Archana Bhardwaj - 2021 - GBIO0002 - Genetics and bioinformatics

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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

UPDATES

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
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.

COURSE SCHEDULE-IN-A-GLANCE & COURSE NOTES (check for updates):

Dates	Topics	Materials	Class links & supplementary info
Sep-14	Meet & Greet	Lecture 1_ Course Administration and Expectations Lecture 1_ HW Organization Lecture 1_Critical Evaluation of a Paper Scientific Communication Lecture 1_In class paper reading R code shown in class Self-study_ Software Introduction (author: Archana Bhardwaj) DATA_FILES Specific_R_CODE_REPORT	First class (Prof 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
Sep-21	Genetics and Genetic Markers: from "DNA blueprint" to variation	Lecture 2 (updated 21.09.2021) - principles of genetics	Prof Dequiedt (in person)
Sep-28	Genetic mapping using GWAS as high-level analysis: Why, What, How?	Lecture 3 - 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 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)	Prof Van Steen (in person) Giada Lalli (in person) 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
Oct-12	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	Lecture 6a- gene expression Lecture 6b - proteomics (updated video lecture via Prof Dequiedt)	Prof Dequiedt(in person)
Oct-26	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	Prof Van Steen: https://global.gotomeeting.com/join/916883981 Background reading I (bridging bioinformatics and genomics - not exam material): McGuire et al. (2020) - The road ahead in genetics and genomics Background reading II (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 Homework assignment 1 (introduced and discussed in class): Bioinformatics & Genetics (by 23 November) Bioinformatics part Genetics part Select your homework style asap (check your mails for the link!) Additional instructions here
Nov -9		Lecture 8a - RNA seq analysis in practice Associated docs & tutos: DESeq2 DGE workshop Lecture 8b - Protein interactions	Arnaud Lavergne (GIGA - Genomics Core Facility; Member of GIGA Bioinformatics Team) Prof Dequiedt (in person)
Nov-16	Systems analytics: principles and examples	Lecture 9 Supporting doc (exam material: what has been covered in class) - Van Steen 2021	Prof Van Steen via https://global.gotomeeting.com/join/916883981 Homework assignment 2 (introduced and discussed in class): Bioinformatics & Genetics (by 14 December) Bioinformatics part Genetics part
Nov-23	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)
Nov-30	Student presentations & discussion	homework assignment 1 - literature style (bioinformatics) Solutions to Q&A style homework assignment 1 (bioinformatics)	Moderated by Prof Van Steen: online via https://global.gotomeeting.com/join/916883981 or postponed to next week (check with student representative Lucie)
Dec-7 from 2-4 PM	Systems analytics: metabolomics	Lecture 10	Guest lecture by Prof Michiel Adriaens (Maastricht University, the Netherlands) ; online via https://global.gotomeeting.com/join/916883981
Dec-14	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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