Thematic Modules

Module 1

Fundamental concepts of bash and R programming

Bash shell e scripting
Fundamental concepts of programming languages
R programming: a language and software tailored for statics data analysis

Module 2

Web resources for bioinformatics

Basics of databases and core biological examples
Genome Browsing. the UCSC Genome Browser
International projects and Consortia: main examples.
Principles of FAIR data for research.

Module 3

Fundamental concepts of statistics for bioinformatics

Data types, distributions and descriptors, frequency and probability, concept of information and entropy.
Main tests of statistical significance, both parametric and non-parametric.
Introduction to complex network theory.
Introduction to Machine learning (ML) and most used ML algorithms.

Introduction to Deep learning (DL)

Module 4

Genomics and Transcriptomics

Microarrays: platforms, data format, main applications (e.g. miRNA microarrays, mRNA microarrays).
High-throughput sequencing (HTS): platforms, data, main applications (WGS, WES, RNA-Seq, ChIP-Seq, scRNA-Seq, etc.).
WGS/WES: purposes, data format, standard analysis pipeline
RNA-Seq: purposes, data format, standard pipeline of analysis
ChIP-Seq: purposes, data format, standard analysis pipeline.
Tutorial: RNA-Seq (from raw sequencing data to normalized data matrix, differential expression analysis, and statistical analysis of over-represented functional annotations in a list of genes of interest)
Tutorial: microarrays (standard analysis pipeline)
Tutorial: WES data analysis
Tutorial: ChIP-Seq data analysis
Tutorial: Cytoscape (visualization and analysis of gene networks)

Module 5

Structural bioinformatics, interactions and biological networks

Substitution matrices; sequence alignment; dynamic programming; scoring matrices.
Multiple alignments; profiles, LOGOs
Database searches: BLAST, PSI-BLAST, HMM
Prediction of: secondary structure; sequence motifs; transmembrane helices; 3D structure; post-translational modifications (glycosylation, etc.). Intrinsically disordered regions.
Structural analysis: programs for visualization, analysis and comparison of 3D structures.
Protein-protein, protein-nucleic acid, protein-peptide, protein-small molecule interactions.
Use of major interaction databases (IntAct and STRING) to build a network of interaction
PPI networks. Analysis of protein interactions using Cytoscape

Module 6

Pharmaceutical chemoinformatics

Protein-protein molecular docking
Structure-based protein, peptide and drug design. Humanization of antibodies.
Protein-small molecule interactions. Drug target-drug interactions. Protein-small molecule docking. Virtual screening.
Introduction to QSAR, PCA for drug design, Fragment-based drug design.

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