Advanced Neurogenomics

08 Nov 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Primer on data distribution and visualization

11 Nov 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

RNA sequencing

15 Nov 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

MApping and counting

18 Nov 2024 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

An introduction to long read Sequencing: Long versus short reads. Theory of Nanopore Sequencing. Hardware description of ONT sequencing. Flow cells and chemistries. Advantages of long-read transcriptomics. Library preparation methods. Targeted sequencing, Adaptive Sampling. Hands-on: running an ONT experiment, familiarization to sequencing hardware.

22 Nov 2024 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

From Signal to Reads - Part 1: A very gentle introduction to neural networks. Training, Forward Pass, Activation and Loss functions. Backpropagation and Gradient Descent (qualitative view). Semi-practical: Tinker with a Neural Network. Feedforward versus Recurrent Neural Networks. Qualitative introduction to Transformers and Self-Attention. Familiarization to ONT data formats. Raw and Basecalled reads. Semi-practical: Squiggle visualization.

25 Nov 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Differential gene expression

25 Nov 2024 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

From Signal to Reads - Part 2: History of ONT basecalling. Signal conditioning and Kmer models. Introduction to Hidden Markov Models. The Viterbi algorithm. Examples of HMM applications in biology. HMM basecallers. RNN basecallers. Modern, Transformer-based basecallers (Dorado). Direct RNA sequencing features. Duplex basecalling.

29 Nov 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Clustering

06 Dic 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Gene Ontology and Gene Set Enrichment

09 Dic 2024 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

Probing RNA life cycle - Part 1: Study of RNA splicing and Isoform Analysis. RNA metabolic labelling. Subcellular localization analysis methods. (Fractionation, proximity labelling). RNA-Protein Interaction Profiling. RNA crosslinking (chemical, UV). Native versus denaturing methods. Enrichment analysis, mutation profiling and noise. CLIP, CRAC, XRNAX techniques.

13 Dic 2024 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

Probing RNA life cycle - Part 2: RNA-RNA interactions: RBP-oriented methods. In situ proximity ligation. Biological applications of interaction studies. High-throughput RNA Structure Determination. SHAPE. RNA polyA tail length estimation by short and long-read sequencing. RNA modifications. Covalent modification profiling. Bulk versus single-molecule methods.

16 Dic 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Network theory and its application to biological problems

20 Dic 2024 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Examples of applications of network theory: selected neurobiology papers

10 Gen 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Hands-on: Analysis of differential expression using DESeq2

13 Gen 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Hands-on: Analysis of GO terms and pathways using WebGestalt

17 Gen 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Riboseq e miRNAs

20 Gen 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Single-cell RNA-seq, methods and analysis

24 Gen 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Single-cell RNA-seq, applications to the nervous system

03 Feb 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Exploration Allen Brain Atlas

07 Feb 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Lecture 14: Spatial transcriptomics

10 Feb 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Lezione 15: Explore the Allen Brain Atlas

14 Feb 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Mass-spectroscopy based proteomics for the neurosciences

24 Feb 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Local translation of synaptic proteins and ribosomes

07 Mar 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

Single cell epigenetics

10 Mar 2025 (2h 00m)

ALESSANDRO Cellerino - Corso (attività didattica) - Mista

StartMAp and PatchSeq

26 Maggio 2025 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

Practical Functional Genomics Data exploration: Hands-on lesson: Exploring the ENCODE database. Multi-omic data formats. How to re-analyse publicly available data, the lazy way. Integrating and visualising ENCODE data in the UCSC web browser.

27 Maggio 2025 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - In presenza

A primer on Genome Assembly - Part 1: The history of the Human Genome Project. HGP versus Celera approach. The legacy of the HGP. The foundation of modern genome assembly. Steps to build a genome. The problem of repeats. Assembler algorithms and their evolution. Genome quality evaluation. Quantitative Metrics (N50, NG50). Sequence-level and Gene Content Completeness. Contamination Screening.

30 Maggio 2025 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - A distanza

A primer on Genome Assembly - Part 2: Genome scaffolding strategies (mate pairs, paired and linked reads, optical mapping, HiC). Long reads and applications in genome assembly. Genome polishing. Towards the Telomere-to-telomere genome. Modern Genome Assembly practice. Assembly of homozygous versus Heterozygous diploid genomes. Collapsed, semi-collapsed and phased genomes. Genome phasing (Trio binning, long read and methylation phasing). Science-driven applications of high-quality genomes).

09 Giu 2025 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - A distanza

Genome Annotation: Transcriptome Assembly, de novo and reference-based approaches. Transcriptome QC metrics. Structural Annotation; Ab initio, evidence-based, homology-based and hybrid methods. Probabilistic parameters of ab initio models. Long Reads for annotation. CAGE and 3P-seq. Functional Annotation; homology transfer, Gene Ontology terms and Protein Domains. HMM representation of sequence profiles and alignment for database searches. Artificial Intelligence and Genomes; Evo2.

10 Giu 2025 (2h 00m)

LUCA Pandolfini - Corso (attività didattica) - A distanza

An overview on Comparative Genomics: Individual Complete genomes. Pangenomes: how to build and represent them; Sequence Tube Map. Pangenomes and human variation. Multi-species analysis and species evolution; Orthologous and Paralogous genes; Evolution by gene duplication. Synteny and Collinearity; Binary Species comparisons; GENESPACE. Comparative analyses of human brain evolution and gyrification. Transposable Element Exonification driving evolution. A glimpse of comparative 3D-Genomics.