Computational Biology, Systems Biology and Biomarker Discovery: Practical Applications in Disease Research and Nanomedicine

Aim

Workshop Objectives

Workshop Structure

🗓️ Day 1 — Python-Based Disease Genomics, Molecular Pathways and Systems Biology

Topics Covered

• Introduction to computational biology and systems biology.
• Molecular mechanisms of lifestyle diseases, including diabetes, obesity and cardiovascular disorders.
• Identification of disease-associated genes.
• Biological databases and molecular information retrieval.
• Introduction to Gene Ontology and pathway enrichment.
• Major signalling pathways: PI3K-AKT, AMPK, insulin signalling and NF-κB.
• Introduction to Python-based biological data analysis and visualisation.

🛠️ Hands-On Session:

Retrieve type 2 diabetes-associated genes using biological databases,
perform functional enrichment analysis using ShinyGO and generate
pathway-related visualisations using Python in Google Colab.

Tools:
GeneCards | DisGeNET | NCBI Gene | UniProt | KEGG | Reactome |
ShinyGO | Google Colab | Pandas | Matplotlib

🗓️ Day 2 — Molecular Network Analysis, Hub Genes and Biomarker Discovery

Topics Covered

• Fundamentals of protein-protein interaction networks.
• Construction and visualisation of biological networks.
• Network topology and centrality measures.
• Identification of hub genes and functional modules.
• Introduction to gene expression datasets.
• Biomarker identification and prioritisation.
• Introduction to Python-based statistical analysis and machine learning applications in biomarker research.

🛠️ Hands-On Session:
Construct a disease-associated protein interaction network using
STRING and Cytoscape, identify hub genes and explore a prepared
gene expression dataset using Python for candidate biomarker
prioritisation.

Tools:
STRING | Cytoscape | cytoHubba | NCBI GEO | GEO2R |
Google Colab | NetworkX | Pandas | Scikit-learn

🗓️ Day 3 — Protein Structure Analysis and Computational Nanomedicine

Topics Covered

• Introduction to protein sequence and structural analysis.
• Retrieval and visualisation of disease-associated protein structures.
• Structure-function relationships in biological systems.
• Introduction to nanomedicine and targeted drug delivery.
• Lipid nanoparticles and polymeric nanocarriers.
• Protein corona formation and nanoparticle-protein interactions.
• Influence of particle size and surface properties on nano-bio interactions.
• Introduction to computational analysis of nanoparticle-associated biological responses.

🛠️ Hands-On Session:
Retrieve and visualise a selected disease-associated protein
structure using RCSB PDB and ChimeraX. Explore a curated nanoparticle
dataset using Python to examine relationships between nanoparticle
properties and available biological response measurements.

Tools:
UniProt | RCSB PDB | ChimeraX | Google Colab |
Python | Pandas | NumPy | Matplotlib

Who Should Enrol?

Important Dates

Workshop Outcomes

Meet Your Mentor(s)

Abhimanyu

Deprtment of Biotechnology

more

Fee Structure