ILAS Seminar-E2 :Introductory Bioinformatics
| Numbering Code | U-LAS70 10002 SE50 | Year/Term | 2022 ・ Second semester | |
|---|---|---|---|---|
| Number of Credits | 2 | Course Type | seminar | |
| Target Year | Mainly 1st year students | Target Student | For all majors | |
| Language | English | Day/Period | Thu.5 | |
| Instructor name | VANDENBON, Alexis (Institute for Frontier Life and Medical Sciences Senior Lecturer) | |||
| Outline and Purpose of the Course | Bioinformatics is an interdisciplinary field in which statistics, machine learning and computer programming are applied to biological data. Nowadays, computational approaches such as bioinformatics have become an essential part of biological research. This course will offer an overview of bioinformatics techniques, including sequence alignment, comparative and evolutionary genomics, protein structure prediction, analysis of sequencing data, systems biology, widely used biological databases, and single-cell data analysis. | |||
| Course Goals | Students will gain insight into a variety of topics within the field of bioinformatics. By taking this course, students will acquire knowledge about fundamental bioinformatics analyses, and will gain understanding about how bioinformatics can contribute to studies in biology. | |||
| Schedule and Contents |
The course will be offered according to the plan below. If face-to-face lectures are not possible because of the pandemic, the course will be online (“on demand”) and I will add new course material (videos and slides) on PandA. I will also hold a weekly Zoom meeting to take questions. Lectures 1 and 2: Introduction to Bioinformatics. What is bioinformatics? We will introduce various topics in bioinformatics, from the use of sequence alignments in making phylogenetic trees, prediction of protein structure, to the modelling of a simple regulatory network. Lectures 3 and 4: Genome organization and evolution. We will introduce the genomes of prokaryotes and eukaryotes and their content. Genome sequencing projects and metagenomics will be covered. Lecture 5 and 6: Alignments. Aligning sequences is one of the fundamental tasks in bioinformatics. We will start with an introduction to alignment, from dotplots to a dynamic programming algorithm. The usage and interpretation of pairwise sequence alignments will be covered. Lecture 7: Phylogenetics. We will extend pairwise alignments to alignments of multiple sequences. We will introduce methods for turning multiple alignments into phylogenetic trees. We will discuss different types of phylogenetic trees, their properties and interpretation. Lectures 8 and 9: Structural bioinformatics. Starting from a review of the properties of amino acids, we will introduce protein structural alignments and approaches for predicting secondary, tertiary and quaternary protein structure from amino acid sequences. In addition, we will briefly cover methods for predicting protein function. Lecture 10: Systems biology. Complex systems have properties that cannot easily be inferred from their individual components. In this lecture, we will introduce holistic approaches to the study of biology. Especially, we will focus on biological networks and their properties. Lecture 11: Metabolic pathways and Review of course material. We will introduce classification systems for enzymes, and popular databases of metabolic pathways. Lecture 12: Gene expression and regulation. Introduction to so-called “next generation sequencing” (NGS, RNA-seq) approaches, and its applications. The information contained in a typical NGS dataset will be introduced, as well as practical steps in its processing, mapping, and interpretation. Lecture 13: Single-cell data analysis. A brief introduction to approaches for sequencing RNA molecules in single cells (single-cell RNA-seq), and several topics related to the analysis of single-cell data. We will also briefly cover spatial transcriptomics, which are approaches that allow us to see where in a tissue each gene is being transcribed. Lecture 14. Review of course material. Lecture 15. Final examination, if the COVID-19 situation allows it. If a face-to-face examination is impossible, the final examination will be replaced by a number of smaller assignments. Lecture 16. Feedback |
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| Evaluation Methods and Policy | Grading will be based on a final examination (50%) and small assignments (50%). If the COVID-19 situation does not allow a face-to-face examination, the grading will be based completely on assignments (100%). | |||
| Course Requirements | Students are expected to have basic knowledge about molecular biology. | |||
| Study outside of Class (preparation and review) | The course lectures will follow the content of this textbook, but it is not compulsory to buy the textbook. I will hand out slides for the content of every lecture. | |||
| Textbooks | Textbooks/References | Introduction to Bioinformatics (5th edition), Arthur Lesk, (Oxford University Press), ISBN:978-0198794141, The course lectures will follow the content of this textbook, but it is not compulsory to buy the textbook. | ||
