Lecture
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08 Nov 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Primer on data distribution and visualization
11 Nov 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
RNA sequencing
15 Nov 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
MApping and counting
18 Nov 2024 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 - Course (teaching activity) - Face to face
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 - Course (teaching activity) - Both face to face and online
Differential gene expression
25 Nov 2024 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 - Course (teaching activity) - Both face to face and online
Clustering
06 Dec 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Gene Ontology and Gene Set Enrichment
09 Dec 2024 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 Dec 2024 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 Dec 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Network theory and its application to biological problems
20 Dec 2024 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Examples of applications of network theory: selected neurobiology papers
10 Jan 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Hands-on: Analysis of differential expression using DESeq2
13 Jan 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Hands-on: Analysis of GO terms and pathways using WebGestalt
17 Jan 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Riboseq e miRNAs
20 Jan 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Single-cell RNA-seq, methods and analysis
24 Jan 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Single-cell RNA-seq, applications to the nervous system
03 Feb 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Exploration Allen Brain Atlas
07 Feb 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Lecture 14: Spatial transcriptomics
10 Feb 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Lezione 15: Explore the Allen Brain Atlas
14 Feb 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Mass-spectroscopy based proteomics for the neurosciences
24 Feb 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Local translation of synaptic proteins and ribosomes
07 Mar 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
Single cell epigenetics
10 Mar 2025 (2h 00m)
ALESSANDRO Cellerino - Course (teaching activity) - Both face to face and online
StartMAp and PatchSeq
26 May 2025 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 May 2025 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Face to face
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 May 2025 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Online
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 Jun 2025 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Online
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 Jun 2025 (2h 00m)
LUCA Pandolfini - Course (teaching activity) - Online
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.
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