Teacher: Rosella Visintin - Dates: 14-15 & 22 March 2024
Format: In-Person only course. Lectures and practical activities
Location: IEO, Milan
Teacher: Rosella Visintin - Dates: 14-15 & 22 March 2024
Format: In-Person only course. Lectures and practical activities
Location: IEO, Milan
Introduction to the course
Critical reading of the literature
How to do a Journal club
Experimental design - From hypothesis to conclusions
Case Study
Gender diversity in scientific experiments - Susanna Chiocca - IEO - Milan
Research integrity module:
Famous cases of alleged scientific misconduct
Seminar by William Teale, EMBO Editor
Paper discussion
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.
Crystallization theory and practical
Sebastiano Pasqualato (HT) & Luigi Scietti (IEO)
Basis of crystallography
Marina Mapelli,
IEO
Structure based drug design
Mario Milani,
UNIMI
Pymol tutorial
Sebastiano Pasqualato (HT) & Luigi Scietti (IEO)
Principles of Cryo-EM SPA
Francesca Coscia,
Human Technopole
Anatomy of the microscopes and sample preparation
Paolo Swuec,
Human Technopole
Challenges of a SPA project “Structural Biology impact in drug discovery"
Chiara Rapisarda,
Sanofi, Paris
Working with Cryo-EM microscopes
Paolo Swuec,
Human Technopole
Group 1: Visit to microscopes
Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial
Simona Sorrentino & Malan Silva,
Human Technopole
Group 1: Negative staining tutorial
Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial
Paolo Swuec & Simona Sorrentino,
Human Technopole
Model building tutorial: Coot for model building and structure interpretation of cryoEM maps
Martin Høgholm Jørgensen,
Aarhus University, Denmark
CLEM: correlative light and electron microscopy
Malan Silva,
Human Technopole
Principles of Cryo-ET: sample prep and theory
Philipp Erdmann,
Human Technopole
A Cryo-ET story: “TBD”
Mirko Cortese,
TIGEM
Cryo-ET workshop and tutorial
Philipp Erdmann,
Human Technopole
Principles of NMR
Giovanna Musco,
San Raffaele Hospital
Mass Spectrometry for Structural Biology: XL-MS
Andrea Graziadei,
IEO & HT
Principles of Alpha-fold
Andrea Graziadei,
IEO & HT
Alpha-fold tutorial
Helen Foster,
Human Technopole
Students’ presentation of articles
Ana Casañal & Marina Mapelli
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.
Introduction
Dario Parazzoli - Nils Gauthier,
IFOM
Fixed sample preparation and artifacts
Sara Barozzi,
IFOM
Flow cytometry basic
Simona Ronzoni,
IEO
Flow cytometry: sample preparation and applications
Maria Grazia Totaro,
IFOM
Moving forward: full spectrum flow cytometry
Maria Grazia Totaro,
IFOM
Seminar by Achille Anselmo (HSR research, Ospedale San Raffaele)
Seminar by Francesca Simoncello (IFOM)
Widefield microscopy and optical sectioning
Dario Parazzoli,
IFOM
Colocalization
Simona Rodighiero,
IEO
Multiplexing
Simona Rodighiero,
IEO
Seminar by Grazisa Rossetti (IFOM)
Introduction live cell imaging
Sara Barozzi,
IFOM
Quantitative fluorescence microscopy techniques (F-techniques)
Zeno Lavagnino,
IFOM
Scale your imaging up, from cells to tissues and beyond
Fabrizio Orsenigo,
IFOM
Optical sectioning in 3D with light sheet microscopy
Zeno Lavagnino,
IFOM
The “perfect” microscope utopia: a discussion on experiment design in optical microscopy
Zeno Lavagnino,
IFOM
Electron microscopy
Alexander Mironov,
IFOM
Super resolution
Nils Gauthier,
IFOM
Mechanobiology
Nils Gauthier,
IFOM
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.
Introduction to the course
Nereo Kalebic,
Human Technopole
Development and function of neocortex
Nereo Kalebic,
Human Technopole
Development and function of cranial placodes
Oliver Harschnitz,
Human Technopole
Neuronal guidance and connectivity
Dario Bonanomi,
San Raffaele Hospital
Genome editing in PSC-derived models
Giovanni Fagà,
Human Technopole
Workshop and tutorial: Genome editing
GEDI facility
PSC models to study evolutionary neurobiology
Elena Taverna,
Human Technopole
From neurodiversity to physiopathology: an introduction
Giuseppe Testa,
Human Technopole & IEO
Human PSC models to study neuroimmunology
Oliver Harschnitz
Human Technopole
Single cell manipulation techniques
Elena Taverna,
Human Technopole
In vivo models of neurological diseases
Manuela Ventura,
Human Technopole
- 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.
Group Work JC
Electrophysiological methods in neuroscience
Diletta Pozzi,
Human Technopole
Neuroglial biology and genomics
Jose Davila Velderrain,
Human Technopole
Workshop and tutorial Neurogenomics part I
Cristina Cheroni,
Human Technopole
Workshop and tutorial Neurogenomics part II
Cristina Cheroni,
Human Technopole
JC: Cancer neuroscience
Nereo Kalebic and Filippo Mirabella,
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.
Introduction to digital images
• How an image is obtained, sampling, monochromatic and color images, Fourier transforms
Zeno Lavagnino,
IFOM
Introduction to Fiji and objects segmentation:
Ambra Dondi,
IEO
Hands-on: Nuclear segmentation and spots detection:
Serena Magni,
IFOM
Introduction to Macro Language
Mattia Marenda (IEO), Fabrizio Orsenigo (IFOM)
Colocalization:
Simona Rodighiero,
IEO
Images for publication and guidelines for best practices in image processing
Fabrizio Orsenigo,
IFOM
Tracking in Biology:
Mattia Marenda,
IEO
Collective Motion:
Emanuele Martini,
IFOM
Wrap-up and Discussion
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.
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
Course Introduction & Working Groups
Introduction to proteomics MS
Angela Bachi,
IFOM
Quantitative Proteomics/Expression proteomics
Alessandro Cuomo,
IEO
Target/DIA
Vittoria Matafora,
IFOM
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)
Interaction and modification proteomics
Tiziana Bonaldi,
IEO
Theory of Data analysis, with statistics
Marta Murgia,
University of Padua & Max Planck Institute Biochemistry, Germany
Data Analysis 1 tutorial (from spectra to protein ID & quantitation and statistics) Es. MaxQuant software
Roberta Noberini,
IEO
Data Analysis 2 functional analysis from quantitative data
Vittoria Matafora,
IFOM
Proteomics in clinical research and Drug Discovery
Roberta Noberini,
IEO
Single cell & Spatial Proteomics
Angela Bachi,
IFOM
Project preparation by WGs (with TB & AB present for problem discussion and briefing)
Tiziana Bonaldi & Angela Bachi
SEMMinar "Spaceflight and bed rest. A proteomic view on skeletal muscle inactivity"
Marta Murgia,
University of Padua & Max Planck Institute Biochemistry, Germany
Project presentation & discussion by working groups
Organizers: R. Visintin - Dates: 3 June 2024
Format: In-person only course.
Location: IEO Campus, Via Adamello 16 - Milan
Preparing and Delivering an Effective Presentation
Rosella Visintin,
IEO
Preparing a good poster
Rosella Visintin,
IEO
Presentation revision
Rosella Visintin,
IEO
Teacher: Myriam Alcalay, IEO - Dates: 4-5-7 June 2024
Format: In person course
Location: IFOM, Via Adamello 16 - Milan
Principles of Effective Writing
Myriam Alcalay,
IEO
Grammar in Scientific English
Myriam Alcalay,
IEO
Exercises (performed individually by students)
Writing an original manuscript
Myriam Alcalay,
IEO
Plagiarism and Copyrights
Myriam Alcalay,
IEO
Discussion of Abstracts and Presentations before/after
Myriam Alcalay,
IEO
Organizers: Francesco Ferrari (IFOM) & Martin Schaefer (IEO) - Dates: 1-5 July 2024
Location: IFOM, Via Adamello 16, Milan
Crash course in data science
Martin Schaefer,
IEO
Genomic data analysis
Giovanni Crisafulli,
IFOM
Practicals on genomic data analysis
Giovanni Crisafulli,
IFOM
Population genetics
Nicola Pirastu,
Human Technopole
Transcriptomic data analysis
Riccardo Rossi,
IFOM
Practicals on transcriptomic data analysis
Riccardo Rossi,
IFOM
Epigenomics
Francesco Ferrari,
IFOM
Practicals on Epigenomics
Francesco Ferrari,
IFOM
Transposable elements in the genome
Alice Eunjung Lee,
Boston Children's Hospital & Harvard Medical School, Boston
SEMMinar by Alice Eunjung Lee
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.
Expression of coding and non-coding genes in mammalian genome
Francesco Nicassio,
IIT
Challenges in measuring RNA expression
Matteo Marzi,
IIT
Capturing specific protein–DNA interactions in biological systems by ChIP
Ivan Dellino,
IEO
DNA Cloning strategies
Chiara Bruckmann,
Thermo Fischer
RNA-based therapies
Chiara Bruckmann,
Thermo Fischer
Working with mammalian genomic DNA
Ylli Doksani,
IFOM
CRISPR technology and its applications in drug discovery
Danilo Maddalo,
Genentech
Protein expression and purification
Marina Mapelli,
IEO
Biochemical and biophysical protein characterization
Sebastiano Pasqualato,
Human Technopole
Protein interactions in vitro
Luigi Scietti,
IEO
Measuring protein interactions in vivo
Sara Sigismund,
IEO
Working with Antibodies
Elena Maspero,
IFOM
Protein-DNA interactions involved in DNA repair and DNA replication
Vincenzo Costanzo,
IFOM
Principles of enzymology
Loredano Pollegioni,
Università degli Studi dell'Insubria
Liquid-liquid phase separation
Philipp Erdmann,
Human Technopole
Proteins on DNA – just look at the thing. What can we learn from using single molecule approach
Joanna Jadwiga Andrecka,
Human Technopole
Case Studies
Teachers: Valeria Ranzani (INGM), Camilla Ugolini (IIT)
Dates: 15-18 July 2024
Location: INGM
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"
Valeria Ranzani,
INGM
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
Valeria Ranzani,
INGM
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
Valeria Ranzani (INGM) & Camilla Ugolini (IIT)
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
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
Introduction to the course
Sergio Abrignani,
INGM
Innate and adaptive immunity
Sergio Abrignani,
INGM
Immunological Tolerance
Jens Geginat,
INGM
Transposable elements dynamics regulate T-cell exhaustion in tumor microenvinroment
Beatrice Bodega,
INGM
Metabolic regulation of T cell function and fate
Teresa Manzo,
University of Turin - Molecular Biotechnology Center "Guido Tarone"
B cells
Stefano Casola,
IFOM
Monoclonal antibodies and immunotherapies
Antonio Lanzavecchia,
INGM
Imaging Immunity
Matteo Iannacone,
San Raffaele Scientific Institute
CAR-T
Andrea Biondi,
University of Milan-Bicocca
COVID-19: immune response and vaccines
Sergio Abrignani,
INGM
Genome editing in T cells for cancer immunotherapy
Chiara Bonini,
San Raffaele Institute
Teacher: M. Cereda (IIGM & UNIMI) - Dates: 23-25 September 2024
Location: Silver & Platinum Room, IEO, Via Adamello 16, Milan
Theoretical lessons and practicals
- Course Introduction
- Programming imprinting
- Code writing
R basics: language structure, data types, object-oriented programming
- Data manipulation
- Performance testing
Writing R Extensions (by Uberto Pozzoli)
- Bioconductor & Data Visualization (by Fabio Iannelli)
- Memory Handling
Data Communication + Build interactive web app: Shiny
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.
Introduction to Python/Jython programming languages:
Hands-on: practice on a nuclei segmentation macro and comparison with Jython language
Emanuele Martini, Fabrizio Orsenigo & Serena Magni,
IFOM
More complex image analysis and Analysis of Multiple Images
Hands-on: nuclei segmentation with spots count and intensity measurement
Fabrizio Orsenigo & Serena Magni,
IFOM
Introduction to machine learning and deep learning in image analysis
Hands-on: Semantic segmentation/pixel classification with Labkit
Damian Edward Dalle Nogare,
Human Technopole
Image restoration and instance segmentation using Deep Learning in Python
Hands-on: Image restoration and nuclear segmentation with Deep Learning algorithms
Joran Deschamps,
Human Technopole
Segmentation in tissues using Stardist with QuPath software:
Hands-on: Cell segmentation in tissues using Stardist and cell-type classification in different populations
Chiara Soriani,
IEO
Cell segmentation using Cellpose software in Python:
Hands-on: Segmentation of cells and nuclei using CellPose and evaluation of cytoplasmic signal using local Jupyter notebooks
Mattia Marenda,
IEO
Organizer: Ugo Cavallaro (IEO)
Dates: 7-9 October 2024
Location: IFOM, Via Adamello 16, Milan - Meeting Room 1-2, bldg. 9
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.
Genetic screens
Luisa Lanfrancone,
IEO
Genomics and big data, from science to medicine and back
Giovanni Tonon,
HSR - Milan
Modeling cancer genetics
Alberto Ciccia,
Columbia University
Alternative splicing in cancer
Juan Valcarcel,
CRG - Barcelona
Viral oncogenesis
Susanna Chiocca,
IEO
Aneuploidy and cancer
Stefano Santaguida,
IEO
The impact of cancer genetics on precision oncology
Pier Francesco Ferrucci,
Gruppo Multimedica, Milan
Cancer genetics in the clinic: implications and applications
Sara Mannucci,
IEO
Teacher: Davide Mazzoni, UNIMI - Dates: 24 & 29 October, 5 November 2024
Location: Cascina Brandezzata, Via Ripamonti, Milan
General principles of qualitative analysis
Collecting and working with different qualitative data
The main approaches to qualitative analysis
The use of software and AI in qualitative research
Applications of qualitative analysis in medical humanities (with Valeria Sebri)
Organizer: Alice Barbaglio (CMCC Foundation) - Date: 30 October 2024
Format: In person course
Location: IEO Gold Room, Via Adamello 16 Milan
Speakers’ introduction and ice breaking
- Proposal writing as a transferable skill and a career tool;
- Proposal writing vocabulary;
- Differences respect to a scientific paper.
Proposal development plan: from scientific hypothesis development to proposal submission
CV/personal statement preparation
Funding opportunities for early stage researchers
Decompression break
Let's try: group work