Argument

Development and function of cranial placodes

Teachers

Oliver Harschnitz,

Affiliations

Human Technopole

Timetable
11.45-12.45
Lesson Argument

Neuronal guidance and connectivity

Teachers

Dario Bonanomi,

Affiliations

San Raffaele Hospital

Timetable
14.00-15.00
Lesson Argument

Genome editing in PSC-derived models

Teachers

Giovanni Fagà,

Affiliations

Human Technopole

Timetable
15.00-17.00
Lesson Argument

Workshop and tutorial: Genome editing

Teachers

GEDI facility

Timetable
9.00-10.00
Lesson Argument

PSC models to study evolutionary neurobiology

Teachers

Elena Taverna,

Affiliations

Human Technopole

Timetable
10.00-11.00
Lesson Argument

From neurodiversity to physiopathology: an introduction

Teachers

Giuseppe Testa,

Affiliations

Human Technopole & IEO

Timetable
11.30-12.30
Lesson Argument

Human PSC models to study neuroimmunology

Teachers

Oliver Harschnitz

Affiliations

Human Technopole

Timetable
13.30-14.30
Lesson Argument

Single cell manipulation techniques

Teachers

Elena Taverna,

Affiliations

Human Technopole

Timetable
14.30-15.30
Lesson Argument

In vivo models of neurological diseases

Teachers

Manuela Ventura,

Affiliations

Human Technopole

Timetable
15.15-16.15
Lesson Argument

- Tour of the microinjection station (E.Taverna, E.Restelli)
- Tour of the Animal research facility (M.Ventura)                             

Either one after another, or split into 2 groups and doing it in parallel and then exchanging.

Timetable
16.15-18.00
Lesson Argument

Group Work JC

Timetable
9.00-10.00
Lesson Argument

Electrophysiological methods in neuroscience

Teachers

Diletta Pozzi,

Affiliations

Human Technopole

Timetable
10.00-11.00
Lesson Argument

Neuroglial biology and genomics

Teachers

Jose Davila Velderrain,

Affiliations

Human Technopole

Timetable
11.30-12.30
Lesson Argument

Workshop and tutorial Neurogenomics part I

Teachers

Cristina Cheroni,

Affiliations

Human Technopole

Timetable
13.30-15.00
Lesson Argument

Workshop and tutorial Neurogenomics part II

Teachers

Cristina Cheroni,

Affiliations

Human Technopole

Timetable
15.30-17.00
Lesson Argument

JC: Cancer neuroscience

Teachers

Nereo Kalebic and Filippo Mirabella,

Affiliations

Human Technopole

Organizers: Emanuele Martini & Mattia Marenda - Dates: 6-7-9 May 2024

Venue: IFOM, Milan

The goal of this course is to teach students the basic theoretical concepts of image analysis and to provide practical tools for most demanding image analysis topics, such as nuclear segmentation, tracking and co-localization. Students will learn how to perform image analysis by using ImageJ/FIJI and will familiarize with automated image analysis through FIJI macro language.

Timetable
9.00-10.45
Lesson Argument

Introduction to digital images
•    How an image is obtained, sampling, monochromatic and color images, Fourier transforms

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
11.00-13.00
Lesson Argument

Introduction to Fiji and objects segmentation:

  • Introduction to Fiji’s key functionalities: installation, basic options, opening of images (Bio-Formats Import), management of simple images, export of analysed images
  • Measurements of images: image calibration, set measurements parameters, creation of selections and Region Of Interest
  • Processing images: geometric transformations, filters, mathematical operations
  • Binarization of images: image thresholding methods, processing of binary images
  • Objects segmentation and detection: Analyse particles/Find Maxima functionalities
Teachers

Ambra Dondi,

Affiliations

IEO

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

Hands-on: Nuclear segmentation and spots detection:

  • Step-by-step creation of an image analysis workflow for nuclear segmentation and nuclear spots detection
  • Step-by-step recording of macro commands within the analysis workflow
Teachers

Serena Magni,

Affiliations

IFOM

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

Introduction to Macro Language

  • Introduction to macro language: What is a macro? Why do we need macros?
  • How can move from a set of recorded commands to a macro for batch processing?
  • Built-in functions in FIJI: basics imaging analysis functions
  • Basics of programming in Fiji macro language with examples: variables, arrays, loops, conditional statements
  • Import and export of files: bio-formats and bio-formats macros extensions
  • Hands-on: Generalization of a series of recorded commands to create a macro for batch nuclear segmentation
Teachers

Mattia Marenda (IEO), Fabrizio Orsenigo (IFOM)

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

Colocalization:

  • Introduction to the concept of colocalization
  • Co-occurrence
  • Hands-on: co-occurence batch analysis
  • Intensity correlation coefficient-based analyses object-based colocalization
  • Hands-on: the JACoP plugin
Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
9.00-9.50
Lesson Argument

Images for publication and guidelines for best practices in image processing

Teachers

Fabrizio Orsenigo,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
10.00-12.30
Lesson Argument

Tracking in Biology:

  • Introduction to the concepts of tracking and biological motivation: tracking of cells and intra-cellular objects (chromatin, proteins, exogenous probes)
  • Introduction to TrackMate Software
  • Technical details for tracking: objects detection & trajectories reconstruction
  • Evaluation of parameters from trajectories: displacement, velocity, directionality, etc
  • Mention of advanced features in tracking: mean square displacement to calculate the motion type (free-diffusion, confined, active motion) and environment material properties
  • Hands-on: Tracking of nuclei using Trackmate
Teachers

Mattia Marenda,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-16.30
Lesson Argument

Collective Motion:

  • Introduction to the concepts of collective cellular mobility and motivation
  • Different ways and parameters to study collective cell motility:
    Wound Healing, Cell Streaming, Particle Image Velocimetry to evaluate speed of wound closure, velocity and coordination of movement
  • Hands-on: Wound Healing speed of closure extraction using Fiji
Teachers

Emanuele Martini,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
16.30-17.00
Lesson Argument

Wrap-up and Discussion

Lesson Location
IFOM - Meeting Room 1-2

Teacher: Arnaud Ceol (IEO). Dates: 14 & 16 May 2024

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
14.00-17.00
Lesson Argument
  1. Aim of the Data management session
  2. Introduction: The Data Management Plan (DMP)
  3. Data management: who is involved?
  4. Analysis of a DPM, focus and relevant sections
  5. Open science & FAIR data
  6. Data
Lesson Location
IEO Platinum Room
Timetable
14.00-17.00
Lesson Argument
  1. Data storage
  2. Data security
  3. Documenting your data
  4. Data management good practices
  5. Research ethics and data protection
  6. Writing a Data Management Plan, Conclusions
Lesson Location
IEO Platinum Room

Organizers: A. Bachi, T. Bonaldi - Dates: 27-29 May 2024

Format: In-person only course. It includes practicals and journal club session.

Location: IEO & IFOM, Milan

Timetable
9.15-9.30
Lesson Argument

Course Introduction & Working Groups

Lesson Location
IEO Silver Room
Timetable
9.30-11.00
Lesson Argument

Introduction to proteomics MS

Teachers

Angela Bachi,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
11.15-12.45
Lesson Argument

Quantitative Proteomics/Expression proteomics

Teachers

Alessandro Cuomo,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
14.00-15.30
Lesson Argument

Target/DIA

Teachers

Vittoria Matafora,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
15.45-17.30
Lesson Argument

1) Sample Prep in proteomics (Cattaneo/Parodi in IFOM MS lab)
2) LC-MS/MS in real life (Cuomo in IEO MS-lab) 

 2 groups alternating (40’ per practical)

Timetable
9.15-11.00
Lesson Argument

Interaction and modification proteomics

Teachers

Tiziana Bonaldi,

Affiliations

IEO

Lesson Location
IEO Gold Room
Timetable
11.15-13.00
Lesson Argument

Theory of Data analysis, with statistics

Teachers

Marta Murgia,

Affiliations

University of Padua & Max Planck Institute Biochemistry, Germany

Lesson Location
IEO Gold Room
Timetable
14.00-16.00
Lesson Argument

Data Analysis 1 tutorial (from spectra to protein ID & quantitation and statistics) Es. MaxQuant software

Teachers

Roberta Noberini,

Affiliations

IEO

Lesson Location
IEO Gold Room
Timetable
16.30-17.30
Lesson Argument

Data Analysis 2 functional analysis from quantitative data

Teachers

Vittoria Matafora,

Affiliations

IFOM

Lesson Location
IEO Gold Room
Timetable
9.30-10.45
Lesson Argument

Proteomics in clinical research and Drug Discovery

Teachers

Roberta Noberini,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
11.00-12.00
Lesson Argument

Single cell & Spatial Proteomics

Teachers

Angela Bachi,

Affiliations

IFOM

Lesson Location
IFOM - Meeting Room 1-2
Timetable
12.00-13.00
Lesson Argument

Project preparation by WGs (with TB & AB present for problem discussion and briefing)

Teachers

Tiziana Bonaldi & Angela Bachi

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-15.00
Lesson Argument

SEMMinar "Spaceflight and bed rest. A proteomic view on skeletal muscle inactivity"

Teachers

Marta Murgia,

Affiliations

University of Padua & Max Planck Institute Biochemistry, Germany

Lesson Location
IFOM - Meeting Room 1-2
Timetable
15.30-17.30
Lesson Argument

Project presentation & discussion by working groups

Lesson Location
IEO Gold Room

Organizers: R. Visintin - Dates: 3 June 2024

Format: In-person only course.

Location: IEO Campus, Via Adamello 16 - Milan

Timetable
9.30-11.00
Lesson Argument

Preparing and Delivering an Effective Presentation

Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
11.15-12.45
Lesson Argument

Preparing a good poster

Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Silver Room
Timetable
14.00-16.30
Lesson Argument

Presentation revision

Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IEO Coral Room

Teacher: Myriam Alcalay, IEO - Dates: 4-5-7 June 2024

Format: In person course

Location: IFOM, Via Adamello 16 - Milan

Timetable
9.30-11.00
Lesson Argument

Principles of Effective Writing

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
11.15-12.45
Lesson Argument

Grammar in Scientific English

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.00-15.30
Lesson Argument

Exercises (performed individually by students)

Timetable
9.30-11.30
Lesson Argument

Writing an original manuscript

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
11.45-12.45
Lesson Argument

Plagiarism and Copyrights

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
9.30-13.00
Lesson Argument

Discussion of Abstracts and Presentations before/after

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2

Organizers: Francesco Ferrari (IFOM) & Martin Schaefer (IEO) - Dates: 1-5 July 2024

Timetable
9.30-11.30
Lesson Argument

Crash course in data science

Teachers

Martin Schaefer,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.00
Lesson Argument

Genomic data analysis

Teachers

Giovanni Crisafulli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.30-12.30
Lesson Argument

Practicals on genomic data analysis

Teachers

Giovanni Crisafulli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.30
Lesson Argument

Population genetics

Teachers

Nicola Pirastu,

Affiliations

Human Technopole

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.30
Lesson Argument

Transcriptomic data analysis

Teachers

Riccardo Rossi,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.30
Lesson Argument

Practicals on transcriptomic data analysis

Teachers

Riccardo Rossi,

Affiliations

 IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.30
Lesson Argument

Epigenomics

Teachers

Francesco Ferrari,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.30
Lesson Argument

Practicals on Epigenomics

Teachers

Francesco Ferrari,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.00
Lesson Argument

Transposable elements in the genome

Teachers

Alice Eunjung Lee,

Affiliations

Boston Children's Hospital & Harvard Medical School, Boston

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.00
Lesson Argument

SEMMinar by Alice Eunjung Lee

Lesson Location
IFOM - Conference Room

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

Working with mammalian genomic DNA

Teachers

Ylli Doksani,

Affiliations

IFOM

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

Capturing specific protein–DNA interactions in biological systems by ChIP 

Teachers

Ivan Dellino,

Affiliations

IEO

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

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

Teachers: Valeria Ranzani (INGM), Camilla Ugolini (IIT)

Dates: 15-18 July 2024

Location: INGM

Timetable
10.00-17.30 with lunch break
Lesson Argument

Usable R fundamentals for biologists

 - Developing a scripting attitude: from GUIs to CLIs
 - 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 Tidyverse. When data are “tidy”?
 - Basic tabular manipulation with dplyr
 - Transformations between wide and long
 - Get quick summarizations with pipes and “group_by"

Teachers

Valeria Ranzani,

Affiliations

INGM

Timetable
10.00-17.30 with lunch break
Lesson Argument

The grammar of graphics with ggplot & data visualization

 - The graphical packages of R
 - The generic R graphic devices, plot command, colours
 - Colours in R, R colour brewer and palettes
 - 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
 - (optional) Other graphical packages

Teachers

Valeria Ranzani,

Affiliations

INGM

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

Teachers

Valeria Ranzani (INGM) & Camilla Ugolini (IIT)

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

Teachers

Valeria Ranzani (INGM) & Camilla Ugolini (IIT)

Organizer: B. Bodega (INGM) - Dates: 18-19-20 September 2024

The course will be held at INGM, c/o Padiglione Invernizzi, Via Francesco Sforza, 35 – Milan

Timetable
9.15-9.30
Lesson Argument

Introduction to the course

Teachers

Sergio Abrignani,

Affiliations

INGM

Timetable
9.30-11.00
Lesson Argument

Innate and adaptive immunity

Teachers

Sergio Abrignani,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

Immunological Tolerance

Teachers

Jens Geginat,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

Transposable elements dynamics regulate T-cell exhaustion in tumor microenvinroment

Teachers

Beatrice Bodega,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
9.30-11.00
Lesson Argument

Metabolic regulation of T cell function and fate

Teachers

Teresa Manzo,

Affiliations

University of Turin - Molecular Biotechnology Center "Guido Tarone"

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

B cells

Teachers

Stefano Casola,

Affiliations

IFOM

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

Monoclonal antibodies and immunotherapies

Teachers

Antonio Lanzavecchia,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
16.00-17.30
Lesson Argument

Imaging Immunity

Teachers

Matteo Iannacone,

Affiliations

San Raffaele Scientific Institute

Lesson Location
INGM Conference Room
Timetable
9.30-11.00
Lesson Argument

CAR-T

Teachers

Andrea Biondi,

Affiliations

University of Milan-Bicocca

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

COVID-19: immune response and vaccines

Teachers

Sergio Abrignani,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

Genome editing in T cells for cancer immunotherapy

Teachers

Chiara Bonini,

Affiliations

San Raffaele Institute

Lesson Location
INGM Conference 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

Organizer: Ugo Cavallaro (IEO)

Dates: 7-9 October 2024

The course aims to provide a link between the molecular pathogenesis of cancer, experimental approaches for genetic analysis, and the clinical relevance and applications of cancer genetics in oncology.

Timetable
11.00-12.30
Lesson Argument

Genetic screens

Teachers

Luisa Lanfrancone,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.30-16.00
Lesson Argument

Genomics and big data, from science to medicine and back

Teachers

Giovanni Tonon,

Affiliations

HSR - Milan

Lesson Location
IFOM - Meeting Room 1-2
Timetable
16.00-17.30
Lesson Argument

Modeling cancer genetics

Teachers

Alberto Ciccia,

Affiliations

 Columbia University

Lesson Location
ONLINE LECTURE
Timetable
9.30-11.00
Lesson Argument

Alternative splicing in cancer

Teachers

Juan Valcarcel,

Affiliations

CRG - Barcelona

Lesson Location
ONLINE LECTURE
Timetable
11.00-12.30
Lesson Argument

Viral oncogenesis

Teachers

Susanna Chiocca,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.30-16.00
Lesson Argument

Aneuploidy and cancer

Teachers

Stefano Santaguida,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2
Timetable
11.00-12.30
Lesson Argument

The impact of cancer genetics on precision oncology

Teachers

Pier Francesco Ferrucci,

Affiliations

Gruppo Multimedica, Milan

Lesson Location
IFOM - Meeting Room 1-2
Timetable
14.30-16.00
Lesson Argument

Harnessing genetic alterations in cancer therapy

Teachers

Livio Trusolino,

Affiliations

University of Turin

Lesson Location
IFOM - Meeting Room 1-2
Timetable
16.00-17.30
Lesson Argument

Cancer genetics in the clinic: implications and applications

Teachers

Bernardo Bonanni,

Affiliations

IEO

Lesson Location
IFOM - Meeting Room 1-2

Organizer: Alice Barbaglio (CMCC Foundation) - Date: 14 October 2024

Format: In person course

Location: IEO, Milan

Timetable
9.30-10.00
Lesson Argument

Speakers’ introduction and ice breaking

Lesson Location
IEO Silver Room
Timetable
10.00-10.30
Lesson Argument

- Proposal writing as a transferable skill and a career tool;
- Proposal writing vocabulary; 
- Differences respect to a scientific paper.

Lesson Location
IEO Silver Room
Timetable
10.30-12.30
Lesson Argument

Proposal development plan: from scientific hypothesis development to proposal submission

Lesson Location
IEO Silver Room
Timetable
13.30-14.30
Lesson Argument

CV/personal statement preparation

Lesson Location
IEO Silver Room
Timetable
14.30-15.30
Lesson Argument

Funding opportunities for early stage researchers

Lesson Location
IEO Silver Room
Timetable
15.30-16.00
Lesson Argument

Decompression break

Lesson Location
IEO Silver Room
Timetable
16.00-18.00
Lesson Argument

Let's try: group work

Lesson Location
IEO Silver Room