Support materials biomedicine master March 2016

Day 1 / 29 February Monday / 9:00 - 17:00 / Hörsaal Anthropologie

Basic concepts from probability and statistics and to learning R

Support files: Uebungen_R_Tag1.R.txt

Lecture slides: VL_Tag_1

 

Day 2 / 1 March Tuesday / 9:00 - 17:00 / Hörsaal Anthropologie

Data analysis methods in R relevant for bioinformatics and biomedicine.

Support files: Uebungen_R_Tag_2.R.txt / size_values / Excercises_R_day_2_Afternoon.R  / Claims.txt / Fever.txt / Patients.txt

Lecture slides: VL_Tag_2

 

Day 3 / 2 March Wednesday / 9:00 - 17:00 / Hörsaal Anthropologie

Advanced concepts from probability and statistics in R

Support files: Exercises_day_3.R.txt

 

Day 4 / 3 March Thursday / 9:00 - 17:00 / Hörsaal Anthropologie

Application of R to GWAS studies

Support files: hyper_QTL.R.txt

R package installation: install_packages.html

Lecture slides: VL_Tag_4

 

Day 5 / 7 March Monday / 9:00 - 17:00 / Hörsaal Anthropologie

5.1 Analysis of ChIP-seq data using R

Lecture slides updated: ChIP-seq lecture The most relevant content for the exam is highlighted with blue background.

Support files: ChIP-seq Exercises
MCF7_FOXA1_binding.bed / MCF7_ER_binding.bed

5.2 Motif detection

Lecture slides updated: Motif Analysis The most relevant content for the exam is highlighted with blue background.

Support files: Motif Analysis Exercises

5.3 Sequence analysis and homology

Exercises: exercises1 / exercises2 / exercises3

 

Day 6 / 8 March Tuesday / 13:00 - 17:00 / IMB seminar room

8 seminars

 

Day 7 / 9 March Wednesday / 9:00 - 17:00 / Hörsaal Anthropologie

Summary of theory Dr. Muro: MuroMB2016

7.1 Multiple sequence alignments

7.2 Phylogenetic analyses

 

Day 8 / 10 March Thursday / 9:00 - 17:00 / Hörsaal Anthropologie

8.1 Protein 3D structure

Slides Chimera: chimera_2 / lesson_domains_2 / lesson_model3D_3_short

8.2 Protein secondary structure

Support files: MR1_fasta / littleMSA_fasta / ferredoxins2_fasta

Slides: lesson_pred2D_4_short

8.3 Non-globular proteins

Slides: lesson_bias_4_short

 

Day 9 / 11 March Friday / 9:00 - 17:00 / Hörsaal Anthropologie

9.1 Microarrays

Slides talk: GE_microarrays

Exercises: gene_expression.html

9.2 Networks

Support files: DEGs after 48-hr-treatment with Estrogen / S. cerevisiae sample network

Lecture slides: Protein interaction networks, STRING and Cytoscape

Day 10 / 14 March Monday / 9:00 - 16:30/ IMB seminar room

13 seminars

 

Files:

file1_fasta / file2_fasta  / file3_fastafile4_fasta

 

Links:

http://blast.ncbi.nlm.nih.gov/

http://myhits.isb-sib.ch/cgi-bin/dotlet

http://matthuska.github.io/biasviz/