Archana Bhardwaj

Start date

20 September 2022

Location

Please join this class from your computer, tablet or smartphone via
https://global.gotomeeting.com/join/916883981

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:
https://global.gotomeeting.com/install/916883981

Time

13:45-17:45

TO DO

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

Sep-20                   

Meet & Greet

• Lecture 1_ Course Administration and Expectations (updated 20/9 10:30 am)
• Lecture 1_ HW Organization

• Lecture 1_Critical Evaluation of a Paper
  

• Scientific Communication
• Lecture 1_In class paper reading
• R code shown in class (updated 20/9 10:30 am)

• Self-study_ Software Introduction (author: Archana Bhardwaj)
  • DATA_FILES
  • Specific_R_CODE_REPORT

• First class (Prof  Kristel Van Steen) via https://global.gotomeeting.com/join/916883981
• Video : Introduction by Prof Van Steen

     Class 1_Admin (ac year 2020-2021)

     Class 1_Admin with R intro

• Video : Software (environments) by Archana Bhardwaj
  

       R_PLINK

• Example Book References and important links

PART I : Genomic Association Studies

Oct-04

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

•  Lecture 2 (updated 21.09.2021) - principles of genetics

Oct-11

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

• Lecture 3a - GWAS (updated 27.09.2021)
• Supporting docs (exam material):
  • Bush et al. (2012) - Computational biology introduction to GWAS
  • Balding et al. (2016) - Statistical introduction to GWAS

• 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)
  • Bioinformatics part
  • Genetics part
    
  • Select your homework style asap: follow this link (contains group formation)
    

•  GWAS (continued)
  • Extra materials on regression (see course mail)
• Real-life experiences from a bioinformaticion: big data handling issues
  • exam material: pay attention in class
  • Slides deck
  • recovered MIRO graphs: one, two, three

• ONLINE via https://global.gotomeeting.com/join/916883981
• Prof Kristel Van Steen
• Giada Lalli
  • Background papers used to build the class:
    • Reference 1
    • Reference 2
    • Reference 3
    • Reference 4
• Video recordings (mp4 files by Archana Bhardwaj):
  
  • GWAS-Part1 
  • GWAS-Part2
    
  • DATASET
• Background:
  
  • Want to know more about multiple testing? Have a look at the following basics: https://uclouvain-cbio.github.io/WSBIM1322/sec-testing.html
  • Lecture 3b - GWAS (continued); extra slides on qq-plots can be downloaded from here

Nov-08

Toward translationof GWAS into clinical practice

• Lecture 4 - 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 in-class paper: example
• Supporting doc - Materials from practical session on PRS/MRS and computational efficiency:
  
  • Slides & reference via WeTransfer (please download asap): https://wetransfer.com/downloads/586d88a4f4d01942c29f4ea98a5488c920221108133214/9e3bc892aa204bd19859ce0bdc69795820221108133215/caf5ef
    

• Prof Kristel Van Steen (in person)
• Federico Melograna (TA - practical recommendations; example of a bioinformatician's workflow)
• Background reading I (DNA rare variant screening viewed from a polygenic risk scoring perspective) : Lu et al. (2021)
  • Processing example (illustration for and prepration to literature style homework assignments; how the tutor has identified main points in the paper): here
• Background reading II (bridging bioinformatics and genomics - not exam material): McGuire et al. (2020) - The road ahead in genetics and genomics
• Background reading III (bioinformatics - not exam material):
  
  • A primer to DNA-based sequence analyses
  • Povysil et al. (2019) - Rare- variant collapsing analyses for complex traits: guidelines and applications

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

and proteomics:  data generation and low-level analyses

• Lecture 5a - Principles of Sequencing (updated 9/11/2022)
  
• Lecture 5b -  RNA seq analysis in practice with linked documents and tutorials:
  
  • DESeq2
  • DGE workshop

• 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)
  • Bioinformatics part
  • Genetics part

Nov-22

 PRESENTATIONS (by group, HMW1)

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

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)
  • SMCCNET
  • ISN

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

ONLINE via: https://global.gotomeeting.com/join/916883981

• 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)
  

Dec-13

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