Archana Bhardwaj - 2020 - GBIO0002 - Genetics and bioinformatics

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2020 - 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

Class of 1 December 2002 will start at 14.30 and will finish at 17.00
31 October 2020: Additional instructions for homework assignment 1 can be downloaded HERE .
12 October 2020: The group memberships for homework assignments can be viewed HERE . Every group should have at least one master student as a member. We propose that master students take the initiative to contact fellow members. As soon as the homework assignments are available, please discuss in your group which style of homework you will take and indicate this in the form (last two columns; dropdown menue). On the basis of this information, further instructions will follow (for instance, about the duration of each presentation in case you selected "literature style").
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	15 September 2020
Location	Online Please join this class from your computer, tablet or smartphone via https://global.gotomeeting.com/join/916883981 This is the link to use for classes by Prof Van Steen (including class 1). Other links will be included in the course schedule below Avoid smartphone connections. 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: View updates here.

COURSE NOTES:

Dates	Topics	Materials	Class links
Sep-15	Meet & Greet	Lecture 1_ Course Administration and Expectations Lecture 1_ HW Organization Lecture 1_Critical Evaluation of a Paper Supporting Book References Important Links Scientific Communication Lecture 1_ Software Introduction(Bhardwaj) DATA_FILES Specific_R_CODE_REPORT	First hour (Prof Van Steen) via https://global.gotomeeting.com/join/916883981 Second through fourth hour (A Bhardwaj) via https://global.gotomeeting.com/join/274762229 Video : Introduction by Prof Van Steen Class 1_Admin Video : R Session R_PLINK
PART I : Genomic Association Studies
Sep-22	Genetics and Genetic Markers: from "DNA blueprint" to variation	Lecture 2	Prof Dequiedt (via Blackboard Collaborate) https://eu.bbcollab.com/guest/d53685ac48c04590a11993fa37bd32ae Important instructions: The virtual classroom should also be available in students myecampus platform, under the GBIO0002 course : Tab: Virtual Classroom, content : Class 09/22. Class will start at 1:45 PM but login is available from 1:30. It is highly recommended to use the Chrome browser, disable your camera during the course and generally, follow the recommendations for Collaborate for students. In case of a problem, please refer to Blackbaord Collaborate help: https://help.blackboard.com/fr-fr/Collaborate
Sep-29	Genetic mapping using GWAS as high-level analysis: Why, What, How?	Lecture 3 Supporting docs (exam material): Bush et al. (2012) - Computational biology introduction to GWAS Balding et al. (2016) - Statistical introduction to GWAS	Prof Van Steen via https://global.gotomeeting.com/join/916883981
Oct-6	GWAS in Practice	Lecture 4_GWAS DATASET	Archana Bhardwaj via https://global.gotomeeting.com/join/427520829 Contact A.Bhardwaj@uliege.be (Kristel.VanSteen@uliege.be in cc) to iterate further about GWAS in Practice Video recordings (mp4 files): GWAS-Part1 GWAS-Part2
Oct-13	Principles of DNA sequencing technologies and low-level analyses	Lecture 5_Principles of Sequencing	Prof Dequiedt (via Blackboard Collaborate) The link to the class is https://eu.bbcollab.com/guest/b52533273cdb4afcaae7a5d87e0b910a In case of a problem, please refer to Blackbaord Collaborate help: https://help.blackboard.com/fr-fr/Collaborate
Oct-20	High-level DNA sequence analyses: Why, What, How?	Lecture 6 Supporting doc (exam material): Povysil et al. (2019) - Rare- variant collapsing analyses for complex traits: guidelines and applications	Prof Van Steen via https://global.gotomeeting.com/join/916883981 Background reading (not exam material):McGuire et al. (2020) - The road ahead in genetics and genomics Homework assignment 1: Bioinformatics & Genetics (by 15th November) Bioinformatics part: papers Bioinformatics part: data Select your homework style here (before 24th October!) Additional instructions here
Oct-27	Principles of gene expression and proteomics: data generation and low-level analyses	gene expression: Lecture 7a proteomics: Lecture 7b	Prof Dequiedt via https://eu.bbcollab.com/guest/2d64a95a0b5142408b6008c5bfc37a41
Nov-10	Systems analytics: principles and examples	Lecture 8 Supporting doc (exam material): Van Steen (short course, Slovenia, 2016): Living in a world of interactions	Prof Van Steen via https://global.gotomeeting.com/join/916883981
Nov-17	Student presentations	homework assignment 1 - literature style (bioinformatics analytics)	Moderated by Prof Van Steen via https://global.gotomeeting.com/join/916883981 Homework assignment 2: Bioinformatics & Genetics (by 6th December) Bioinformatics part: papers Select your homework style here (asap!)
Nov-24	Student presentations	homework assignment 1 - literature style (genetics) Lecture 9: RNA seq analysis in practice Associated docs & tutos: DESeq2 DGE workshop	Moderated by Prof Dequiedt via https://eu.bbcollab.com/guest/5bc0e4b482ed4499b2c8101d63f5829d Practical session: Arnaud Lavergne (GIGA - Genomics Core Facility; Member of GIGA Bioinformatics Team) video via ecampus (virtual rooms, "enregistrements") Missing additional Q (Q&A - bioinformatics) to homework 2: included in homework assignment Nov-17
Dec-1	Systems Analyses	Lecture 10	Guest lecture by Prof Michiel Adriaens (Maastricht University, the Netherlands) video via campus Via https://global.gotomeeting.com/join/916883981 Class starts at 14:30 !
Dec-8	Student presentations	homework assignment 2 - literature style (genetics)	Moderated by Prof Dequiedt via https://eu.bbcollab.com/guest/7bb42f1a518542759dc2cf746c2117 Feedback on homework assignment 1 (genetics & bioinformatics analytics): see mail
Dec-15	Student presentations	homework assignment 2 - literature style (bioinformatics analytics)	Moderated by Prof Van Steen via https://global.gotomeeting.com/join/916883981 Want to know more about multiple testing? Have a look at the following basics: https://uclouvain-cbio.github.io/WSBIM1322/sec-testing.html Feedback on homework assignment 2: see mail (pending)

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