Genomics, Proteomics, Transcriptomics & Metabolomics

The Omics Revolution — From Genomes to Systems Biology

Course Overview

The omics sciences represent one of the most transformative revolutions in modern biology. By studying entire classes of biological molecules simultaneously — genomes, transcriptomes, proteomes, and metabolomes — researchers can now understand living systems at an unprecedented scale and resolution.

This comprehensive course covers 20 detailed chapters spanning four major omics disciplines and their integration through systems biology and bioinformatics. From DNA sequencing technologies and RNA-Seq to mass spectrometry-based proteomics and metabolic profiling, you will learn the principles, technologies, and computational methods that drive modern biomedical research.

20 ChaptersMathJax Equations4 Omics DisciplinesMulti-Omics Integration

Course Structure

Part I: Genomics

Genome organization, DNA sequencing technologies (Sanger, NGS, third-generation), assembly, annotation, and functional genomics

4 chapters — from genome architecture to GWAS and comparative genomics

Part II: Transcriptomics

Gene expression analysis, microarray technology, RNA-Seq pipelines, single-cell and spatial transcriptomics

4 chapters — from microarrays to 10x Genomics and Visium spatial data

Part III: Proteomics

Protein separation, mass spectrometry (MALDI, ESI, tandem MS), quantitative approaches, interactomics

4 chapters — from 2D-PAGE to SILAC, TMT labeling, and Y2H screens

Part IV: Metabolomics

Metabolic profiling, NMR and mass spectrometry platforms, flux analysis, clinical applications

4 chapters — from targeted/untargeted metabolomics to biomarker discovery

Part V: Multi-Omics Integration

Systems biology, bioinformatics tools, machine learning approaches, precision medicine applications

4 chapters — from network analysis to AI-driven biomarker discovery

Mathematics in Omics

Modern omics sciences rely heavily on quantitative methods. Here are some of the key mathematical frameworks you will encounter throughout this course:

Sequence Alignment (Smith-Waterman)

$$H(i,j) = \max\begin{cases} 0 \\ H(i-1,j-1) + s(a_i,b_j) \\ H(i-1,j) - d \\ H(i,j-1) - d \end{cases}$$

Differential Expression (Fold Change)

$$\log_2\text{FC} = \log_2\!\left(\frac{\bar{x}_{\text{treatment}}}{\bar{x}_{\text{control}}}\right)$$

Mass-to-Charge Ratio

$$\frac{m}{z} = \frac{M + z \cdot m_H}{z}$$

Phred Quality Score

$$Q = -10 \log_{10}(P_e)$$

What You Will Learn

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Genomics

  • - Genome structure & chromatin organization
  • - NGS & third-generation sequencing
  • - De novo assembly & gene prediction
  • - GWAS & functional annotation
📊

Transcriptomics

  • - Microarray design & normalization
  • - RNA-Seq: alignment, quantification, DE
  • - scRNA-seq clustering & trajectory
  • - Spatial transcriptomics methods
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Proteomics

  • - 2D-PAGE & chromatography separation
  • - MALDI-TOF & ESI tandem MS
  • - Label-free & isotope-labeling quantification
  • - Protein-protein interaction networks
⚗️

Metabolomics

  • - Targeted vs untargeted approaches
  • - NMR & LC-MS/GC-MS platforms
  • - Metabolic flux analysis (MFA)
  • - Clinical biomarker discovery

Related Courses

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Biochemistry

Amino acids, enzymes, metabolism

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Molecular Biology

DNA, RNA, gene regulation

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Cell Physiology

Cell structure, signaling, transport

Start Chapter 1: Genome Organization