Day 1 – November 21, 2016

• Exercise: Multiple Sequence Alignment and Analysis (PDF)
• Exercise: Multiple Sequence Alignment and Analysis (ODT)

Handouts: nbic-phd-course-comp-genomics-day1-af4-handout_shrunk

Literature:

• Multi-Harmony: detecting functional specificity from sequence alignment (Berndt Brand)
• Sequence comparison by sequence harmony identifies subtype-specific functional sites (Walter Pirovano)

Zipfile with reference sequence sets

Day 2 – November 22, 2016

• BioSB Questions Day 2
• QIl1-AIM5 – Zipfile
• extra-question-orthology-and-domain-composition

Handouts/lectures:

• biosb-homologyorthology
• biosb-orthology

Day 3 – November 23, 2016

Lecture Jaap Heringa: biosb-phd-course-comp-genomics-2016-day3-jh

• Practical assignment: compgenomics_2016_day3_biological_networks_practical
• Answers: compgenomics_2016_day3_short_answers_biological_networks_practical

Lecture Martijn Huynen (Bayesian): bayesian-integration-simple

• question-bayesian-integration
• ciliacarta_table_for_students_negative_set
• ciliacarta_table_for_students_positive_set
• ciliacarta_table_for_students_candidates

Day 4 – November 24, 2016

Lecture/slides Berend Snel:

• http://bioinformatics.bio.uu.nl/snel/BEG/BioSB_tree_reconciliation.pdf
• http://bioinformatics.bio.uu.nl/snel/BEG/WGD_2016.pdf

Exercises:

• http://bioinformatics.bio.uu.nl/snel/BEG/exercises_WGD.html
• http://www-binf.bio.uu.nl/snel/BEG/exercise_peroxisome.html
• http://www-binf.bio.uu.nl/snel/BEG/exercise_RPL22.html

Day 5 – November 25, 2016

Lectures/slides Martijn Huynen:

• nbic-phd-course-day-5-2016

Exercises:

• questions-biosb-course

Literature:

• Positive Selection of Tyrosine Loss in Metazoan Evolution
• Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”
• Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”