2026 Program
Block 1: Bioinformatics for genomic medicine - variant calling and classification
Day 1: DNA sequencing and germline variant calling
When: April 20, 10.00-17.00
Where: Building 202, room R1020 how to get there?
Program:
10.00 - 10.15: Intro to the course
(Carolina Barra Quaglia)
10.15 - 11.00: Bioinformatics in Genomic
Medicine (Frederik Otzen Bagger)
11.00 - 11.15: Coffee Break
11.15 - 12.00: Somatic variant calling and RNA sequencing (Frederik
Otzen Bagger)
12.00 - 13.00: Lunch
13.00 - 13.30: Introduction
to germline variant characterization (Carolina Barra Quaglia)
13.30
- 17.00: Exercises in germline variant classification (Carolina Barra
Quaglia)
15.00 - 15.15: Coffee Break
Preparation:
Whole
genome sequencing in clinical practice
Slides:
Welcome
Bioinformatics
pipelines + Burrows Wheeler transformation
Variant
Not Found
Material:
Burrows-Wheeler
transformation explained (youtube video)
Extra Material on Protein Structure
Visualisation:
Pymol
software
Pymol basics
tutorial
Pymol wiki
Pymol
license file
Bioinformatics resources and databases:
ClinVar
Virtual
Ribosome
UniProt
Variant effect
predictor
AlphaFold
String
Exercise:
Burrows-Wheeler
Transformation and GATK - answers
Variant
not found - answers
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* The
following file formats: fastq, bam, sam, cram, vcf, vcf.gz (what’s in
them)
* Of the file formats above, which should you store for your
own data and why?
* The bioinformatics database and web services
listed above (from a basic usage perspective)
Day 2: Variant Interpretation and Classification Methods
When: April 21, 9.00-17.00
Where: Building 202, room R1014
Program:
9.30 - 10.00: Exercise summary
10.00 - 10.15: Coffee Break
10.15 - 11.15: Clustering +
Classification algorithms (Carolina Barra Quaglia)
11.15 - 12.00:
Microbial genomics in personalized medicine (Rasmus Lykke Marvig)
12.00 - 13.00: Lunch
13.00 - 17.00: Exercises in variant
interpretation, clustering and classification (Carolina Barra
Quaglia)
15.00 - 15.15: Coffee Break
Social Dinner Event
Tuesday 21 April, 19hs
RizRaz, Store Kannikestræde 19, 1169 København
Slides:
Klinisk
variant klassificering
Clustering
Classification
Talk:
Microbial Genomics
Material:
Principal
component analysis explained
Paper describing
bioinformatics pipelines for molecular subtyping of cancer
Paper:
“Delivering precision oncology to patients with cancer”
Paper
describing machine learning algorithms for breast cancer classification
(very technical paper, but it provides a good overview - voluntary
reading)
Exercise:
Clustering
and classification
R
script
R
data
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* Euclidean
distance (and knowing that there are other distance metrics out
there)
* Basic concept of data distributions
* Hierarchical
agglomerative clustering
* knn classification
* Distance to
centroid classification
* The fact that classifiers have tweakable
parameters (e.g. the “k” in knn) and how to decide on the best
settings
* Principal component analysis (in broad strokes, not the
math of it)
Block 2: Immunoinformatics for precision therapeutics – Epitopes and Immunotherapy
Day 3: Assessing chimeric antigen receptor targets for cancer immunotherapy
When: April 22, 9.00-17.00
Where: Building 202, room R1014
Program:
9.00 - 9.30: Exercise summary
9.30
- 10.00: Immunoinformatics and CAR T cells
10.00 - 10.15: Coffee
Break
10.15 - 11.15: Bioinformatics tools for assessing CAR targets
(Lars Rønn Olsen)
11.15 - 12.00: Exercises in CAR target assessment
(Carolina Barra Quaglia)
12.00 - 13.00: Lunch
13.00 - 17.00:
Exercises in CAR target assessment (Carolina Barra Quaglia)
15.00 -
15.15: Coffee Break
Slides:
Online
bioinformatics tools for assessing CAR therapy targets
Material:
Blog
post describing the prediction of signal peptides
Overview
of post-translational modifications
Paper
describing the importance of target isoforms in CAR cell therapy
Introduction
to Xenabrowser
Bioinformatics resources and databases:
Xenabrowser
Clustal Omega
(Protein) BLAST
DeepLoc
SignalP
TopCons
BepiPred
NetPhosP
UniProt
Exercise:
Evaluating
targets for chimeric antigen receptor therapy
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* The FASTA
format and why we use it
* The purpose of the web servers and
databases listed above (if you use any of them for your final project,
you will also need to be able to provide a high level explanation of how
it works)
Day 4: Neo epitope prediction and vaccine development (on-line)
When: April 23, 9.00-15.00
Where: Zoom link
Program:
9.00 - 9.30: MHC binding and T cell
epitopes (Carolina Barra Quaglia)
Exercise: Making Sequence
logos
10.00 - 10.30: MHC binding predictions (Carolina
Barra Quaglia)
Exercise: Calculate the weights of a neural
network
11.00 - 11.30: MHC binding predictions and medical
applications (Carolina Barra Quaglia)
Exercise: IEDB
database search
12.00 - 14.00: Lunch + Exercise T cell
epitope prediction (off-line time)
14.00 - 15.00:
Walk-through T cell Epitope prediction Exercise (Carolina Barra
Quaglia)
Slides:
Predicting
T cell epitopes
Material:
T
cell epitope prediction book chapter
IEDB
Lecture
Bioinformatics resources and databases:
Sequence
Logo generator
Predictor
of MHC-I presented peptides
Predictor
of MHC-II presented peptides
Allele
Frequencies
Exercise:
Making
sequence logo
Neural
network exercise
Immune
Epitope Database exercise
Prediction
of T cell epitopes - answers
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* What is
visualized using logo plots and what do the axes of the plot mean
*
How are HLA binders predicted? (General method and training data)
*
What is the content of the immune epitope database and what is the
source of these data?
Block 3: Fundamental bioinformatics algorithms: BLAST and MSA
Day 5: Pairwise sequence alignment and BLAST (on-line)
When: April 27, 9.00-14.00
Where: Self study and Zoom
Program:
9.00 - 10.00: Video lecture: Pairwise
alignment summary + BLAST
10.00 - 12.00: Exercise: BLAST
13.00 - 14.00: Q&A time on Zoom
Slides:
Blast
updated slides
Exercises
Pairwise
alignment - answers
BLAST
- answers
Material:
Pairwise
alignment tool on google colab
Blast
exercise in Python using google colab
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* What is
achieved using pairwise sequence alignment
* What is achieved using
BLAST?
* What is an e value?
* What is % identity?
Day 6: Multiple Sequence alignment and Phylogenetic trees (on-line)
When: April 28, 9.00-14.00
Where: Self study and Zoom
Program:
9.00 - 10.00: Video lecture: Multiple
sequence alignment + Phylogenetic trees
10.00 - 12.00: Exercise:
building phylogenetic trees
13.00 - 14.00: Q&A time on Zoom
Slides:
Phylogeny
slides
Exercises
Phylogeny
- answers
Hand-out
answers
Material:
Tree
building help manual
Understanding
evolutionary trees
Curriculum summary
Out of the material covered
today, the following is in the curriculum for the exam:
* What is
achieved using multiple sequence alignment
* What are the steps for
building a phylogenetic tree
* Trees can be used to investigate
evolutionary relationships, how does this tool relates to hierarchical
clustering seen on day2?
Block 4: Project work
Introduction
to project work
When: April 29 - May 25
Where: Self-organized
Program:
Q&A times on Zoom
TBD
Exam
When: Submission of written assignment in Digital
Eksamen: 12:00 noon, Monday, May 25, 2026
When:
Oral exam May 29, 9.00-12.00 (exact program TBD)
Where: Online