ABOUT THE COURSE: The course begins with a historical perspective to genomics and how the human genome project catalyzed the development of Next-Generation sequencing technologies. Instead of following a standard textbook format of chapters, the course is designed to use the latest articles in leading journals to keep the course focused on the recent advances in the field. However, the course is well grounded in the basics and exposes the students to practical NGS data analysis. In contrast to traditional course on genomics and proteomics, this course has a strong evolutionary flavor.INTENDED AUDIENCE: BE/ME/MS/BSc/MSc/PhDPREREQUISITES: Basics of biological molecules
Overview
Syllabus
Week 1:Introduction to genomics: Historical perspective with examples from Human genome project and Advent of NGS. Genomic assembly approaches.
Week 2:Detailed discussion of the principles of sequencing technologies and comparison of advantages and disadvantages. Applications and Challenges in the use of NGS technologies
Week 3:Omics data avalanche: 1000 genomes project, ENCODE project, ExAC, TCGA
Week 4:Importance of evolutionary viewpoint in genomics, Signatures of selection in primates (with prominent examples from Human studies), Whole-genome duplication, comparative and population genomics, tests of selection (codon based and site frequency-based tests).
Week 5:Introduction to transcriptomics, proteomics and Integration of Multi-Omic data. Other types of omic datasets resulting from high-throughput use of assays (Ex: Repli-Seq, Ribo-Seq, Tag-Seq)
Week 6:Omics databases organization and utility. NCBI, UCSC genome browser, Short Read Archive, Proteome Exchange, Peptide Atlas, KEGG
Week 7:Introduction to linux, use of command line interface, Tutorial on analysis of NGS data (Genomics, Transcriptomics)
Week 8:Course summary and Exam
Week 2:Detailed discussion of the principles of sequencing technologies and comparison of advantages and disadvantages. Applications and Challenges in the use of NGS technologies
Week 3:Omics data avalanche: 1000 genomes project, ENCODE project, ExAC, TCGA
Week 4:Importance of evolutionary viewpoint in genomics, Signatures of selection in primates (with prominent examples from Human studies), Whole-genome duplication, comparative and population genomics, tests of selection (codon based and site frequency-based tests).
Week 5:Introduction to transcriptomics, proteomics and Integration of Multi-Omic data. Other types of omic datasets resulting from high-throughput use of assays (Ex: Repli-Seq, Ribo-Seq, Tag-Seq)
Week 6:Omics databases organization and utility. NCBI, UCSC genome browser, Short Read Archive, Proteome Exchange, Peptide Atlas, KEGG
Week 7:Introduction to linux, use of command line interface, Tutorial on analysis of NGS data (Genomics, Transcriptomics)
Week 8:Course summary and Exam
Taught by
Prof. Nagarjun Vijay
