GENOMICS

Second cycle degree in MOLECULAR BIOLOGY

Campus: PADOVA

Language: English

Teaching period: Second Semester

Lecturer: GIORGIO VALLE

Number of ECTS credits allocated: 9


Syllabus
Prerequisites: The content of the course has been defined keeping in mind the program of the first level degree in Molecular Biology of the University of Padua. In particular it is expected that the students have a good knowledge of Genetics, Molecular Biology and Bioinformatics. The course is in English, therefore the students should have a reasonable command of spoken and written English.
Examination methods: The exam will be written, but a continuous process of assessment will be carried out throughout the course, to verify the level of understanding of the students.
Course unit contents: This is a 9 credit course, 7 of which will be lessons, the remaining 2 will be practicals. Each title reported below corresponds to approximately two hours of classroom teaching plus four hours of home study. The lessons will be articulated as follows.

Part 1.
Presentation of course and practicals
Introduction: Life, Biology, Information, Genomes, Evolution
History of genomics
Next Generation sequencing (NGS)
NGS: data formats for reads
Classical sequence alignment and assembly algorithms
NGS read alignment
Alignment formats: gff, sam and bam
Genome assembly with NGS data
Mate pair libraries and scaffolding
Metagenomics

Part 2
Transcriptome: Northern, EST, Full length, Microarrays
RNAseq
Analysis of RNAseq data
Proteomics
miRNA,
miRNA target prediction; lincRNA
Interactomics, and functional associations
Gene prediction, gene ontology and gene annotation
DNA methylation and methylome analysis
Histone modification and ChIP analysis"

Part 3
Analysis of human mutations and polymorphisms
GWAS
Genome re-sequencing and Exome sequencing
Personalized medicine and related bioinformatics
Genome browsers
Data integration and systems biology
General summary, discussion and conclusions