Universitat Internacional de Catalunya
Bioinformatics for Omics
Other languages of instruction: Catalan, Spanish
Introduction
The biotechnological explosion of recent years has crystallized in a huge number of new experimental techniques, characterized by their complexity and by the variety of biological problems they address. Today we can sequence a complete genome, analyze the levels of gene expression in different tissues, explore cellular behavior in different clinical situations, etc. Each of these experiments generates varied and extensive information and, at a technical level, with very different characteristics. The objective of this course is to familiarize the student with the main massive experiments in biomedicine, and show them how to process their data to give them clinical value.
Pre-course requirements
Introduction to Bioinformatics
Objectives
To explain the main massive experiments in the field of biomedicine and the clinical value that arises from their analysis.
Competences/Learning outcomes of the degree programme
- CN14 - Identify the principles of biomedical sciences related to health, as well as the basic concepts and tools that have an impact on Biomedical Sciences and allow them to work in any of its fields (biomedical companies, bioinformatics labs, research laboratories, clinical analysis companies, etc.).
- CP05 - Apply biological foundations in the search for practical solutions to health problems, following ethical standards and scientific rigour and respecting fundamental equal rights between men and women, and the promotion of human rights and the values inherent in a peaceful society of democratic values that includes inclusive, non-discriminatory language without stereotypes.
Learning outcomes of the subject
The following is contemplated as a specific learning outcome of this course:
- The student will become familiar with the most widely used or most promising mass experiments in biomedicine and will learn to use the bioinformatics programs used to analyze them.
Syllabus
1.- The concept of large-scale experiments in biomedicine: the exhaustive characterization of biological phenomena.
2.- Next-generation Sequencing (NGS)
2.1.- A historical overview
2.2.- The main techniques in Next-Generation sequencing
2.3.- The outcome in NGS experiments. Quality controls. Interpretation.
2.4.- NGS in the clinical: from gene panels to Whole Genome Sequencing. Diagnostics yield.
3.- Measuring gene expression: RNA-Seq
3.1.- Understanding the basics of gene expression. Role in health and disease.
3.2.- How to measure gene expression massively: RNA-Seq
3.3.- The outcome of RNA-Seq experiments. Quality controls. Interpretation.
3.4.- Building gene expression signatures for disease and drug therapy.
4.- Single-cell experiments: a revolutionary look at biological processes
4.1.- Technical and historical overview
4.2.- The main single-cell techniques
4.3.- Single-cell RNA-seq: understanding how gene expression varies within cell populations
4.4.- Analyzing single-cell data: a challenging problem with open solutions
5.- Epigenomics
5.1.- Reviewing the role of epigenetics in health and disease
5.2.- Main techniques in epigenetic studies. ChIP-seq, Cut&Run, etc.
5.3.- Looking for relevant epigenetic marks and patterns: the role of bioinformatics
6.- Can we integrate all these data to obtain an overall view of biomedical problems: the growing field of multi-omics studies
Teaching and learning activities
In person
Lectures: lectures for 2 hours in blocks of 50 minutes on a theoretical topic by the teacher.
Clinical cases or case methods (CM): Presentation of a real or imaginary situation. Students work on the questions posed in small groups or in active interaction with the teacher and the answers are discussed. The teacher actively intervenes and, if necessary, contributes new knowledge.
Virtual education (EV): Online material that the student can consult from any computer, at any time, and which will contribute to self-learning of concepts related to the subject.
Evaluation systems and criteria
In person
Students in the first call:
Case methods: 20%
Midterm exam: 30%
Final exam: 40%
Students in the second or subsequent call: the grade for the case methods will be saved and the final exam will represent 75% of the final grade. Repeating students who wish to repeat the midterm in the 3rd or 5th call may do so by previously communicating this to the professor.
General points to bear in mind about the evaluation system:
In order to be able to make an average, a minimum grade of 5 must be obtained in the final exam.
In addition to what was mentioned above, to pass the subject, the average of all the grades must be 5 or higher.
The continuous nature of this evaluation means that it is not possible to evaluate the subject if you have not participated in 75% of the hours.
Improper use of electronic devices (such as recording and sharing information about students and teachers during the different sessions, as well as the use of these devices for recreational and non-educational purposes) may lead to expulsion from class.
Teachers reserve up to 10% of the grade to be awarded based on subjective arguments such as: involvement, participation, respect for basic rules, etc.