Archana Bhardwaj

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2021 - 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



  • 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

14 September 2020


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 Dequiedt (in person)


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

  • Prof Van Steen (in person)


 Oct-5 GWAS in Practice
  •  Lecture 4 - GWAS (continued)
    • extra slides on qq-plots can be downloaded from here
  • Real-life experiences from a bioinformaticion (materials retrospectively posted here)
    • interoperability
    • TPOT
  • Q&A self-study (see Class 1)


Principles of DNA sequencing technologies and low-level analyses

  • Lecture 5 - Principles of Sequencing (updated 13 October 7:39PM)
  • Prof Dequiedt (in person)
Oct-19 Principles of gene expression and proteomics:  data generation and low-level analyses
  • Prof Dequiedt(in person)


High-level DNA sequence analyses: Why, What, How?

  • Lecture 7 - performing polygenic score analyses
    • In class reading and discussion
    • aims: increase GWAS concepts understanding and their links to DNA-seq rare variants analysis.
    • Processing the paper: example
  • Supporting doc - DNA rare variant screening viewed from a polygenic risk scoring perspective (exam material): Lu et al. (2021)
    • Processing example (illustration for and prepration to literature style homework assignments): here
Nov -9   Lecture 8a -  RNA seq analysis in practice
Associated docs & tutos:
Lecture 8b - Protein interactions
  • Arnaud Lavergne (GIGA - Genomics Core Facility; Member of GIGA Bioinformatics Team)
  • Prof Dequiedt (in person)




Systems analytics: principles and examples


Student presentations & discussion
  • homework assignment 1 - literature style (genetics)
  • Q&A about the genetics course
  • Solutions to Q&A style homework assignment 1 (genetics)
  • Moderated by Prof Dequiedt (in person)


Student presentations & discussion
  • homework assignment 1 - literature style (bioinformatics)
  • Solutions to Q&A style homework assignment 1 (bioinformatics)


from 2-4 PM

Systems analytics: metabolomics


Student presentations & discussion
  • homework assignment 2 - literature style (genetics)
  • homework assignment 2 literature style (bioinformatics)
  • Course closure: feedback & exam preparation
  • Moderated by Prof Dequiedt & Prof Van Steen (in person)


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