Medical Bioinformatics and e-Bioscience

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AMC Graduate School: Introduction to Bioinformatics

Schedule and registration

• Schedule
• Register via the AMC graduate school

Introduction to Bioinformatics

Teacher: prof. dr. Antoine van Kampen

• Introduction to Bioinformatics (pptx)

Biological Databases

Teacher: prof. dr. Antoine van Kampen

• Biological databases (pptx)
• Computer exercises.

Bioinformatics of sequencing

Teacher: Fred van Ruissen

• Bioinformatics of sequencing (pdf)

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

Statistical analysis of transcript counts

Teacher: Dr. Jan Ruijter

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

DNA microarray analysis

Teacher: Dr. ir. Perry Moerland

• Lecture notes and slides
• Computer exercises

Gene finding

Teacher: prof. dr. Antoine van Kampen

• Gene finding (ppt)
• Exercises (doc)
• Exercise sequences

• Sequence analysis
  • EMBOSS toolbox
  • Readseq
  • Blast 2 sequences
• Gene finding programs
  • GeneMark
  • GLIMMER
  • BPROM. Prediction of bacterial promotors
    • BPROM Documentation
• Hemoglobin and Sickle cell disease (Chime plugin required)
• Genetic code

Sequence alignment and Blast

Teacher: Aldo Jongejan

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

Phylogenetics

Teacher: prof. dr. Antoine van Kampen

• Phylogenetics (pptx)

SNPs and genome-wide association

Teacher: Dr. ir. Perry Moerland

• Slides

Pathways

Teacher: Miranda Stobbe

• Pathways (ppt) and pdf