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 lectures (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, performing data analyses and implementing the relevant algorithms
Assessment methods
The evaluation is based on a 2-3 evaluated practicals throughout the semester.
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
- Physical Biology of the Cell / Rob Phillips et al.
Ressources en bibliothèque
- A primer of genome science / Gibson
- Bioinformatics and functional genomics
- Biological sequence analysis
- Bioinformatics / David W.Mount
- Physical Biology of the Cell / Rob Phillips et al.
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
- 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