From Genomics to Systems Biology
Theory: 3 hours/week | Tutorials: 1 hour/week | Practicals: 2 hours/week | ECTS Units: 5
Learning outcomes
Going through the post-genomic era, the course aims to educate students in the latest trends in Genomics, as well as to extend them to Systems Biology. The ultimate goal is to create competitive bioscientists with knowledge about the structure, organization and function of the genome along the evolutionary scale as well as the manipulation of the databases that accompany them.
Upon completion of the course, students are expected to:
- distinguish the individual branches of Genomics and their applications in modern basic and applied research
- know the operating principles and technical characteristics of the main sequencing technologies
- be introduced to Genome navigation and analysis using Genomic navigators and the analysis tools they offer
- become familiar with the basic principles and concepts of Systems Biology and their interconnection with multi-omic genomic analyses
Syllabus
- Introduction to genomics, along with a description of the categories and subbranches of the subject (comparative, functional, etc.).
- Structure and organization of eukaryotic genomes (plants, insects, invertebrates, fish, birds, mammals, primates and Neanderthals), gene density, effect of agriculture and livestock on the genome.
- Structure and organization of viral genomes, adaptive strategies of viral genomes of DNA and RNA, applications in basic research.
- Organization and function of prokaryotic genomes, differences in the genome of pathogenic and non-pathogenic bacteria, sequencing and treatment of super-resistant bacteria.
- Strategies for adaptation and genomic function of Archaea, thermophilic genomes and differences in transcribed and non-transcribed sequences
- Principles of large-scale sequencing, BAC-to-BAC and random access sequencing, comparison and limitations with Sanger sequencing, reference genomes and applications
- Construction of NGS libraries, adapters and bar codes, one-way and two-way sequencing, multiplexing.
- Principle of operation and main features of next generation sequencing methods, Illumina, Ion Torrent, PacBio, Nanopore, comparison with microarrays, advantages and applications by sequencing length.
- Population genomics, mapping of quantitative traits with sequencing or TILLING microarrays, molecular map construction and applications in agriculture.
- Comparative genomics and evolution, duplication and evolution of genomes, C-value paradox, gene degeneration, functional deviation and gene density.
- Functional genomics, transcriptomics and epigenomics, detection of regulatory elements in the genome, methodologies of transcriptome analysis. applications in biomedicine.
- Basic principles of proteomics, principle of operation of mass spectrometry, introduction to normalization with SILAC, peptidomics, protein microarrays of analytical and functional type.
- Introduction to metagenomics, applications in paleontology, microbiome in cancer and applications in diagnosis.
- Introduction to systems biology, transcriptional networks and physical or logical interactions, directed and highlighted network graphs, transcriptional noise and self-regulation, feedback loops and logic gates.
Within the framework of the tutorial, exercises are solved with the use of genomic databases. Within the framework of the laboratory, functional genomics data analysis and individual work are carried out by students.
Practicals
Practical lecture 1 : Genome browser I – Introduction to genome navigation (UCSC, WashU)
Practical lecture 2 : Genome browserII – Operation of basic tools (BLAT, insilicoPCRetc)
Practicallecture 3 : Genome browserIII – Comparative visualization of diverse NGS data
Practical lecture 4 : Principles of NGS library construction
Practical lecture 5 : Quantitative PCRΙ – Analysis of gene expression
Practical lecture 6 : QuantitativePCRΙΙ – TaqmanandHRManalysis
Practical lecture 7 : Meta-analysis of transcriptomics data
Laboratory exercise 1 : Dotblot
Laboratory exercise 2 : RNA electrophoresis and Quality Control
Student performance evaluation
Performance in the course is assessed on the basis of the written examination in the laboratory/tutorial part of the course (30%) and the written examination in the theoretical part of the course during the examination period (70%).
The written examination includes:
General questions that include critical thinking with graded difficulty (60 credits). Targeted questions requiring short and accurate answers (30 credits). Problem solving (10 credits). For students with learning disabilities there is provision for a blended examination method in all parts of the course.
The total of correct answers corresponds to 100 points, which is reduced to a grade of 10. Based on this reduction, the grade of each student in the theoretical examination of the course is calculated. This grade corresponds to 70% of the total grade of the course.
Suggested bibliography
- Εισαγωγή στην Γονιδιωματική και την Βιολογία Συστημάτων, Arthur Lesk Δεύτερη έκδοση, Πανεπιστημιακές εκδόσεις Utopia, (ISBN 978-618-5173-18-0)
- Γονιδιώματα – σύγχρονες ερευνητικές προσεγγίσεις, Brown Τ. Α. (ISBN 9603998563)
- ΑΝΑΣΥΝΔΥΑΣΜΕΝΟ DNA, James D. Watson κ.α. (ISBN 978-960-88412-5-3)
Teaching Material / E-class
Lecturer
