Difference: TranslationalMedicine (1 vs. 23)

Revision 22
16 Oct 2015 - Main.PerryMoerland
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Bioinformatics for Translational Medicine

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The story of Nicholas Volker
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RNA-seq

Revision 21
11 May 2015 - Main.PerryMoerland
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Revision 20
29 Sep 2014 - Main.PerryMoerland
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Medical Bioinformatics

 
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Revision 19
11 Sep 2014 - Main.PerryMoerland
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Medical Bioinformatics

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Bioinformatics for Translational Medicine: exome sequencing
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Bioinformatics for Translational Medicine: exome and RNA sequencing
 

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    • Exercises
    • For the exercises you will need access to the Cloud. An IP number, login name and password will be provided to you
    • References
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Revision 18
09 May 2014 - Main.PerryMoerland
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Medical Bioinformatics

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RNA-seq

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Revision 17
08 May 2014 - Main.PerryMoerland
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Medical Bioinformatics

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Location

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    • All lectures are in WN-P647, on the sixth floor in the W&N building.
 

Lecturers

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RNA-seq (2013)

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RNA-seq

 

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  • Please read the instructions carefully and don't forget to email your answers to Perry Moerland
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  • For the exercises you will need access to the Cloud. An IP number, login name and password will be provided to you
 
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Revision 16
02 May 2014 - Main.PerryMoerland
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Medical Bioinformatics

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RNA-seq

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RNA-seq (2013)

 

  • Lecture Documents
  • Please read the instructions carefully and don't forget to email your answers to Perry Moerland
Revision 15
02 May 2014 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Please read the instructions carefully and don't forget to email your answers to Antoine van Kampen
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    • Supplementary documents
      • User manual of the Linux 'pico' editor
      • Excel file with all variants found in four patients with Nicolaides-Baraitser syndrome
Revision 14
07 May 2013 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Please read the instructions carefully and don't forget to email your answers to Perry Moerland
  • For these exercises you will need access to our Linux server. The host name, login name and password will be provided to you
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Revision 13
07 May 2013 - Main.PerryMoerland
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Medical Bioinformatics

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    • For those who want to know more about Unix and R (DESeq package):
 
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Revision 12
06 May 2013 - Main.PerryMoerland
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Exome sequencing

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Revision 11
06 May 2013 - Main.PerryMoerland
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Medical Bioinformatics

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Location

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Lecturers

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17 Sep 2012 - Main.PerryMoerland
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Medical Bioinformatics

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Revision 9
19 May 2012 - Main.PerryMoerland
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Medical Bioinformatics

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Lectures + computer lab

Exome sequencing

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  • Please the the instructions carefully and don't forget to email your answers to Antoine van Kampen
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  • Please read the instructions carefully and don't forget to email your answers to Antoine van Kampen
 
  • For these exercises you will need access to the Cloud. An IP number, login name and password will be provided to you
  • Computer lab:
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RNA-seq

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  • Please the the instructions carefully and don't forget to email your answers to Perry Moerland
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  • Please read the instructions carefully and don't forget to email your answers to Perry Moerland
 
  • For these exercises you will need access to our Linux server. The host name, login name and password will be provided to you
  • Computer lab:
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    • Data for Exercise 2 (DESeq). Make sure that you are using R2.13 for this exercise.
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    • Data for Exercise 2 (DESeq). Make sure that you are using R v2.13 for this exercise.
 
Revision 8
14 May 2012 - Main.PerryMoerland
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Medical Bioinformatics

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Lecturers

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  • Dr. Perry Moerland (Bioinformatics Laboratory, AMC)
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Lectures + computer lab

Exome sequencing

Revision 7
14 May 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • For these exercises you will need access to our Linux server. The host name, login name and password will be provided to you
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    • Data for Exercise 2 (DESeq). Make sure that you are using R2.13 for this exercise.
 
Revision 6
14 May 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Please the the instructions carefully and don't forget to email your answers to Perry Moerland
  • For these exercises you will need access to our Linux server. The host name, login name and password will be provided to you
  • Computer lab:
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Revision 5
14 May 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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RNA-seq

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Revision 4
06 May 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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The story of Nicholas Volker
 

RNA-seq

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Revision 3
01 May 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Admin. code FDBA
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Aims

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Course objective

Observations from biological high-throughput experiments will allow us to improve diagnosis and give a personalised treatment plan for patients. However, integrating data from several sources and using this data for predictions is non-trivial.
This is a theoretical and practical Bioinformatics course on computational methods for Translational Medicine; we will focus on Bioinformatics algorithms that are used to predict the clinical outcome for patients and analysis methods to obtain deeper understanding of complex diseases, by combining data from various high-throughput experiments such as proteomics, microarrays and next-generation sequencing as well as existing biological databases.

Next Generation Sequencing: Exome sequencing and RNA-seq

  Next Generation Sequencing (NGS) allows a range of applications. Two of these applications are exome sequencing and RNAseq. With exome sequencing we aim to detect variants that cause rare disorders. RNAseq is used for gene expression studies. You will be introduced to Next Generation Sequencing after which we will explain exome sequencing and RNAseq in detail. In the computer labs you will be able to try it yourself.

Schedule

Revision 2
23 Apr 2012 - Main.AntoineVanKampen
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Medical Bioinformatics

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Bioinformatics for Translational Medicine: exome sequencing
 
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Bioinformatics for Translational Medicine

  • Master Bioinformatics and Systems Biology
  • VU
  • Admin. code FDBA
  • Studielast 6 EC

Aims

Next Generation Sequencing (NGS) allows a range of applications. Two of these applications are exome sequencing and RNAseq. With exome sequencing we aim to detect variants that cause rare disorders. RNAseq is used for gene expression studies. You will be introduced to Next Generation Sequencing after which we will explain exome sequencing and RNAseq in detail. In the computer labs you will be able to try it yourself.

Schedule

Location

  • Free University.
    • All lectures are in WN-C659, on the sixth floor in the W&N building.

Lecturers

  • Prof dr Antoine van Kampen (Bioinformatics Laboratory, SILS/AMC, a.h.vankampen@amc.uva.nl)
  • Dr. Perry Moerland (Bioinformatics Laboratory, AMC)

Lectures + computer lab

Exome sequencing

RNA-seq

 
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