Genomics and bioinformatics
Summary
This course covers various data analysis approaches associated with applications of DNA sequencing technologies, from genome sequencing to quantifying gene expression, transcription factor binding and chromosome conformation.
Content
- Genome sequencing and assembly
- Genome annotation, gene prediction
- Hidden Markov Models
- Comparative genomics
- Phylogenetic trees
- Models of molecular evolution
- Transcription
- Gene expression profiling
- Gene regulation
- Chromosome conformation
Learning Prerequisites
Recommended courses
Molecular biology, genetics, linear algebra, ordinary differential equations, basic statistics, computer programming
Important concepts to start the course
DNA and RNA, replication, transcription and translation.
Learning Outcomes
By the end of the course, the student must be able to:
- Choose a method or algorithm to analyse different kinds of genomic data
- Design an analysis strategy to interpret complex, heterogenous genomic data
- Assess / Evaluate a publication based on genomic data
Transversal skills
- Access and evaluate appropriate sources of information.
- Summarize an article or a technical report.
- Communicate effectively with professionals from other disciplines.
- Use both general and domain specific IT resources and tools
Teaching methods
2 hours lecture (theoretical concepts) followed by 2 hours practical exercises (review the theory and practice with bioinformatics tools and data)
Lecture notes, slides and exercises provided on Moodle.
Expected student activities
Following the lectures, completing exercises, doing a project
Assessment methods
The evaluation is based on a written test at week 7 and a personal project between week 7 and week 14. Each counts for 50% of the grade.
Resources
Bibliography
- A primer of genome science / Greg Gibson, Spencer V. Muse
- Bioinformatics: sequence and genome analysis / David W. Mount
- Bioinformatics and functional genomics / Jonathan Pevsner
- Biological sequence analysis: probabilistic models of proteins and nucleic acids / Richard Durbin
Ressources en bibliothèque
- A primer of genome science / Gibson
- Bioinformatics / David W.Mount
- Biological sequence analysis
- Bioinformatics and functional genomics
Moodle Link
In the programs
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Genomics and bioinformatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Genomics and bioinformatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks
- Semester: Spring
- Exam form: During the semester (summer session)
- Subject examined: Genomics and bioinformatics
- Lecture: 2 Hour(s) per week x 14 weeks
- Exercises: 2 Hour(s) per week x 14 weeks