Week 1: Proteogenomics overview- Part I, Proteogenomics overview- Part II, Introduction to Genomics- Part I : Gene sequencing and mutations Introduction to Genomics-Part II : Sequence alignment, Introduction to Genomics-Part III :Transcriptome, SL1: Advancement in Cancer Genomics, SL2: Advancement in Cancer Genomics
Week 2: Introduction to Genomics IV : Epigenome, Introduction to Genomics : cBioPortal, Genotype, Gene expression & Phenotype - Part I, Genotype, Gene expression & Phenotype- Part II, An overview of NGS technology, SH1: NGS-Sequencing by synthesis, SH2: NGS- Sequencing by synthesis
Week 3: Introduction to Proteomics, Proteomics: Sample Prep & Protein Quantification, Proteomics: Sample Prep & Protein Quantification (Hands-on), Introduction to MS-based Proteomics- Part I, Introduction to MS-based Proteomics- Part II, SL 3: Applications of NGS – Ion Torrent, SL4: Applications of NGS – Ion Torrent
Week 4: Introduction to MS-based Proteomics- Part I (Hands-on), Introduction to MS-based Proteomics- Part II (Hands-on), Data analysis: Normalization, Data analysis: Batch Correction and Missing values, Data analysis: Statistical Tests, SH3: NGS- Ion Torrent, SH4: NGS- Ion Torrent
Week 5: Machine learning and Clustering, Hypothesis testing, ProTIGY- Part I, ProTIGY- Part II, Proteogenomics approach to unravel proteoforms, SL5: Genomic Analysis using Droplet PCR, SL6: Genomic Analysis using Droplet PCR
Week 6: Workflow to Automated Data Processing, Introduction to Fire Cloud, Fire Cloud and Data Model, Bioinformatics solutions for ‘Big Data’ Analysis- Part I, Bioinformatics solutions for ‘Big Data’ Analysis-Part II, SH5: Genomic Analysis using Droplet PCR, SH6: Genomic Analysis using Droplet PCR
Week 7: Data Science infrastructure management- Part I, Data Science infrastructure management- Part II, Data Science infrastructure management- Part III, DIA-SWATH Atlas-Part I, DIA-SWATH Atlas-Part II, SL7: Introduction to Targeted Proteomics, SH7: Data Analysis using Skyline
Week 8: Human Protein Atlas-Part I Clinical, Human Protein Atlas-Part II, Affinity based proteomics & HPA, Clinical Considerations for OMICS-Part I, Considerations for OMICS- Part II, SL8: Proteomics: PTMs, SL9: Clinical Proteomics
Week 9: ntroduction to Proteogenomics-Part I, Introduction to Proteogenomics-Part II, Sequence centric proteogenomics, Gene Variant Analysis, Proteomics in Clinical studies,SH8: ProTIGY
Week 10:Supervised Machine learning- Predictive Analysis Part I, Supervised Machine learning- Predictive Analysis Part II, Supervised Machine learning- Marker Selection, Gene Set Analysis using WebGestalt- Part I, Gene Set Analysis using WebGestalt- Part II, SH9: Supervised Machine Learning
Week 11:Biological Network Analysis- Part I, Biological Network Analysis- Part II, Mutation and Signaling - Part I, Mutation and Signaling- Part II, Pathway Enrichment,SH10: Pathway Enrichment and Network Analysis
Week 12:Gene Set Enrichment Analysis (GSEA), Pathway enrichment: GSEA, Linked Omics, Linked Omics (Hands-on), Proteogenomics Conclusions, SL10: Topics in Proteogenomics- Malaria and Cancer case study
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