Medical Bioinformatics and e-Bioscience

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AMC Graduate School: Introduction to Bioinformatics Schedule and registration Introduction to Bioinformatics Biological Databases Bioinformatics of sequencing RNA sequencing Gene detection and genome annotation Statistical analysis of transcript counts Sequence alignment and Blast DNA microarray analysis Human Genome Project SNPs and genome-wide association Pathways Preprocessing of metabolomics data e-Science Topics from previous editions Score matrices Phylogenetics

AMC Graduate School: Introduction to Bioinformatics

Schedule and registration

• Schedule
• Register via the AMC graduate school
• Black board UvA

Introduction to Bioinformatics

Teacher: Barbera van Schaik

• Introduction to Bioinformatics (pptx)

Biological Databases

Teachers:

• Barbera van Schaik
• Aldo Jongejan
• Umesh Nandal

• Biological databases (pptx)
• Computer exercises 2013

Bioinformatics of sequencing

Teacher: Prof Dr Frank Baas

• Bioinformatics of sequencing (pdf)

RNA sequencing

Teacher: Marcel Willemsen

• RNA sequencing (pptx)

Gene detection and genome annotation

Teacher: Prof Dr Antoine van Kampen

• Lecture
  • Gene finding (pptx)

• Tutorial
  • Tutorial (doc)
  • Answers (first make tutorial before looking into these files)
  • Tutorial sequences

• Sequence analysis programs
  • EMBOSS toolbox
  • Readseq
  • Blast 2 sequences
  • ORF finder

• Gene finding programs
  • GeneMark
  • GLIMMER (not used in the exercises)
  • BPROM. Prediction of bacterial promotors
    • BPROM Documentation

• Other programs
  • Hemoglobin and Sickle cell disease (Chime plugin required)

• Background information
  • Genetic code

Statistical analysis of transcript counts

Teacher: Dr Jan Ruijter

• Teacher notes and exercises (pdf)
• Handouts (pdf)
• Exercises_SAGEstatistics.xls
• Exercises_SAGEstatistics_with_results.xls

Sequence alignment and Blast

Teacher: Dr Aldo Jongejan

• Slides - sequence alignment (pptx)
• Slides - Blast & Galaxy (ppt)
• Slides - overview nextgen sequencing bioinformatics (pdf) (not presented during course)
• Exercises (pdf)
• Solution exercises (pdf)

DNA microarray analysis

Teacher: Dr ir Perry Moerland

• Lecture notes and slides
• Computer exercises

Human Genome Project

Teacher: Prof Dr Rogier Versteeg and Dr Jan Koster

To be added

SNPs and genome-wide association

Teacher: Dr ir Perry Moerland

• Slides

Pathways

Teacher: Umesh Nandal and Perry Moerland

• Pathways (ppt)
• Exercises
• Answers to exercises
• Cytoscape: program for network data integration, analysis, and visualization
• Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network, Ideker et al, Science (2001) html pdf
• Biological networks video link

Preprocessing of metabolomics data

Teacher: Prof Dr Antoine van Kampen Presentation:

• Metabolomics (pptx)

e-Science

Teacher: Mark Santcroos

Presentation:

• Slides (ppt) Slides (pdf)

Topics from previous editions

Score matrices

Teacher: Prof Dr Antoine van Kampen

• Scores (ppt). The basics of score matrices and their statistical evaluation.
  • Exercises Score Matrices (doc)
  • Teacher Notes Exercies (doc)
  • Exercise.xls
  • Exercise+Answers.xls
  • PAM_Exercise.xls
  • PAM_Exercise+Answers.xls
  • Generation of PAM matrices

Phylogenetics

Teacher: Prof Dr Antoine van Kampen

• Phylogenetics (pptx)