Admission requirements
This course is mandatory for and restricted to students who do the Minor ‘Computational approach to Disease Signaling and Drug Targets’ (CADSDT; the entire Minor or only Part 2) or the ‘Elective Module DSDT’. The same admission criteria apply to this course as for the respective afore mentioned programs.
Description
With the emergence of high throughput DNA sequencing technologies, the complete genome sequences of many organisms are deciphered and are being analyzed. Despite the progress, understanding the cellular functions of most of identified genes remains a challenge. The emerging field of “Functional Genomics” aims at providing comprehensive approaches to understand the genome functions, to develop and promote high throughput and large scale approaches to investigate the function of the genomes, their products and the interactions between the two.
Indeed, high-throughput techniques such as high-throughput genome-scale DNA, RNA sequencing or protein analysis by mass spectrometry, are successfully applied to diverse biological questions with the goal of reaching a comprehensive description of their molecular regulation. Yet, they cannot provide temporal or spatial resolution nor directly show that the identified molecules have a function in the dynamic cellular process investigated. Quantitative fluorescence-microscopy in living cells overcomes these limitations because it can probe the function of macromolecules in living cells with ever increasing spatial and temporal resolution.
Imaging-based assays enable genome-wide functional analyses by high-throughput microscopy if combined with standardized reagents that systematically interfere with gene expression or protein activity (e.g. siRNAs, sgRNAs in conjunction with CRISPR/Cas9, chemical inhibitor libraries). In addition, new GFP-tagging genome-editing-based approaches now also allow systematic direct characterization of the abundance, localization, dynamics and interaction of proteins in intact cells, and therefore hold the promise of imaging-based proteomics in single living cells.
This course will provide an overview of the concept of Functional Genomics, how to link a genotype to a phenotype. Contemporary approaches used to understand the genome function will be described and exemplified in this course.
Course Objectives
After completing the course, the student will be able to:
describe what is meant by functional genomics and how this area of research contributes both to new basic biomedical knowledge and to new developments in biomedicine and biotechnology, including improved diagnostics and treatment of disease
describe and discuss how functional genomics contributes to systems biology and systems medicine
explain the different state-of-the-art “omics” technologies that are currently applied to perform global analyses at a system level (high throughput transcriptomic and genomic analysis RNA-seq, proteomics and metabolomics)
explain main principles of bioinformatic tools used for data analysis, biological background knowledge management and modeling
explain how the researcher can apply high-content screening for functional genomics (RNAi high-throughput screening, high-throughput live cell imaging, high-content imaging systems and tools, high-content image analysis)
Timetable
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
PLEASE NOTE
Always check the detailed schedule on the Brightspace module of each Course 2-3 weeks before the start of the Course for group-specific meetings, (intermediate) deadlines, etc..
Mode of instruction
The course will use a combination of lectures, discussions of assigned literature and computer-based exercises (workshops). Most of the course will be offered in the morning and will focus on Functional Genomics approaches and their application in (pre-)clinical studies. Students will be expected to critically read assigned papers beforehand. There will also be hands-on experience how bioinformatics tools can be applied to analyze omics and screening data output.
Assessment method
The course will be concluded by a written exam. Students will be graded for their work in groups (30%) and for the individual written exam (70%). Both partial grades need to be ≥5.0 and their weighted average ≥5.5 in order to pass the course.
Reading list
Literature will be provided during the course.
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Mw. Dr. S.E. Le Dévédec
Remarks
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.