Elements of Bioinformatics: definitions and concepts. Dynamic cointegration and correlations among “omics” Sciences and Bioinformatics. Genomics and Bioinformatics. The Human Genome Project. Principles of sequence analysis. Gene finding and Genome assembly. Genome annotation. Genomic database generation. Gene and genome comparison and variability.
The role of Bioinformatics in: phylogeny and evolution, population genetics and biodiversity, genetic archeology: mitochondrial Eve. Genome data integration applying bioinformatics tools. Mendelian genetic disorders and effect of genetic background in phenotypic variability (e.g. Osteogenesis imperfecta), genome wide association studies (GWAS) (hypercholesterolemia, type I diabetes, hypertension and Crohn's disease).
Metagenomics and metatranscriptomics. Microbiome and clinical implications (obesity).
Systems theory and biological complexity. Systems Biology: Complexity Sciences, computational modelling, and data integration. Bioinformatics tool development and implementation, and “information flow” through genomics, transcriptomics, and proteomics. Bioinformatics and protein dynamics’ complexity. Proteomics versus Genomics.
Functional analysis. Cluster analysis: DAVID bioinformatics resources; pathway analysis: MetaCore, String. Expression matrix.
Internet, World Wide Web, server web, web browser, URL, web page, hypertext, website, web search engine. Keywords and Boolean operators.
Database: logical database structure, data storage, redundancy and database crosstalk. Molecular biology databases. INSDC: EMBL, GenBank, and DDBJ; dbEST. NCBI (National Centre for Biotechnology Information), Entrez, and NCBI databases. Medline and PubMed (PubMed Central). Literature search in PubMed.
The SIB Bioinformatics Resource Portal ExPASy: tools and databases for Life Sciences applications.
UniProt consortium (EMBL-EBI, SIB, PIR). UniProtKB: SwissProt and TrEMBL databases.
UniRef, UniParc, UniMES, Proteomes. Gene Ontology (GO).
Functional sequence annotation: automatic and reviewed-manually annotation. Main secondary databases: PROSITE, HAMAP, IntEnz, IntAct, InterPro, PRIDE, PeptideAtlas, PDB. Other databases: Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, CATH-Gene3D, PANTHER Treefarm, PhylomeDB.
Principles of 2D SDS polyacrylamide gel electrophoresis (PAGE); Swiss-2D-PAGE and Siena-2D-PAGE databases.
Principles of mass spectrometry: peptide mass fingerprinting and tandem mass spectrometry. Intra- and inter-species identification applying Mascot software.
Sequence analysis by the use of proper ExPASy provided prediction tools: Compute pI/Mw, NetPhos, PeptideCutter, and PeptideMass.
Morphological and molecular bases of organism classification. Fundamentals of deterministic and stochastic models of evolution. Genetic drift. Divergent and Convergent evolution. Forward and back mutation. Gene duplication, pseudogene. Gene/protein family and superfamily. Similarity, identity, and homology (orthology, paralogy, xenology). Protein evolution: molecular clock, fixation of mutations, insertion and deletion events (gap occurrence).
Sequence alignment. Sequence function prediction. Manual, local, and global sequence alignment. Dot plot, PAM and BLOSUM substitution matrices.
Heuristic and dynamic algorithms. FASTA and BLAST alignment tools. Protein sequence alignment applying BLASTp algorithm. Statistical and biological value of produced alignments and correlated sequence functional annotation.