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
Course schedule and location
Please consult current course schedule here
Start date | 23 Sept 2014 (Tuesday) |
Location | Room 1.21, building B28 |
Time | from 14:00 til 18:00 |
Professors | Kristel Van Steen & Franck DEQUIEDT |
Anouncements
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
Introductory lecture: course details, R-language, databases
BioDatabases Assignment - Demo
September 23, 2014 - RETAKE of the 1st class Class starts at 2pm
LECTURE 1: Bioinformatics as a Discipline
September 30, 2014 Class starts at 2pm
LECTURE 2: Principles of Molecular Biology and Genetics + Genome Structure and Mapping
October 7, 2014 Class starts at 3pm
Programming of Life Video Lecture
October 14, 2014 Class starts at 2pm
PRACTICAL 1: Practical aspects of GWAS and GENABEL library
- Option 1: Anderson, Carl A., et al. "Data quality control in genetic case-control association studies." Nature protocols 5.9 (2010): 1564-1573.
- Option 2: Balding, David J. "A tutorial on statistical methods for population association studies." Nature Reviews Genetics 7.10 (2006): 781-791.
- 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.
- 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
- Phenotype file: ACRN_phenoData.phe
- Genotype file: genoeData_GenABEL.raw
HW1b - type 3 (Q&A on GWAS and GenABEL)
- Phenotype file: wgDat.phe
- Genotype file: wgDat.raw
- R-fucntion to plot Venn Diagram: plot-VennDiagram.R
October 21, 2014 Class starts at 2pm
LECTURE 4: Principles of DNA sequencing data
October 28, 2014 Class starts at 2pm
LECTURE 5: DNA sequence descriptive and comparative analysis
Nov 4th, 2014 Class starts at 2pm
Practical 2: on sequence analysis and alignment
- 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.
- 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
- Option 3: Shendure, Jay, and Hanlee Ji. "Next-generation DNA sequencing." Nature biotechnology 26.10 (2008): 1135-1145
- Option 4: Martin, Jeffrey A., and Zhong Wang. "Next-generation transcriptome assembly." Nature Reviews Genetics 12.10 (2011): 671-682
- Option 5: Ding, Li, et al. "Expanding the computational toolbox for mining cancer genomes." Nature Reviews Genetics 15.8 (2014): 556-570
HW 2b - Seq Alignment type 2 (computer)
HW 2b - Seq Alignment type 3 (QandA)
Nov 18th, 2014 Class starts at 2pm
Lecture 6a: Principles of gene expression
Lecture 6b: Protein- protein interactions
Nov 25th, 2014 Class starts at 2pm
Practical: Gene Co-expression Networks and WGCNA package
HW 3a - Principles of Gene expression (option 1)
HW 3a - Protein-Protein interaction (option 2)
HW 3b - Gene networks (WGCNA) (Literature)
- 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
- 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.
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.
Presentation 1 by DERYA,LUC and,RAYAN