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
Understand 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
- CB01 - Students must demonstrate that they have and understand knowledge in an area of study that is based on general secondary education, and it tends to be found at a level that, although it is based on advanced textbooks, also includes some aspects that involve knowledge from the cutting-edge of their field of study.
- CB03 - Students must have the ability to bring together and interpret significant data (normally within their area of study) to issue judgements that include a reflection on significant issues of a social, scientific and ethical nature.
- CB04 - That students can transmit information, ideas, problems and solutions to specialist and non-specialist audiences.
- CB05 - That students have developed the necessary learning skills to undertake subsequent studies with a high degree of autonomy.
- CE07 - To apply statistical tools to Health Science studies.
- CE19 - To be aware of the principles of biomedical science related to health and learn how to work in any field of Biomedical Sciences (biomedical companies, bioinformatics laboratories, research laboratories, clinical analysis companies, etc.).
- CG07 - To incorporate basic concepts related to the field of biomedicine both at a theoretical and an experimental level.
- CG10 - To design, write up and execute projects connected to the field of Biomedical Sciences.
- CG11 - To be aware of basic concepts from different fields connected to biomedical sciences.
- CT01 - To develop the organisational and planning skills that are suitable in each moment.
- CT02 - To develop the ability to resolve problems.
- CT03 - To develop analytical and summarising skills.
- CT04 - To interpret experimental results and identify consistent and inconsistent elements.
- CT05 - To use the internet as a means of communication and a source of information.
- CT06 - To know how to communicate, give presentations and write up scientific reports.
- CT07 - To be capable of working in a team.
- CT08 - To reason and evaluate situations and results from a critical and constructive point of view.
- CT09 - To have the ability to develop interpersonal skills.
- CT10 - To be capable of autonomous learning.
- CT11 - To apply theoretical knowledge to practice.
- CT12 - To apply scientific method.
- CT13 - To be aware of the general and specific aspects related to the field of nutrition and ageing.
- CT14 - To respect the fundamental rights of equality between men and women, and the promotion of human rights and the values that are specific to a culture of peace and democratic values.
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.