Systems biology and network analysis
A.A. 2024/2025
Obiettivi formativi
Systems biology is the study of interrelationships between molecular constituents of a living cell through the integration of experimental and computational approaches. Most biological characteristics arise from complex interactions between the cell's functional elements; to understand how genes determine phe¬notypes, both in physiology and disease, it is necessary to adopt quantitative methods that allows a holistic approach. The course describes the principles useful to explore interactions by introducing methods for the analysis of gene-regulatory and large-scale networks exploiting availability of big functional genomics data sets. Analysis and modelling of genetic and epigenetic determinants of gene expression regulation will be considered.
Risultati apprendimento attesi
At the end of the course, students will be able to apply systems biology techniques and pipelines to the analysis and characterization of regulatory (genetic and epigenetic) and interaction networks.
Periodo: Primo semestre
Modalità di valutazione: Esame
Giudizio di valutazione: voto verbalizzato in trentesimi
Corso singolo
Questo insegnamento non può essere seguito come corso singolo. Puoi trovare gli insegnamenti disponibili consultando il catalogo corsi singoli.
Programma e organizzazione didattica
Edizione unica
Periodo
Primo semestre
Programma
Biological networks and basic concepts of graphs.
Hill function. Negative and positive autoregulation.
Network motifs: feed-forward loop, single input modules and dense overlapping regulons (DORs). Positive and negative feedback loops. Oscillators.
Modelling of circadian rhythms in cellular networks.
Annotation and pathway analysis (over-representation, functional class scoring, topology based).
Network analytics. Scale-free nature of cellular networks. Biological small worlds.
Dependencies estimation in co-expression networks (WGCNA).
Network modularity.
Network rewiring and comparative genomics to study gene essentiality.
Identification of DNA sequence alterations: statistical genetics for linkage analysis and genome wide association studies (GWASs). Linkage disequilibrium. Expression quantitative trait loci (eQTLs).
Hill function. Negative and positive autoregulation.
Network motifs: feed-forward loop, single input modules and dense overlapping regulons (DORs). Positive and negative feedback loops. Oscillators.
Modelling of circadian rhythms in cellular networks.
Annotation and pathway analysis (over-representation, functional class scoring, topology based).
Network analytics. Scale-free nature of cellular networks. Biological small worlds.
Dependencies estimation in co-expression networks (WGCNA).
Network modularity.
Network rewiring and comparative genomics to study gene essentiality.
Identification of DNA sequence alterations: statistical genetics for linkage analysis and genome wide association studies (GWASs). Linkage disequilibrium. Expression quantitative trait loci (eQTLs).
Prerequisiti
The course Bioinformatics and Computational Biology must be successfully completed to take the exam of this class.
Metodi didattici
The course consists of 24 hours of theoretical lectures and 24 hours of practical lessons in Matlab environment.
Materiale di riferimento
The slides presented during the course along with additional material recommended for specific topics will be available on the Webeep portal (https://webeep.polimi.it/login/index.php), accessible to students registered to the course.
Modalità di verifica dell’apprendimento e criteri di valutazione
The assessment is based on an oral exam concerning a preliminary exercise (writing of a Matlab script) and general questions about the topics covered during the course along with the discussion of an assignment developed during the semester.
ING-INF/06 - BIOINGEGNERIA ELETTRONICA E INFORMATICA - CFU: 6
Lectures: 48 ore
Docente:
Pattini Linda