(Algorithms in) Computational biology and bioinformatics

INFO-F-439

 

Syllabus

  1. VUB course description

  2. Goals

  3. Short description

  4. Staff

  5. Schedule

  6. Syllabus

  7. Information concerning the projects and the exam

  8. Practical information

  9. Reference books

Course content

Staff

Tom Lenaerts (MLG ULB and AI-lab, VUB), telephone 02 650 60 04,

email: tlenaert@ulb.ac.be


Wim Vranken (MoRe, DBIT & VIB), telephone 02 629 10 25,

email:wvranken@vub.ac.be


Matthieu Defrance (MLG ULB) telephone 02 629 58 68

email :  matthieu.dc.defrance@ulb.ac.be


Assistants : Sofia Papadimitriou, Andrea Gazzo and Gabriele Orlando (IB2 ULB-VUB),

Prof. T. Lenaerts and Prof. W. Vranken

2011-2017

Goals

The goal of this course is to introduce students to some of the  most relevant algorithms and techniques within the area of Computation Biology and Bioinformatics


The general aims are to provide them with the necessary skills i) to understand computational biology and bioinformatics research, ii) to grasp the workings of some of  the key algorithms that were developed to solve particular problems in molecular biology iii) to understand the role of different computational methods in solving these problems, iv) to know where certain molecular data can be found and how to combine this, v) to be able to develop a project that tries to solve some problem in this domain.  This knowledge will allow you to understand the literature on bioinformatics and computational biology, which will be checked during the exam.

The course is divided in three blocks, addressing questions related to algorithm development, data preparation and prediction within the context of sequence, structural and genome analysis.  


The first block will train you in the basics of sequence alignment and motif detection, wherein you will implement the algorithms and test their performance in relation to the state-of-the-art.  At the same time you will apply your newly acquired knowledge to understand computational biology articles related to this topic.


The second block works in a similar manner and focusses on the role of prediction in computational biology. As a case-study we will examine the field of secondary structure prediction wherein we will first discuss the data preparation and then the algorithms that can be used to make the predictions.  Specific attention will be given to the evaluation of the predictive quality (ROC analysis, precision-recall analysis, ...).  You will implement your own secondary structure predictor and also examine articles to ensure that you can read and understand them.


The final block of the course focusses on the genomic aspects of bioinformatics.  An introduction to genomics and transcriptomics will be provided and you will receive insight into the technologies that produce the data through the study of certain articles.  Afterwards RNA-seq and Chip-seq will be investigated in detail.


This training should provide you the skills to read and understand the bioinformatics/computational biology literature.  As such the exam will consist in selecting a paper from either the journal Nucleic Acids Research, PLOS computational biology or (BMC) Bioinformatics and to present the biological question, the informatics methodology and the results in a clear and pedagogic manner. The exam will be in groups of 2 students.


The grade for this course is based on the 2 assignments (50%) and the exam (50%).

Schedule

Sessions :

  1. Thursdays between 10:00 and 12:00, (starting February 16, 2017) at the VUB campus, room D2.19 (Building D, second floor) except on 9/3/2017, when the room will be E3.03 (Building E, third floor)

List of sessions (provisional)

Assignments

Reference books