Archana Bhardwaj

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2022 - GBIO0002 - Genetics and bioinformatics


In this course genetic concepts are introduced that are necessary to understand a selection of bioinformatics related data analysis problems. To solve these problems a variety of analytic tools will be explained and exemplified.

The course is in part based on interactive ex-cathedra lectures and in part on interactive practical sessions. The exercise sessions allow students to become familiar with the theoretical concepts introduced during the theory classes. They prepare students to successfully carry out their homework assignments.

This course is organized by Kristel VAN STEEN and Franck DEQUIEDT



  • Note the extended due date for the 2nd homework assignment
  • Class of 25 October includes a guest speaker and will be organized as an online class.
  • Course notes may be updated based on detected typographical errors with no  impact on the content or discussions in class; Course notes are uploaded as soon as the course contributor makes them available. Please stay tuned. In case of doubt, contact the course tutors.
  • Prepare yourself for the first class: Please follow the instructions HERE to pre-install on your computer the software that will be used in class 1 and/or subsequent classes.

Start date

20 September 2022


Please join this class from your computer, tablet or smartphone via

This is the link to use for Class 1 by Prof Van Steen. The subsequent classes will be in person, unless communicated otherwise. Check CELCAT and UPDATES above.

Avoid smartphone connections for the online class.

New to GoToMeeting? Get the app now and be ready when your first meeting starts:




Please complete the following administrative form by clicking HERE. It will be used to manage group formation for homework assignments.



Dates Topics Materials Class links & supplementary info


Meet & Greet



     Class 1_Admin (ac year 2020-2021)

     Class 1_Admin with R intro

  • Video : Software (environments) by Archana Bhardwaj


PART I : Genomic Association Studies


Genetics and Genetic Markers: from "DNA blueprint" to  variation

  •  Lecture 2 (updated 21.09.2021) - principles of genetics

  •  Prof Franck Dequiedt (in person)


Genetic mapping using GWAS as high-level analysis: Why, What, How?

  • Prof Kristel Van Steen (in person)
  • Homework assignment 1 (example discussed in class as; final version will follow on Oct 15): Bioinformatics & Genetics (by 15 November)


 Oct-25 GWAS in Practice
  •  GWAS (continued)
    • Extra materials on regression (see course mail)
  • Real-life experiences from a bioinformaticion: big data handling issues


Toward translationof GWAS into clinical practice


Principles of RNA sequencing and gene expression with low-level data analysis techniques

and proteomics:  data generation and low-level analyses

  • Prof Franck Dequiedt (in person)
  • Arnaud Lavergne (GIGA - Genomics Core Facility; Member of GIGA Bioinformatics Team)
  • Homework assignment 2 (introduced and discussed in class): Bioinformatics & Genetics (Q&A or final version of slides by 20 December)



(depending on the number of groups; an additional presentation moment can be foreseen)

Nov -29 Biological and analytic networks

  • Prof Franck Dequiedt(in person)

Dec -6

Systems analytics: full circle;

Case study on metabolomics

  • Lecture 7 - modeling the genetics and metabolism of heart failure (slides from last year)
  • feedback homework 1 bioinformatics: presentations; solutions Q&A assignment
  • Lecture 8 - living in a world of interactions (updated slides)
  • Lecture 9: Networks and network analysis (novel class; a bioinformatician's workflow)

Several guest speakers: for ease of organization this class will be 


  • Prof Kristel Van Steen
  • Showcase of network analyses: Federico Melograna & Zuqi Li (TranSYS Marie Sklodowska Curie Early Stage Researchers)
  • Case study: Guest lecture by Prof Michiel Adriaens (Maastricht University, the Netherlands)



(depending on the number of groups; an additional presentation moment can be foreseen)

  • Feedback homework 1 genetics: presentations; solutions Q&A  assignment
  • Preparing for the exam
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