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Genomic Architecture

Vak
2024-2025

Admission requirements

BSc degree containing basics in biochemistry and molecular genetics

Description

How is genetic information organized in genomes? How are genes organized in organisms? What fraction of their genomes consists of genes? How does horizontal gene transfer work? Why do salamanders have much more DNA per cell than we have? How does the genome of related species differ? How is the DNA of different individuals different? How well can we make predictions on health and personalized medicine on the basis of DNA?

With the advance of innovative genome sequencing technologies, those questions and more about DNA, genetics and evolution can, in principle, be answered. Starting from the basics (introns, exons, gene families, recombination, QTLs, sequencing) we address those questions, discuss various examples and ask what all those new insights mean in terms of evolution, development maintainance and health of species.

In individual desk assignments you will get acquainted with modern bioinformatics and genomics analysis while solving several conceptual genomic questions and puzzles, both at a basic and at a more advanced level.

In a small-group project you will analyze and apply genomic information in the context of the biology, behaviour and ecology of various organisms. This analysis will be presented by the group via a poster during a mini-symposium with which we finalize the course.

Course objectives

After completion of this course, students are able to:

  • Explain and apply knowledge (theory of genetics, gene transfer, inheritance) and insight (examples of gene function, speciation) in the field of genomics

  • Explain and apply the basics of genetic regulatory mechanisms

  • Explain, value and discuss state of the art methodology (next generation sequencing, metagenomics analysis) used in genomics

  • Apply basic bioinformatics to analyze, compare and organize genomic information for groups of organisms

  • Analyze and evaluate genomic information for answering scientific questions about evolution, development and health of different species.

Timetable

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).

For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

Mode of instruction

The course will start with an introductory lecture and facultative assessment through which all enrolled students can evaluate themselves whether they comprehend all basic knowledge required at the start of this course. If not, students are encouraged to strengthen their basic knowledge via selfstudy of several specified chapters of ‘Biology; a Global Approach” (Campbell). The course will consist of interactive lectures, with reference to specified chapters of “Introduction to Genomics” (Lesk, 2017, 3rd Edition), individual bioinformatics desk assignments and genome analysis and a hands-on Genomic Architecture analysis and evaluation project performed in small groups (last course week), finalized with a group presentation during a minisymposium.

Assessment method

Formative assessment of individual assignments, digital final exam consisting of multiple choice and open questions (graded), and small group assignment and poster presentation (peer-review and graded).

Reading list

Advised to buy as specific support literature for studentsthis course:

  • Lesk AM (2017) Introduction to genomics. Oxford UP, third3rd edition

Registration

All students have to register for courses with the enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.

Please note that it is compulsory to register your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Enrolling is possible until ten days before the exam.

Extensive FAQ's on MyStudymap can be found here.

Exchange and Study Abroad students, please see the Prospective students website for more information on how to apply.

Contact

Coordinator: Prof. dr. J.H. de Winde
Email: j.h.de.winde@science.leidenuniv.nl

Remarks

First 3 weeks: lectures, self study (DNA, RNA, proteins, genomes throughout the Tree of Life, human evolution) and individual assignments. Week 4 small-group project and final exam. The A detailed course schedule will be placed available on Brightspace.