Advanced Neurogenomics

Registro delle lezioni

Anno accademico 2021/2022
Docente Alessandro Cellerino

Lecture

  • 05 Nov 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Primer on data distribution and visualization. Definition of probability, Poisson's distribution, gaussian distribution, definition of p-value, one sample t-test, two samples t-test, sign test as an example of non-parametric test. Box plot, gaussian kernel, violin plot. 2D plot. log-transform. Venn diagrams.

  • 08 Nov 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    RNA-sequencing. Illumina method. RNA isolation and quality check, removal of unwanted RNAs, cDNA synthesis, library construction, bridge amplification, sequencing on flow cell, paired end vs. single end, sequencing depth and optimal experimental design. Pacific Bioscience and Oxford Nanopore.

  • 16 Nov 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Quality check, FASTQ, alignment, BWT, SAM files, coverage vectors

  • 19 Nov 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Detection of differentially expressed genes. Negative binomial distribution. DESeq. Linear regression generalized linear models. DESeq2. Type I and Type II errors. Correction for multiple testing. Benjamini-Hochberg. Block design.

  • 29 Nov 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Hierarchical clustering, heat maps, K-means clustering, principal component analysis, multi dimensional scaling, elements of machine learning: overfitting, cross-validation, elastic net regression, epigenetic clock, linear discriminant analysis

  • 03 Dic 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Kyoto Encyclopedia of Genes and Genomes, Reactome, Gene Ontology, GO as an acyclic graph, the problem of redundancy, clustering of GO terms. Hypergeometric distribution, Gene Set Enrichment Analysis, Generally Applicable Gene Enrichment analysis

  • 06 Dic 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Network theory and application. Edges and NOdes. Random netrowrs and scale-free networks. Types of biological networks: metabolic network, protein-protein interaction, connectome. Correlation-based networks: gene co-expression and neural activity correlation. Metrics of centrality and modularity. Weighted-gene coexpression network analysis. Example of application of WGCNA to identify pathways controlling longevity.

  • 10 Dic 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    WGCNA applications in Neuroscience: Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Networks associated to neuronal activity and mitochondria. Allen brain atlas. Concordance of functional and transcriptomic networks. Networks in psychiatric disorders.

  • 13 Dic 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Use of DESeq2: data import, exploratory analysis, data normalization, plotting of counts, differential expression analysis with single and multiple factors

  • 21 Dic 2021 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - A distanza

    Practical exercises with WEBGESTALT and REVIGO

  • 10 Gen 2022 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Biology of microRNAs. Ribosome footprinting. Assay of translational efficiency. Small RNA sequencing. IsomiRs. Examples of microRNA-29 biological functions. CLIP and CLASH.

  • 18 Gen 2022 (2h 00m)

    Alessandro Cellerino - Corso (attività didattica) - Mista

    Single-cell RNA-seq (1): Library construction, trade-off between depth and number of cells, quality control.10x vs. Smart-seq, non-linear embeddings: t-SNE and UMAP. Clustering for single cells. Trajectory reconstruction.