BC

Bioinformatics and Computational Biology Program

Chulalongkorn University
ไทย

Course Catalog

Core Courses

BC5001 - Fundamentals of Bioinformatics (3 credits)

Introduction to bioinformatics concepts, biological databases, sequence analysis, and common tools.

Prerequisites: None Offered: Every semester

Topics:

  • Introduction to molecular biology for computer scientists
  • Biological databases (NCBI, Ensembl, UniProt)
  • Sequence alignment algorithms (BLAST, FASTA)
  • Multiple sequence alignment
  • Phylogenetic analysis basics

BC5002 - Computational Biology (3 credits)

Computational approaches and algorithms for analyzing biological data.

Prerequisites: BC5001 or instructor permission Offered: Every semester

Topics:

  • Algorithm design for biological problems
  • Dynamic programming in biology
  • Graph algorithms for biological networks
  • Genome assembly
  • Gene prediction algorithms

BC5003 - Statistics for Bioinformatics (3 credits)

Statistical methods and data analysis techniques for biological data.

Prerequisites: Basic statistics Offered: Every semester

Topics:

  • Probability and statistical distributions
  • Hypothesis testing in biology
  • Multiple testing correction
  • Statistical modeling
  • R programming for statistical analysis
  • Data visualization

BC5004 - Programming for Bioinformatics (3 credits)

Programming skills and tools essential for bioinformatics analysis.

Prerequisites: None Offered: Every semester

Topics:

  • Python programming fundamentals
  • Perl/Biopython libraries
  • Data structures and algorithms
  • File parsing and data processing
  • Workflow automation
  • Version control (Git)

Genomics & Sequencing

BC5101 - Next-Generation Sequencing Analysis (3 credits)

Analysis of high-throughput sequencing data including quality control, alignment, and variant calling.

Prerequisites: BC5001, BC5004 Offered: Fall semester

Topics:

  • NGS technologies overview
  • Quality control and preprocessing
  • Read mapping and alignment
  • Variant calling and annotation
  • Copy number variation analysis
  • Structural variant detection

BC5102 - Transcriptomics and RNA-seq (3 credits)

Analysis of gene expression data from RNA sequencing experiments.

Prerequisites: BC5001, BC5003 Offered: Spring semester

Topics:

  • RNA-seq experimental design
  • Read quantification
  • Differential expression analysis
  • Alternative splicing analysis
  • Long non-coding RNA analysis
  • Single-cell RNA-seq

BC5103 - Comparative Genomics (3 credits)

Computational methods for comparing genomes across species.

Prerequisites: BC5002 Offered: Fall semester

Topics:

  • Genome evolution
  • Synteny analysis
  • Orthology and paralogy
  • Horizontal gene transfer
  • Pan-genome analysis
  • Evolutionary genomics

BC5104 - Epigenomics (3 credits)

Analysis of epigenetic modifications and chromatin structure.

Prerequisites: BC5101 Offered: Spring semester

Topics:

  • ChIP-seq analysis
  • DNA methylation analysis (BS-seq)
  • ATAC-seq and chromatin accessibility
  • Histone modification analysis
  • Enhancer prediction
  • Epigenetic regulation

Structural Bioinformatics

BC5201 - Protein Structure Prediction (3 credits)

Computational methods for predicting and analyzing protein structures.

Prerequisites: BC5001 Offered: Fall semester

Topics:

  • Protein structure fundamentals
  • Homology modeling
  • Threading and fold recognition
  • Ab initio structure prediction
  • AlphaFold and deep learning approaches
  • Structure validation

BC5202 - Molecular Modeling and Simulation (3 credits)

Computational techniques for simulating biomolecular systems.

Prerequisites: BC5201 Offered: Spring semester

Topics:

  • Molecular dynamics fundamentals
  • Force fields and energy functions
  • MD simulation setup and analysis
  • Free energy calculations
  • Protein-ligand interactions
  • Membrane protein simulations

BC5203 - Drug Design and Virtual Screening (3 credits)

Computational methods for drug discovery and molecular design.

Prerequisites: BC5202 Offered: Fall semester

Topics:

  • Drug discovery pipeline
  • Molecular docking
  • Virtual screening strategies
  • Structure-based drug design
  • Ligand-based drug design
  • ADMET prediction
  • AI in drug discovery

Systems Biology & Networks

BC5301 - Network Biology (3 credits)

Analysis of biological networks including protein interaction and metabolic networks.

Prerequisites: BC5002, BC5003 Offered: Fall semester

Topics:

  • Graph theory basics
  • Protein-protein interaction networks
  • Metabolic networks
  • Gene regulatory networks
  • Network topology analysis
  • Community detection
  • Network visualization

BC5302 - Mathematical Modeling in Biology (3 credits)

Mathematical and computational modeling of biological systems.

Prerequisites: BC5003, Calculus Offered: Spring semester

Topics:

  • Ordinary differential equations in biology
  • Kinetic modeling
  • Boolean network models
  • Agent-based modeling
  • Stochastic simulations
  • Parameter estimation

BC5303 - Pathway Analysis (3 credits)

Methods for analyzing biological pathways and functional enrichment.

Prerequisites: BC5001, BC5003 Offered: Fall semester

Topics:

  • Pathway databases (KEGG, Reactome)
  • Gene Ontology analysis
  • Gene set enrichment analysis (GSEA)
  • Pathway topology analysis
  • Flux balance analysis
  • Pathway crosstalk

Machine Learning & AI

BC5401 - Machine Learning in Biology (3 credits)

Application of machine learning methods to biological problems.

Prerequisites: BC5003, BC5004 Offered: Every semester

Topics:

  • Supervised learning algorithms
  • Classification and regression
  • Feature selection and engineering
  • Model evaluation and validation
  • Random forests and SVM
  • Ensemble methods
  • Applications in genomics

BC5402 - Deep Learning for Genomics (3 credits)

Deep learning techniques applied to genomic and biological data.

Prerequisites: BC5401 Offered: Spring semester

Topics:

  • Neural network fundamentals
  • Convolutional neural networks (CNNs)
  • Recurrent neural networks (RNNs)
  • Transformers and attention mechanisms
  • DNA sequence modeling
  • Protein sequence analysis with DL
  • Image analysis in biology

BC5403 - Data Mining in Life Sciences (3 credits)

Data mining techniques for discovering patterns in biological data.

Prerequisites: BC5003, BC5004 Offered: Fall semester

Topics:

  • Clustering algorithms
  • Dimensionality reduction (PCA, t-SNE, UMAP)
  • Association rule mining
  • Text mining in biomedical literature
  • Integrative data analysis
  • Big data in biology

Specialized Topics

BC5501 - Metagenomics (3 credits)

Analysis of microbial community sequencing data.

Prerequisites: BC5101 Offered: Spring semester

Topics:

  • 16S rRNA analysis
  • Shotgun metagenomics
  • Taxonomic classification
  • Functional profiling
  • Metagenome assembly
  • Microbiome analysis

BC5502 - Proteomics and Mass Spectrometry (3 credits)

Computational analysis of protein mass spectrometry data.

Prerequisites: BC5001, BC5003 Offered: Fall semester

Topics:

  • Mass spectrometry fundamentals
  • Peptide identification
  • Protein quantification
  • Post-translational modifications
  • Proteomics data analysis pipelines
  • Proteogenomics

BC5503 - Clinical Bioinformatics (3 credits)

Application of bioinformatics in clinical and medical settings.

Prerequisites: BC5101 Offered: Spring semester

Topics:

  • Variant interpretation
  • Cancer genomics
  • Pharmacogenomics
  • Genetic disease diagnosis
  • Clinical data standards
  • Precision medicine

BC5504 - Single-Cell Omics (3 credits)

Analysis of single-cell sequencing data.

Prerequisites: BC5102, BC5401 Offered: Fall semester

Topics:

  • Single-cell technologies
  • Quality control and normalization
  • Cell type identification
  • Trajectory inference
  • Spatial transcriptomics
  • Multi-modal single-cell analysis

Seminar & Research

BC5901 - Bioinformatics Seminar (1 credit)

Weekly seminars featuring research presentations from faculty, students, and invited speakers.

Prerequisites: None Offered: Every semester

Requirements:

  • Attend weekly seminars
  • Present own research once per semester
  • Active participation in discussions

BC5902 - Research Methodology (2 credits)

Training in research design, execution, and communication.

Prerequisites: None Offered: Fall semester

Topics:

  • Research question formulation
  • Experimental design
  • Literature review
  • Scientific writing
  • Presentation skills
  • Research ethics
  • Grant writing

BC5903 - Special Topics in Bioinformatics (3 credits)

Advanced topics based on current research trends and student interests.

Prerequisites: Varies by topic Offered: As needed

Recent Topics:

  • Graph neural networks in biology
  • Quantum computing for bioinformatics
  • CRISPR screen analysis
  • Long-read sequencing analysis
  • Multi-omics integration

Independent Study & Thesis

BC5911 - Independent Study (3-6 credits)

Supervised research project culminating in a written report.

Prerequisites: Completion of core courses For: M.Sc. Plan B students

BC5921 - Thesis (12 credits)

Independent research project culminating in a thesis and defense.

Prerequisites: Completion of core courses For: M.Sc. Plan A students

BC5931 - Ph.D. Dissertation (36 credits)

Original research culminating in a doctoral dissertation and defense.

Prerequisites: Completion of qualifying exam For: Ph.D. students

Course Schedule

Typical Fall Semester

  • Fundamentals of Bioinformatics
  • Computational Biology
  • Statistics for Bioinformatics
  • Programming for Bioinformatics
  • NGS Analysis
  • Protein Structure Prediction
  • Network Biology
  • Machine Learning in Biology

Typical Spring Semester

  • RNA-seq and Transcriptomics
  • Molecular Modeling
  • Mathematical Modeling
  • Deep Learning for Genomics
  • Clinical Bioinformatics
  • Single-Cell Omics

Note: Course offerings may vary by semester based on enrollment and faculty availability.

Prerequisites Chart

BC5001 (Fundamentals) ──┬──> BC5002 (Comp. Biology)
                        ├──> BC5101 (NGS Analysis)
                        └──> BC5201 (Protein Structure)

BC5004 (Programming) ───┬──> BC5101 (NGS Analysis)
                        └──> BC5401 (Machine Learning)

BC5003 (Statistics) ────┬──> BC5102 (RNA-seq)
                        └──> BC5401 (Machine Learning)

For detailed syllabi and current course schedules, contact the program office.