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.