Course Information
| Course Code | Course Name | Credit Type |
|---|---|---|
| CUBI2548 | FUNCTIONAL GENOMICS | 2 + 1 + 1 |
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| Course Code | Course Name | Credit Type |
|---|---|---|
| CUBI2548 | FUNCTIONAL GENOMICS | 2 + 1 + 1 |
This course provides a comprehensive exploration of functional genomics, focusing on theoretical principles and practical applications. Students will gain insights into computational approaches, experimental methodologies, and data analysis techniques essential for understanding gene function within a genome.
| CO \ PO | PO1 | PO2 | PO3 | PO4 | PO5 | PO6 | PO7 | PO8 | PO9 | PO10 | PO11 | PO12 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CO1 | 3 | 2 | 2 | - | - | - | - | - | - | - | - | - |
| CO2 | 3 | 3 | 2 | 2 | 2 | 2 | - | - | - | - | - | - |
| CO3 | 3 | 3 | 2 | 2 | 2 | 2 | 3 | 2 | 2 | - | - | - |
| Session No. | Module | Topic | Sub-Topics |
|---|---|---|---|
| 1 | Module I | Introduction to Functional Genomics | Definition, Scope |
| 2 | Module I | History & Evolution | Relation with genomics & molecular biology |
| 3 | Module I | Central Dogma Refresher | DNA–RNA–Protein concepts |
| 4 | Module I | Bioinformatics Tools Overview | Genomics applications |
| 5 | Module I | Databases for Functional Genomics | NCBI, Ensembl, UCSC |
| 6 | Module I | BLAST & Sequence Retrieval | Types, Scoring, Use cases |
| 7 | Module I | Genome Browsers | UCSC Browser deep dive |
| 8 | Module I | Annotation & Feature Interpretation | Genes, CDS, Promoters |
| 9 | Module I | Comparative Genomics Basics | Orthologs, Paralogs |
| 10 | Module I | Genomic Data Formats | FASTA, GFF, BED, VCF |
| 11 | Module II | Introduction to NGS | Platforms: Illumina, Nanopore, PacBio |
| 12 | Module II | NGS Workflow | Library prep, Sequencing chemistry |
| 13 | Module II | Quality Control | FastQC, Phred scores |
| 14 | Module II | Data Preprocessing | Trimming, Filtering, Adaptor removal |
| 15 | Module II | Alignment Algorithms | BWA, HISAT2, STAR |
| 16 | Module II | Assembly Concepts | Reference vs De Novo assembly |
| 17 | Module II | NGS Case Studies | Agriculture & Disease genomics |
| 18 | Module II | Introduction to Transcriptomics | Gene expression basics |
| 19 | Module II | RNA-Seq Experimental Design | Controls, Replicates, Biases |
| 20 | Module II | RNA-Seq Data Processing | Alignment, Counting Reads |
| 21 | Module II | Differential Gene Expression | DESeq2, EdgeR |
| 22 | Module II | Interpreting DEGs | Biological significance |
| 23 | Module II | Pathway Analysis | GO, KEGG, Reactome |
| 24 | Module II | Data Visualization | Heatmaps, PCA, Volcano |
| 25 | Module II | Transcriptome Case Study | Interpreting real datasets |
| 26 | Module III | Introduction to Proteomics | Concepts, Types, Applications |
| 27 | Module III | Mass Spectrometry | Principles, Workflow |
| 28 | Module III | Protein Identification | Mascot, Sequest, MS Databases |
| 29 | Module III | Protein-Protein Interactions | STRING, BioGRID |
| 30 | Module III | CRISPR-Cas9 | Mechanism, Design, Applications |
| 31 | Module III | Genome Editing | Off-target effects, Validation |
| 32 | Module III | siRNA & shRNA | Knockdown strategies |
| 33 | Module III | Functional Screens | Guide Libraries, Hit Discovery |
| 34 | Module III | Multi-Omics Integration | Genomics + Transcriptomics + Proteomics |
| 35 | Module III | Systems Biology | Network modelling, Dynamic systems |
| 36 | Module III | Pathway Enrichment | GSEA, DAVID Analysis |
| 37 | Module III | Signal Transduction | Key regulators, Pathway cascades |
| 38 | Module III | Disease Genomics | Cancer, Neurogenomics |
| 39 | Module III | Multiomics Case Study | Interpretation of real datasets |
| 40 | Module III | Revision & Integration | Final summary + Q&A |
| Practical No. | Module | Title / Experiment | Activities / Tasks |
|---|---|---|---|
| P1 | Module I | Bioinformatics Hands-on | Tool usage, Database searching |
| P2 | Module I | Data Retrieval Troubleshooting | Handling errors, fixing missing fields |
| P3 | Module II | NGS Data Handling | FASTQ files, Quality checks |
| P4 | Module II | Differential Expression | DESeq2 / EdgeR workflow |
| P5 | Module III | CRISPR-Cas9 Editing | Design, Target selection, Editing |
| P6 | Module III | siRNA / shRNA Activity | Gene silencing hands-on |
| P7 | Module III | Functional Screens | Guide libraries, Hit identification |
| Project No. | Project Title | Description |
|---|---|---|
| 1 | Functional Genomics Experiment | Design & conduct a functional genomics experiment using real datasets. |
| 2 | Systems Biology Integration | Integrate genomics, transcriptomics, and proteomics for systems-level insights. |
| 3 | Network & Pathway Analysis | Perform network analysis and enrichment to identify key regulators. |