BIOINFORMATICS AND CHEMOGENOMICS
Learning outcomes of the course unit
ACQUIRING KNOWLEDGE AND UNDERSTANDING.
Students are expected to acquire a good knowledge of methods for biological sequence analysis and of query sequence and domain databases, and a good familiarity with public databases and software for analysis and results visualization
APPLYING KNOWLEDGE AND UNDERSTANDING.
Through guided exercises, students will gain the basic skills necessary to face the study of new biological sequences, hypothesizing their function, evolutionary history, structure and localization.
Students will also acquire basic information and specific application examples on one of the most advanced fields of post-genomic research, with special reference to the new frontiers of molecular pharmacology and toxicology, “systems biology” and other modern applications of biotechnology to drug discovery.
Students should have a solid background in Biochemistry and Molecular Biology
Course contents summary
The course is developed on two principal and complementary topics: bioinformatics and chemogenomics. The main topics are: the search in biological databases using different tools, the analysis of biological sequences and the interpretation of data coming from high-throughput experiments (transcriptomic or genomic phenotyping)
1. Biological sequences and databases.
2. Substitution matrices and alignment scores.
3. Local and global pairwise alignments.
4. Methods for query sequences in databases.
5. Oligonucleotides design for real-time PCR application.
6. Multiple alignments of protein sequences and their use for functional and structural inference.
7. Creating patterns and profiles from multiple alignments. Query profile, domains and motifs databases.
8. Molecular evolution, phylogeny.
9. Predictions of protein biochemical-structural features. Prediction of intracellular localization. Hydropathy plots and topology of membrane proteins.
10. Basic knowledge of chemistry, biochemistry, molecular biology and genomics and pharmaceutical chemistry
11. Goals and fields of application of chemogenomics
12. Chemogenomics applied to “drug discovery”, “target/mode of action identification” and “drug validation”
13. Chemogenomics based transcriptomics, proteomics and phenomics.
14. Chemogenomic technologies in the yeast S. cerevisiae: microarrays and the “compendium” approach; yeast two hybrid and its variants; the yeast gene deletion mutant collections
15. Mechanism of action, offtarget effects and new applications for “old drugs” or “lead compounds” discarded in advanced phase of (pre)clinical development
16. New drugs and bioactive compounds of molecularbiological origin: nucleotide and peptide aptamers, interfering RNAs
17. Drugs and vaccines based on recombinant proteins/peptides
18. Features of pathways, network and gene ontology databases and their interrogation
19. “Genomic phenotyping” of small molecule drugs (or toxicants) in yeast and use of interactomics databases and of specific software for data analysis
“BIOINFORMATICA”, TRAMONTANO Anna, Ed. Zanichelli
“INTRODUZIONE ALLA BIOINFORMATICA”, VALLE Giorgio-HELMER CITTERICH
Manuela-ATTIMONELLI Marcella-PESOLE Graziano, Ed. Zanichelli
Specialized articles, slides and presentations of specialists and companies, available to the students in electronic format
The course is organized in lectures that provide a theoretical basis, flanked with exercises in computer classroom for learning the use of software for analysis and visualization of the results.
Assessment methods and criteria
The assessment of learning outcomes is based on an oral examination, which will be conducted in the form of presentation of results obtained during exercises, and integrated with questions about the theoretical background. During the examination, the knowledge of the theoretical basis, the understanding of the exercises, and the ability to apply knowledge and to interpret results will be evaluated.