Content of lectures: 1. Overview of what is genomics, basic genome structure and features, organellar vs. nuclear genomes, viral vs. prokaryotic vs. eukaryotic genomes 2. Genomic databases. General vs. specific, data downloading, genome browsers 3. Genome evolution. Factors affecting genome structure, stabilizing vs. destabilizing forces, coding capacity, C-value paradox 4. Towards your own genome I. How to prepare genomic project, Sequencing platforms, Single cell genomics 5. Towards your own genome II. Read processing, QC, assembling strategies and assemblers, read quantification and mapping 6. Genome annotation. Structural annotation: gene prediction in prokaryotes and eukaryotes, repeats identification. Functional annotation: Blast, PFAM, COG/GO calling, GO Enrichment test. 7. Genome and metabolism. Mapping of genes and transcripts to biochemical pathways, KEGG maps, 8. Cytogenomics. Chromosome structure, gene and chromosome duplications, sex chromosomes vs. Autosomes 9. Meta-omics I. Metabarcoding vs. Metagenomics, amplicon sequencing, prokaryotes vs, eukaryotes, QC and amplicon linking, reference databases, taxonomic binning, alpha/beta diversity 10. Meta-omics II. Metagenomics, metatranscriptomics, taxonomic binning, 11. Phylogenomics. Basic phylogenetic concepts, phylogenetics vs. phylogeno/transcriptomics, dataset compilation, contamination and paralog discovery and removal, LGT detection. Alignment and phylogenomic SW 12. Population Genomics. Future of genomics.
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Hartwell, Goldberg, Fischer, Hood. Genetics From Genes to Genomes 6th Edition. McGraw Hill, 2018.
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Lesk. Introduction to Genomics, 2nd edition, Oxford University Press, 2012.
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Pevsner. Bioinformatics and Functional Genomics 3rd Edition, 2015 Brown. Genomes, Garland Science, 2017.
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