GBIO0002-1: Genetics and Bioinformatics 2014-15

This course is intended for students who registered for GBIO009-1 Bioinformatics 2014 OR GBIO0002-1 Genetics and Bioinformatics 2014-15

Exam information (re-write)

The exam is open book. This written exam will count for 40% of the final mark. This is exam re-write is only for students that did not obtain the passing grade in Jan 2015.

Date 28 Aug 2015 (Friday)
Location Room R157 (B28)
Time 10:00 am

Corrected HWs

The corrected HWs and feedback are found in this section. PartA HW comments would be posted later. To download the *.zip archive you need to login with the same credentials you used for HW submission

download link

Course schedule and location

Please consult current course schedule here

Start date23 Sept 2014 (Tuesday)
LocationRoom 1.21, building B28
Timefrom 14:00 til 18:00
ProfessorsKristel Van Steen & Franck DEQUIEDT


• Sept 22th:The next class of "Genetics and Bioinformatics" (GBIO0002/9) will be given THIS WEEK, on TUESDAY at 2pm. All GBIO0009 students should follow the GBIO00002 "Genetics and Bioinformatics" class instead. Both courses take place at the same moment.

• Oct 6th: Please note that this week class will start at 3pm. This week is an exception.

• Oct 22th: Guiding questions for some the HW1b papers were posted. You are welcome to come by my office 1/16 and ask me HW realted questions the following weeks between 29Oct - Nov 4th

• Dec 9th: This our last class. The 3 groups will give oral presentations. Presentations will be graded based on originality, presentation skills and ability to answer questions. Prof. Kristel Van Steen is available to address questions related to the theory in preparation to the exam. Please send a message her ULg mail address to make an appointment. If there is a need for an additional session, then Prof. Van Steen will organize this.

• Dec 23th:The exam info and student presentations posted. The corrected HWs and partial marks will be posted in 2-3 days

Assignment submission

Assignments for this course are submitted on-line via specially dedicated website. One needs to create a new account to be able to login and submit your assignments. In the event of passed deadlines and/or thechnical difficulties, please send your work via email to Kyrylo Bessonov (TA).


Course material

September 18, 2014 - the 1st class . Class starts at 2pm

pdf Introductory lecture: course details, R-language, databases

pdf BioDatabases Assignment - Demo

September 23, 2014 - RETAKE of the 1st class Class starts at 2pm

pdf LECTURE 1: Bioinformatics as a Discipline

September 30, 2014 Class starts at 2pm

pdf LECTURE 2: Principles of Molecular Biology and Genetics + Genome Structure and Mapping

pdf HW 1a - option 1

pdf HW 1a - option 2

October 7, 2014 Class starts at 3pm

pdf LECTURE 3: Genome-wide Association Studies What? How? Hurdles? Relation to bioinformatics? Variable (pre-) selection?

video Programming of Life Video Lecture

October 14, 2014 Class starts at 2pm

pdf PRACTICAL 1: Practical aspects of GWAS and GENABEL library

pdf HW 1b - type 1 (literature)

    1. Option 1: Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.
    2. Option 2: Balding, David J. "A tutorial on statistical methods for population association studies." Nature Reviews Genetics 7.10 (2006): 781-791.
    3. Option 3: Ziegler, Andreas, and Yan V. Sun. "Study designs and methods post genome-wide association studies." Human genetics 131.10 (2012): 1525-1531. AND Ambrosone, Christine B. "The promise and limitations of genome-wide association studies to elucidate the causes of breast cancer." Breast Cancer Res 9.6 (2007): 114.
    4. Option 4: Slatkin, Montgomery. "Linkage disequilibrium—understanding the evolutionary past and mapping the medical future." Nature Reviews Genetics 9.6 (2008): 477-485.

Guiding questions to help with paper

  1. Anderson2010 questions
  2. Balding2006 questions

pdf HW 1b - type 2 (programming)

ppt HW1b - type 3 (Q&A on GWAS and GenABEL)

October 21, 2014 Class starts at 2pm

ppt LECTURE 4: Principles of DNA sequencing data

October 28, 2014 Class starts at 2pm

pdf LECTURE 5: DNA sequence descriptive and comparative analysis

Nov 4th, 2014 Class starts at 2pm

ppt Practical 2: on sequence analysis and alignment

pdf HW 2a - option 1

pdf HW 2a - option 2

pdf HW 2b - type 1 (literature)

    1. Option 1: Cirulli, Elizabeth T., and David B. Goldstein. "Uncovering the roles of rare variants in common disease through whole-genome sequencing." Nature Reviews Genetics 11.6 (2010): 415-425.
    2. Option 2: Do, Ron, Sekar Kathiresan, and Gonçalo R. Abecasis. "Exome sequencing and complex disease: practical aspects of rare variant association studies." Human molecular genetics 21.R1 (2012): R1-R9
    3. Option 3: Shendure, Jay, and Hanlee Ji. "Next-generation DNA sequencing." Nature biotechnology 26.10 (2008): 1135-1145
    4. Option 4: Martin, Jeffrey A., and Zhong Wang. "Next-generation transcriptome assembly." Nature Reviews Genetics 12.10 (2011): 671-682
    5. Option 5: Ding, Li, et al. "Expanding the computational toolbox for mining cancer genomes." Nature Reviews Genetics 15.8 (2014): 556-570

pdf HW 2b - Seq Alignment type 2 (computer)

pdf HW 2b - Seq Alignment type 3 (QandA)

Nov 18th, 2014 Class starts at 2pm

ppt Lecture 6a: Principles of gene expression

ppt Lecture 6b: Protein- protein interactions

Nov 25th, 2014 Class starts at 2pm

ppt Lecture 7: Gene Networks

ppt Practical: Gene Co-expression Networks and WGCNA package

pdf HW 3a - Principles of Gene expression (option 1)

pdf HW 3a - Protein-Protein interaction (option 2)

pdf HW 3b - Gene networks (WGCNA) (Literature)

    1. Option 1: Barabasi, Albert-Laszlo, and Zoltan N. Oltvai. "Network biology: understanding the cell's functional organization." Nature Reviews Genetics 5.2 (2004): 101-113
    2. Option 2: Udyavar, Akshata R., et al. "Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer." BMC systems biology 7.S-5 (2013): S1.

pdf HW 3b - Co-expression networks (WGCNA) (Q&A)

Dec 9th, 2014 Class starts at 2pm

Students will give oral presentations of chosen papers followed by discussion in class. In addition, exam details will be given.

pdf Presentation 1 by DERYA,LUC and,RAYAN

pdf Presentation 2 by Coralie and Hervé

pdf Presentation 3 by Eva and Funny