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

All Courses

Teacher: Rosella Visintin - Dates: 7, 8, 21 January 2021

Format: The course will be held online, with lectures and practical activities

Thursday, 7 January, 2021
9.30-13.00

- Critical reading of the literature
- How to read a scientific paper
- How to do a Journal Club

14.00-18.00

- Experimental Design
- Scientific methods and experimental design
- Standard of conduct – scientific integrity vs scientific misconduct
- Time management

Friday, 8 January, 2021
9.30-13.00

- Science communication
- How to make a good presentation
- How to make a good poster

14.00-18.00

How to write a good paper

Thursday, 21 January, 2021
9.30-13.00

Group Practical Activity (part 1)

14.00-18.00

Group Practical Activity (part 2)

Organizer: Ylli Doksani & Marina Mapelli

Dates: 11-15 January 2021

Format: The course will be held online

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

Monday, 11 January, 2021
9.30-15.30

Working with DNA and RNA

9.30-10.15

Working with mammalian genomic DNA

Ylli Doksani - IFOM
10.15-11.00

Visualization of DNA structures in Electron Microscopy

Massimo Lopes - UZH
11.00-11.45

Cloning strategies

Daniele Piccini - IFOM
14.00-14.45

Expression of coding and non-coding genes in mammalian genome

Francesco Nicassio - IIT
14.45-15.30

Challenges in measuring RNA expression

Matteo Marzi - IIT
Tuesday, 12 January, 2021
9.30-16.00

Genetic Engineering

9.30-10.15

Fundamentals of gene targeting

Stefano Casola - IFOM
10.15-11.00

Gene therapy

Giuliana Ferrari - HSR Milan
15.00-15.45
CRISPR technology and its applications in drug discovery
Danilo Maddalo - Roche
Wednesday, 13 January, 2021
9.30-12.00

Protein Biochemistry

9.30-10.15

Protein expression

Marina Mapelli - IEO
10.15-11.00

Measuring protein interactions in vitro

Marina Mapelli - IEO
11.00-11.45

Measuring protein interactions in vivo

Sara Sigismund - IEO
Thursday, 14 January, 2021
9.30-15.00

Protein Biochemistry

9.30-10.30

Working with antibodies

Simona Polo - IFOM
10.45-11.45

Capturing specific protein–DNA interactions in biological systems by Chromatin Immunoprecipitation

Ivan Dellino - IEO
14.00-15.00

Principles of enzymology

Loredano Pollegioni - University of Insubria
Friday, 15 January, 2021
9.30-13.00

Protein Biochemistry

9.30-10.30

Biochemistry of Ubiquitin

Sebastiano Pasqualato - IEO
10.45-13.00

Case studies

Teachers: Virginia Sanchini, UNIMI & Silvia Camporesi, Kings' College London

PART ONE – Basics of bioethical reasoning V. Sanchini: 11,13,14,15 January 2021;

PART TWO – Reproductive Ethics S. Camporesi 18,25 January; 1,8,15 February 2021 The course aims to provide a brief overview of the main areas of bioethics reasoning. After some introductory notions on the origin of the word “bioethics”, the main historical cases related to its development, and the presentation of the main ethical theories and approaches used in bioethics reflection, the course will explore the main ethical issues related to the fields of clinical ethics and research ethics. A specific module will be devoted to reproductive ethics.
Monday, 11 January, 2021
9.30-13.30
-Introduction to the course. -Dilemmas and disagreements: the toolbox of bioethics reasoning. -An introduction to moral theories.
Virginia Sanchini - UNIMI
Wednesday, 13 January, 2021
9.30-11.30
Bioethics: origin, domains, and paradigmatic cases
Virginia Sanchini - UNIMI
14.30-16.30
Papers' presentation
Virginia Sanchini - UNIMI
Thursday, 14 January, 2021
9.30-13.30
-The ethics of clinical research: informed consent; therapeutic misconception; clinical equipoise -Papers' presentation
Virginia Sanchini - UNIMI
Friday, 15 January, 2021
9.30 - 13.30
-An introduction to clinical ethics: clinical ethics committees; ethics consultation; patient-physician relationship models. -Papers' presentation
Virginia Sanchini - UNIMI
Monday, 18 January, 2021
10.30-12.30
Naturalness
Silvia Camporesi - Kings College - London UK
Monday, 25 January, 2021
10.30-12.30
Moral status, 14-day limit
Silvia Camporesi - Kings College - London UK
Monday, 1 February, 2021
10.30-12.30
Personhood
Silvia Camporesi - Kings College - London UK
Monday, 8 February, 2021
10.30-12.30
Disability and Impairment
Silvia Camporesi - Kings College - London UK
Monday, 15 February, 2021
10.30-12.30
Performativity
Silvia Camporesi - Kings College - London UK

Dates: 18-20, 22 January 2021

Organizers: Dario Parazzoli and Nils Gauthier

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.

 

Monday, 18 January, 2021
9.00-12.45

- Introduction to the course
  Dario Parazzoli - IFOM

- Fixed sample preparation and fluorescence tagging
  Sara Barozzi - IFOM

- From samples to histopathology
  Claudio Tripodo - IFOM

- Molecular Pathology and translational research
  Salvatore Pece - IEO

14.30-16.30

- Flow Cytometry: basics and applications
  M.Grazia Totaro-Simona Ronzoni - IFOM, IEO

Tuesday, 19 January, 2021
9.00-12.30

- Widefield Microscopy
  Dario Parazzoli- IFOM

- Optical sectioning methods
  Simona Rodrighiero - IEO

14.00-15.00

Colocalization
  Massimiliano Garrè - IFOM

Wednesday, 20 January, 2021
9.00-11.30

- Super resolution: STED, STORM, PALM, SIM
  Dario Parazzoli, Mario Faretta - IFOM, IEO

- Electron Microscopy, basics
  Alexandre Mironov - IFOM

Friday, 22 January, 2021
9.00-13.00

- Image analysis
  Emanuele Martini - IFOM

- Applications of advance microscopy techniques: from tissue to cell to molecular scale
  Nils Gauthier - IFOM

Organizers: A. Bachi, T. Bonaldi, D.Pasini - Dates: 1-8 February 2021

Monday, 1 February, 2021
9.30-11.00

Introduction to proteomics MS

Angela Bachi - IFOM
11.15-12.45

Quantitative Proteomics

Alessandro Cuomo - IEO
14.00-15.30

Targeted Proteomics

Vittoria Matafora - IFOM
15.45-17.00

PTM analysis by MS

Tiziana Bonaldi - IEO
Tuesday, 2 February, 2021
9.30-10.30

Proteomics in epigenetic research

Tiziana Bonaldi - IEO
10.45-12.00

Proteomics in clinical research and Drug Discovery

Roberta Noberini - IEO
14.00-17.00

Open discussion preparation

Wednesday, 3 February, 2021
9.30-12.00

Proteomics data analysis and Systems biology

Mauro Fasano - University of Insubria
14.00-16.00

Open discussion: proteomics in practice

Thursday, 4 February, 2021
9.00-10.30

Trascription and Epigenomics

Serena Ghisletti - IEO
14.00-16.00

Journal Club session

Matteo Marzi - IIT
Friday, 5 February, 2021
9.00-10.30

Next Generation Sequencing

Diego Pasini - IEO - Milan
11.00-12.30

Single Cell Analyses

Giuseppe Testa - IEO
14.00-15.30

The Genomics Unit

Luca Rotta - IEO
15.45-17.00

Clinical Genomics

Luca Mazzarella - IEO - Milan
Monday, 8 February, 2021
9.00-10.30

Bioinformatics approaches

Giulio Pavesi - UNIMI
11.00-12.30

non-coding RNAs

Francesco Nicassio IIT - Milan
14.00-16.00

Metagenomics

Nicola Segata - IEO

Teacher: Nicholas Del Grosso - Dates: 2-5 February 2021

The free, open-source R programming language is currently the most popular computational statistics environment, and is used heavily in a wide variety of scientific fields and industries. In this introductory-level course, we’ll use R to review core concepts in statistics, both learning the simple mathematics underlying statistics and how to apply statistics as a tool for making decisions during scientific data analysis. While R is a programming language, this course will focus purely on the math and visualization aspects of R in order to develop a stronger foundation in statistics, with the goal of developing confidence in statistical reasoning for the purpose of scientific data analysis and reporting. No prior mathematics or programming knowledge is required for this workshop.

Tuesday, 2 February, 2021
9.30-11.15

Course Orientation: Statistics and R

11.15-12.30

Levels of Measurement:
- How do we compare numbers to each other? How do we visualize these numbers to match these descriptions?
- Using built-in R functions and an RMarkdown worksheet, groups describe and visualize some data

 

14.00-15.30

Sample Variance:
Ways to describe data sets according to the data's distribution.
- Moments of Ratio data (mean, variance, skew, kurtosis)
- Moment of Ordinal Data (median, rank ordering, percentile)
- Descriptive Data Visualization (Point, Hist, Cum. Hist, Box, Boxen, Violin, etc)

15.40-17.30

Probability Arithmetic:
- What is probability
- Calculating joint probability
- Data Distributions vs. Probability Distributions
- Joint Probability Distributions
- Marginal Probability
- Visualizing Probability Distributions

Wednesday, 3 February, 2021
9.30-10.40

Warmup and Review over Day1: Data Description
- Review of terminology, build statistical communication skills
- What is tabular data
- What is a dataframe
- How is tabular data stored on the computer
- How can we load/save the data into/out of R
- Data classes in R
- How do we organize and explore dataframes in R?

10.55-12.10

Inference from Data:
- What is statistical inference
- Sample vs. Population
- Data Collection, Randomness, Bias, and Noise
- Generative Models
- Sample Size
- Data Rejection and Outliers
- The Law of Small Numbers, The Law of Large Numbers
- Data Generation in R

13.40-14.45

The Central Limit Theorem:
- the Central Theorem
- The Normal Distribution
- Z Scores and T Scores
- qqplots
- Demonstration of Central Theorem

15.00-17.30

Error Bars, Confidence Intervals, and the Central Limit Theorem:
- Confidence Intervals (Bootstrap demonstration)
- Selecting and Interpreting Error Bars (Descriptive vs Inferential, SD vs. SEM vs. CI)
- RMarkdown Project

Thursday, 4 February, 2021
9.30-10.35

Warmup and Review over Day 2: Confidence Intervals

10.50-12.00

T-Tests:
- Null-Hypothesis Testing
- What is the t-test
- Independent Samples vs - Paired Samples
- P-Values
- Reporting T-test results
- Nonparametric comparisons of two samples (Mann-Whitney and Wilcoxen)

13.30-15.10

Correlations and the Normal Distribution:
- Definition
- Correlations and Heteroscadiscity
- Pearson, Spearman, etc.
- Visualizing Correlations
- Reporting Correlations

15.25-17.40

Linear Regression:
- Regression vs Correlation
- Data Modelling
- R Formula Syntax
- R-squared
- Visualizing and Reporting Regression Analysis

Friday, 5 February, 2021
9.30-11.00

Warmup and Review Over Day 3

11.20-12.30

ANOVA:
- Sum of Squares
- Variance Minimization
- Calculation of Univariate ANOVA
- Reporting ANOVA

14.00-14.20

- The Problem of Multiple Comparisons
- Tukey's Post-Hoc Test

14.20-15.55

Special Topic: The Grammar of Graphics

15.55-17.25

Final Project: Real-World Data Analysis

Dates: 9-12 February 2021

 

Organizers: Francesco Ferrari  & Martin Schaefer

The course will focus more on lecture, not on practical tutorials, unless the presenter wants to show some tools during the lecture.

 

Tuesday, 9 February, 2021
9.30-17.30

FOCUS ON GENOMICS

9.30-12.30

Genomics sequence search and alignment

Fabio Iannelli - IFOM - Milan
14.30-17.30

- Mutations calling (including copy number variations and structural variants)

- Cancer genomics resources and databases (e.g. cancer genome portal, TCGA, ICGC resources and datasets)

Fabio Iannelli - IFOM - Milan
Wednesday, 10 February, 2021
9.30-17.30

FOCUS ON TRANSCRIPTOMICS

9.30-12.30

RNA-seq (including expression quantification and splicing)

Tommaso Leonardi - IIT Milan
14.30-17.30

Single cell RNA-seq

Giulio Pavesi - UNIMI
Thursday, 11 February, 2021
9.30-17.30

FOCUS ON EPIGENOMICS

9.30-12.30

- Bioinformatics data analysis for ChIP-seq and other techniques to study 1D chromatin organisation

- Annotations of TFBS (annotation of ChIP-seq peaks e.g. to find the target gene of a TF)

Marco Morelli - San Raffaele - Milan
14.30-17.30

- Large scale collaborative projects as a source of datasets (ENCODE, Roadmap epigenomics, FANTOM, IHEC etc)

- Other epigenomics data (e.g. DNA methylation)

Margherita Mutarelli - CNR
Friday, 12 February, 2021
9.30-12.30

FOCUS ON INTEGRATIVE/FUNCTIONAL ANALYSES

9.30-12.30

- Integrative and functional pathway-level analysis of genomics data

- Functional classes analysis (e.g. GO analysis)

- Pathway level analysis of genomics data

- Topological pathways and gene regulatory networks

Chiara Romualdi - University of Padova

Organizer: Myriam Alcalay & Ugo Cavallaro IEO Milan

Dates: 15-17 February 2021

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

Monday, 15 February, 2021
9.30-12.00

Approaches for the discovery of genetic abnormalities in cancer

9.30

Genomics and big data, from science to medicine and back

Giovanni Tonon - HSR - Milan
11.00

Genetic Screens

Luisa Lanfrancone - IEO
14.30-17-30

Issues in Cancer Genetics

14.30

Alternative splicing in cancer

Juan Valcarcel - CRG - Barcelona
16.00

Cancer stem cell genetics

Giuseppe Testa - IEO - Milan
Tuesday, 16 February, 2021
9.30-15.30

Translational aspects of Cancer Genetics

9.30

Translational and therapeutic implications of tumor heterogeneity

Livio Trusolino - University of Turin
11.00

How the environment affects cancer genomics

Luca Mazzarella - IEO - Milan
14.00

Harnessing genetic alterations in the clinic

Alberto Bardelli - Dept of Oncology - Univ of Torino and IRCCs - Candiolo
Wednesday, 17 February, 2021
9.30-12.30

Cancer Genetics in medical practice

9.30

Perspectives of clinically oriented cancer genetics

Salvatore Pece - IEO - Milan
11.30

Cancer genetics in the clinic: implications and applications

Bernardo Bonanni - IEO - Milan

Teacher: Myriam Alcalay, IEO

Dates: 22-23-25 February 2021

Monday, 22 February, 2021
9.30-12.30

Principles of Effective Writing

Grammar in Scientific English

14.00-15.00

Exercises (performed individually by students)

  • Multiple choice exercises
  • Sentence rewrites
Tuesday, 23 February, 2021
9.30-11.30

Writing an original manuscript

11.45-12.45

Plagiarism and Copyrights

afternoon

Abstract rewrite: Students will re-write their abstract on the basis of what they learned and send it to Prof. Alcalay by 18.00.

Thursday, 25 February, 2021
9.30-12.30

  Abstracts: before/after

Organizer: Fabio Stella (University of Milan Bicocca) - Dates: 8-12 March 2021

The course aims to provide a gentle introduction to different components of machine learning. In particular, the course will first give the framework of machine learning and then will devote specific lectures to different models and techniques. Attention will be devoted to Bayesian networks, machine learning methods and models for the analysis of single cell data analysis, for analyzing the spread of infectious diseases, and to reinforcement learning to solve sequential decision-making problems.

 

Monday, 8 March, 2021
15.00-18.00

What is Machine Learning?

Understanding what machine learning is, where it comes from and what are its goals is crucial in designing data-driven applications in the life and clinical sciences. We will discuss these points, as well as the general workflow of setting up a machine learning model, illustrating them with a toy example supported by R code.

Marco Scutari - Dalle Molle Inst. for Artificial Intelligence - Switzerland
Tuesday, 9 March, 2021
15.00-18.00

Practical Bayesian Networks for Clinical Data

We will explore how to use network models to analyse clinical data by reproducing the paper "Bayesian Networks Analysis of Malocclusion Data", from learning the model to using inference to assess it and produce clinical insights.

Marco Scutari - Dalle Molle Inst. for Artificial Intelligence - Switzerland
Wednesday, 10 March, 2021
15.00-18.00

Basic Machine Learning for single-cells data analysis

The important points on single cell RNAseq data preprocessing; Data reduction and clustering, Cluster's stability, Extracting biological knowledge from clustered cells: from XL-mHG test to partially connected autoencoders.

Marco Beccuti / Raffaele Calogero / Francesca Cordero - University Turin
Friday, 12 March, 2021
15.00-18.00

A gentle introduction to reinforcement learning

Reinforcement learning is responsible of probably the most amazing recent achievement in artificial intelligence, i.e., the defeat of Lee Sedol, a master player of the game of Go. In this lecture we introduce different types of machine learning including multi-armed bandits and deep reinforcement learning. We provide concrete examples where reinforcement learning is used to address and solve complex sequential decision problems in health and other application domains.

Fabio Stella - University Milan Bicocca
Monday, 15 March, 2021
15.00-18.00

Building an Infectious Disease Model: SIR and Beyond

We begin by introducing the most basic Susceptible–Infectious–Removed (SIR) model to build up the framework for compartment-based models which capture the key features of infection dynamics. The theory will be illustrated using the data on the suppression of COVID-19 outbreak in the municipality of Vo’, Italy, using the free software environment for statistical computing and graphics R.

Alessandra R. Brazzale - University Padua

Teachers: U. Pozzoli, F. Iannelli, M. Cereda

Teorethical lessons and practicals held online

 

Monday, 22 March, 2021
9.30-10.00

Course Introduction: description and objectives

10.00-12.30

Programming Languages: similarities and differences

14.30-17.30

R: language structure, data types, examples

Tuesday, 23 March, 2021
9.30-11.00

Bioconductor for genomic data

11.00-12.30

Data Visualization

14.30-16.30

Data Communication - R Markdown

16.30-17.30

Implementing a data analysis pipeline using Bioconductor and R Markdown

Wednesday, 24 March, 2021
9.30-10.30

Data Communication - Shiny

10.30-12.30

Code writing and performance testing

14.30-17.30

Parallelization

Thursday, 25 March, 2021
9.30-12.30

R-package development

14.30-17.30

Extending R through C/C++: Rcpp

Friday, 26 March, 2021
9.30-12.30

Assignment presentation and discussion with students

Teacher: Nicholas Del Grosso - Dates: 14-16 April 2021

The free, open-source Python programming language is currently the most popular tool for computational research and data analysis. In this introductory-level course, we’ll develop both programming and data analysis skills through hands-on projects, learning both the core Python syntax and the key scientiϐic libraries in the Python ecosystem. Along the way, we’ll also explore best practices in computational research, including transparent reporting, open research data management, and tool validation, exploring how these practices both make our research work more effective and produce higher-quality science.
 

Wednesday, 14 April, 2021
9.30-18.00

Exploratory Tabular Data Analysis with Pandas, Holoviews, Seaborn, and Jupyter Lab
• How to perform automated Excel-like analyses in the Python programming language using that Pandas Python package and the DataFrame data structure.
• How to efficiently produce accurate graphs and charts from Pandas DataFrames using the Holoviews and Seaborn plotting packages.
• How to apply good scientific practices to exploratory data analysis using the Jupyter Lab Python programming environment.
 

Thursday, 15 April, 2021
9.30-18.00

Numerical and Statistical Simulation and Visualization with Numpy, Matplotlib, and Scipy-Stats
• How to manipulate data using the array data structure using the Numpy Python package and visualize it with publication-quality figures using the Matplotlib Python package.
• How to generate data with different probability distributions and perform statistical analysis (t-tests, anova, binomial tests, etc) on the data.
• How to test intuitions about statistics by translating real-world reasoning into code.
 

Friday, 16 April, 2021
9.30-18.00

Custom Analysis Software Tool Creation with Python and PyTest
• How to write reusable functions in order to perform reproducible analysis on similar datasets
• How to apply core programming principles (functions, loops, and conditionals) to abstract scineitic problems in bioinformatics.
• How to use the scientific method to conϐidently produce validated, reproducible research tools via code testing frameworks and the test-driven-development approach.

Organizer: Jernej Zupanc, Seyens Ltd. - Dates: 3-4 June 2021

This is an interactive webinar, where you will learn to effectively communicate your own scientific ideas and results by applying best visual communication practices to your research communication. You will understand the principles and useful design approaches used by experts. You will get actionable advice and feedback on your own pre-submitted materials.

 

Thursday, 3 June, 2021
9.00-16.30 (with lunch break)
  • Communicating with scientific vs non-scientific audiences
  • Visual perception and what humans find intuitive
  • Visual organization: how to structure to simplify comprehension
  • Eye-flow: effortlessly guide the audience through the design
  • Colors: how to amplify, not ‘fancify’
  • Feedback and discussion on your pre-submitted figures
  • Graphical abstract drawing exercise & group work: draw a sketch of your research and get feedback from peer scientists and the facilitator
Friday, 4 June, 2021
9.00-13.30
  • Slides that amplify your messages when presenting
  • Feedback and discussion on your pre-submitted slides
  • Posters: strategy and process for creating posters that attract and explain
  • Feedback and discussion on your posters

Teachers: D. Monzani (IEO) - Dates: 9-16-23-30 June 2021; 7 July 2021

The course aims at providing an introduction to Structural Equation Modelling (SEM) using Mplus for social and behavioral sciences. The course will cover basic principles of SEM, introduction to Mplus, exploratory and confirmatory factor analysis, exploratory structural equation modeling, multiple group analysis and test of measurement invariance, mediation and moderation with observed and latent variables. It includes theoretical training, tutorials and practical examples with real data.

 

Wednesday, 9 June, 2021
14.00-18.00
  • Theoretical introduction to SEM
  • Practical introduction to Mplus language
Wednesday, 16 June, 2021
14.00-18.00
  • Path analysis and SEM
  • Output reading and interpretation
Wednesday, 23 June, 2021
14.00-18.00
  • Exploratory Factor Analysis (EFA)
  • Exploratory Structural Equation Modeling (ESEM)
Wednesday, 30 June, 2021
14.00-18.00
  • Confirmatory Factor Analysis (CFA)
  • Comparison of competing models
  • Test of invariance
Wednesday, 7 July, 2021
14.00-18.00
  • Mediation models with observed and latent variables
  • Moderation models with observed and latent variables

Teacher: M. Masiero (UNIMI) - Dates: 5-6-8 July 2021.

The communication process has a pivotal role in healthcare, and it is a milestone in the relationship between doctors and patients. Even though, communication skills are not innate, they can be learned and enhanced. This course will focus on the classic theory of the psychology of communication and on how communication may be used to create a good relationship between doctor and patient.

Monday, 5 July, 2021
9.00-13.00

- Doctor-Patient communication: why is it important?

- The Shannon and Weaver model

- Grice’s Conversational maxims

- Verbal and Nonverbal communication

Tuesday, 6 July, 2021
9.30-12.30

- Pragmatic of Human Communication

- Mis-communication

- The communication of the bad news

- The SPIKES model.

Thursday, 8 July, 2021
9.30-12.30

- Risk Perception

- Prospect Theory

- Framing effect and Communication

Organizer: F. Ciccarelli - Dates: 20-22 September 2021

Schedule to be communicated

Teachers: Paola Galimberti (UNIMI) & Arnaud Ceol (IEO). Dates: 27-28 September; 4-5 October 2021.

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

The course is organized in the context of the ENABLECARES European project (https://enablecares.eu/).

Schedule to be communicated.