NWI-BB064B
Functional Genomics
Course infoSchedule
Course moduleNWI-BB064B
Credits (ECTS)6
Category03 (Advanced)
Language of instructionEnglish
Offered byRadboud University; Faculty of Science; BioWetenschappen;
Lecturer(s)
PreviousNext 1
Lecturer
dr. J.H.A. Martens
Other course modules lecturer
Lecturer
prof. M.M.K. Mhlanga
Other course modules lecturer
Lecturer
dr. K.W. Mulder
Other course modules lecturer
Examiner
dr. K.W. Mulder
Other course modules lecturer
Coordinator
dr. K.W. Mulder
Other course modules lecturer
Academic year2023
Period
KW3  (29/01/2024 to 07/04/2024)
Starting block
KW3
Course mode
full-time
Remarks-
Registration using OSIRISYes
Course open to students from other facultiesYes
Pre-registrationNo
Waiting listNo
Placement procedure-
Aims
At the end of the course
  1. The student understands the field of functional genomics, its key terms and concepts, and is able to explain these terms and concepts in a way that demonstrates a correct understanding of the relevant molecular and biological processes and mechanisms
  2. The student has a good understanding of the experimental approaches that are relevant for research questions on the subject, as shown by the ability to design experiments to address a relevant research question and the ability to explain the possibilities and limitations of specific experimental approaches
  3. The student is also able to interpret and evaluate experimental results related to this field, as shown by the ability to derive and justify meaningful and legitimate conclusions from experimental data
Content
To allow students to attain the level of knowledge and understanding described in the course objectives, the lectures will treat the following topics: 
    
• To provide insight in the historical and technology-driven development of the genome sciences, the (recent) technological advances in sequencing will be briefly reviewed (lecture topic: Sequencing & Genomics). 
    
• The molecular mechanisms and networks that regulate the genome constitute another major component of the course (lecture topics: Epigenetics, Chromosomal interactions, Systems biology)
    
• A third major component of course content concerns high-throughput screens of interactions and functions that help to characterize genes on a genome-wide scale and how we can exploit genomic analyses to improve our understanding of cancer (lecture topics: Cancer genomics, Genome Engineering, Genome-wide disease screens, Single-cell Genomics)
    
The Questions & Answers (Q&A) sessions (two hours each) are designed to provide a deeper insight in each of these topics. To this end the students will prepare answers to questions, discuss these answers in small groups, followed by a plenary discussion with teaching staff. The Q&A questions are also meant to prepare for the exam. In addition a practice exam is provided.The Computer Practical complements the students' experience of Functional Genomics and is designed to train and assess students for course objective 3. In this practical experimental genomic data is visualized and analyzed to introduce the students to bioinformatic analyses and to deepen their knowledge and understanding of epigenetics using real datasets. This computer practical consists of an interactive R-studio programming environment where students will get familiar with statistical and computational methods to extract meaningful insight from (epi-)genomics data. Note: coding experience is not a requirement and your coding proficiency will not be part of the Computer Final Assignments. Nonetheless you will be changing and filling-in code-snippets during the computer practicals.

As part of the practical the students will work with the UCSC genome browser and R-Studio, develop an understanding of what types of genomic data can be analyzed and how the input and output are formatted. The students will develop their critical-thinking, problem-solving and communication skills in the area of genomics and will develop an ability to interpret genomic data, report the results and explain, discuss and justify their conclusions. The computer practical is concluded with a Final Assignment in Brightspace in which the students have to use the results of the the experimental data they have analyzed during the computer practicals to interpret, explain and key concepts from the theoretical component of the course.

Instructional Modes
  • Lectures
  • Q&A sessions
  • Computer Practicals
  • Self-study
Level

Presumed foreknowledge
The student is expected to have prior knowledge corresponding to the subject matter of the course Advanced Molecular Biology II (AMB, see Lodish 7 chapters 4, 7, 8, 19 and 24)
Test information
  • exam with open and multiple choice questions and with computer practical assignments, counts for 80%. minimum grade 5.00.
  • computer practical assignment, counts for 20%, no minimum grade
  • highly recommended participation in Questions and Answers ('werkcolleges')
  • mandatory participation in Computer practical, copies of the results to be handed in after completion each time.
Specifics
The course is scheduled on Thursdays and Fridays, but all course activities will be recorded or can be completed by the participants on other times during the week as well.
Therefore the course can be taken together with, .e.g. NWI-MOL055 Molecular Basis of Diseases.
Make sure you plan well.
Required materials
Learning Management System (Brigthspace)
Selected texts (on Brightspace)

Recommended materials
Book
Lodish et al.: Molecular Cell Biology, 6th edition (Freeman and Company, New York, 2008)

Instructional modes
Course occurrence

Practical computer training
Attendance MandatoryYes

Tests
Digi-Cirrus
Test weight4
Test typeDigital exam with CIRRUS
OpportunitiesBlock KW3, Block KW4

Assignments
Test weight1
Test typeAssignment
OpportunitiesBlock KW3, Block KW4