22145 Immunological Bioinformatics Course Programme Fall 2026: Difference between revisions

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=== Where and when ===
=== Where and when ===


Wednesday from 9 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 3 at 9:00'''. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material provided on DTU Learn
Classes are held on Wednesdays from 8:00 to 12:00 in '''Building 208, Holdlokale 3/065''', beginning on '''Wednesday, 2 September 2026, at 09:00'''.  
 
The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.


=== Teachers ===
=== Teachers ===


* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible.
* [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate Professor and course responsible.
 
* [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor and course responsible.
* [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsible.


=== Teaching assistant ===
=== Teaching assistant ===


* [https://www.dtu.dk/english/person/sebastian-nymann-deleuran?id=117549&entity=profile Sebastian Nymann Deleuran] — PhD student
* [https://orbit.dtu.dk/en/persons/eric-bautista-farrerons/ Eric Bautista Farrerons] — PhD student.


=== Course content ===
=== Course content ===


The course aims to introduce the students to state-of-the-art methods within computational immunology.
The course introduces students to state-of-the-art methods in computational immunology.


There is a strong focus on introducing the methods in context with immunology as a domain-specific knowledge area. Furthermore, an introduction to the theory of the methods will be followed by practical exercises, enabling the student to independently perform analyses. The course covers immunological bioinformatics and computational vaccinology with an outlook on infectious diseases, cancer immunotherapy, and autoimmunity.
The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.


The course is taught in two parts. Part 1 covers lectures and group-based exercises, and part 2 will cover a group-based research project with the output being a poster presentation on the last day of the course.  
The course is taught in two parts:
* Part 1 consists of lectures and group-based exercises. Part 1 ends with a "in class" written exam on November 11th.
* Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.


See also [http://kurser.dtu.dk/course/22145 the course base about 22145].
See also [https://kurser.dtu.dk/course/2026-2027/22145 the DTU course description for course 22145].


=== Curriculum ===
=== Curriculum ===


There is no formal textbook. The curricula consist of lectures and exercises performed in class, supplemented with various papers and book chapters which will be made available on DTU Learn. Please note that ''all'' exercise guides are mandatory curriculum — including the ''answers'' to the exercises which will be made available on DTU Learn after each exercise.
There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that ''all'' exercise guides are part of the mandatory curriculum, including the ''answers'', which will be made available on DTU Learn after each exercise.


=== Hand-ins ===
=== Hand-ins ===


Regardless of your choice of writing software, the result ''' must be handed in as a PDF file'''.
Regardless of the software used to prepare your work, '''all submissions must be handed in as PDF files'''.


It is possible (and recommended) to hand in as a group.
Group submissions are permitted and recommended.


''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.
''The hand-ins are mandatory however, they do not affect your grade.'' Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.


=== Exam ===
=== Exam ===


The exam consists of a group oral project presentation with individual questions at the end of the course, and a final 2-hour written exam. The grade is based on an overall assessment of both parts of the exam. It is a requirement that the oral presentation is completed, and the written exam is passed, to pass the entire course. The questions will be made available as a PDF file on the DTU online exam system. ''' The only accepted hand-in format is PDF'''.  
The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.
 
 
All aids are permitted during the written exam, including books, papers, and notes.  
'''Internet is not allowed in the written exam'''
You are ''not'' permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.


All aids are allowed at the exam; you can bring any books, papers, or notes. You will have '''open access to the internet''' which includes all the materials and websites we have used during the course. You are also allowed to search for information on ChatGPT,  Google, Wikipedia, etc., but you are ''not'' allowed to communicate with others through e-mail, Facebook, chat, or file-sharing websites. The internet traffic will be logged during the exam to ensure that these restrictions are kept.
The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in [https://www.bibliotek.dtu.dk/en/research-service/reference-management/kunstig-intelligens DTU guidelines].


AI bots are allowed but you should state in your answer where and how you have used them. A word of wisdom here: AI generative models will give very general answers which might make you loose precious time of the exam, so be careful on their use.
Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built.


=== DTU Learn Link ===
Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected.  
* Link to this year's DTU Learn page: https://learn.inside.dtu.dk/d2l/home/271397


=== Evaluation and feedback ===
You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and [https://www.inside.dtu.dk/en/research/good-scientific-conduct Principles for good scientific conduct].
We will be very happy to receive comments, suggestions, criticisms, or praise at any time during the semester. You can:
* send them by email to the teachers, or
* write them under "General feedback" in "Discussion" in DTU Learn.
If somebody writes a message in "Discussion", you can comment on it. If you see a message you agree with, please comment "Agree!" so that we can see that it is not just one person's opinion.  


In addition, we will conduct a mid-term evaluation just after the autumn break in [https://evaluering.dtu.dk/ DTU evaluation].
=== DTU Learn link ===


== Lecture & exercise plan ==
* DTU Learn page: https://learn.inside.dtu.dk/d2l/home/325135


Note: This is a ''preliminary'' plan, changes may occur!
== Lecture and exercise plan ==


=== Wednesday, Sep 3 — Introduction &  databases ===
'''Note:''' This is a ''preliminary'' plan and may be subject to changes. Check the page regularly for updates.
:'''Lectures:'''
 
=== Wednesday, 2 September 2026 — Introduction and databases ===
 
:'''Preparation material:'''
:* ''Video: Immunology Recap''
:* ''Video: Adaptive Immunity''
:* ''Book chapter: The adaptive Immune system''
 
:'''Lectures: We start at 9am'''
:* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.
:* ''Introduction to immunological bioinformatics'' — Carolina Barra Quaglia.
:* ''Databases'' — Carolina Barra Quaglia.
:* ''Databases'' — Carolina Barra Quaglia.
:'''Slides:''' All slides will be made available on DTU Learn.
:'''Slides:''' All slides will be made available on DTU Learn.
<!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.
:'''Test of prior knowledge:''' Go to  https://evaluering.dtu.dk/, click "Test of prior knowledge" under 22111, and fill out the form (it's anonymous). Spend max. 10 minutes on it.
-->
:'''Exercise:'''
<!--:# [[Plain text files and Geany]]
:# [[Taxonomy databases]]
:'''Extra material'''
:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.
:*"[https://doi.org/10.1093/nar/gkac1032 Database resources of the National Center for Biotechnology Information in 2023]" — article from the annual database issue of Nucleic Acids Research, 2023
-->


=== Wednesday, Sep 10 — Antigen Processing and Presentation ===
:'''Exercise:[https://teaching.healthtech.dtu.dk/22145/index.php/IEDB IEDB]'''
:'''Lecture:''' ''Antigen Processing and Presentation'' — Carolina Barra Quaglia
 
:'''Slides:''' on DTU Learn.
=== Wednesday, 9 September 2026 — MHC binding prediction, Part 1 ===
<!--:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/DNA_SequencingTutorial.pdf DNA sequencing tutorial] — source: IDT Tech Vault
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/HandoutEx_BaseCalling_Simple.pdf "Base-calling" exercise (for printing)] [PDF] / [https://teaching.healthtech.dtu.dk/material/22111/BaseCalling_on_screen_version.pdf "Base-calling" exercise (version for on-screen viewing)] [PDF].
-->


:'''Exercise:'''  
:'''Lecture:''' ''MHC binding prediction, Part 1'' — Morten Nielsen.
<!--:# [[ExGenbank-new|Using the GenBank database]]
:'''Slides:''' Available on DTU Learn.
:'''Reference material''' for the exercise: [https://teaching.healthtech.dtu.dk/material/22111/GenBank+FASTA_handout_revised.pdf GenBank + FASTA format] [PDF]  
:'''Exercise: [https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part1.php MHC binding prediction]'''


:'''Background material''' (supposedly known):
=== Wednesday, 16 September 2026 — MHC binding prediction, Part 2 ===
:*[[File:Phone_34.gif‎]] [http://www.youtube.com/watch?v=YgmoHtLGb5c mRNA splicing] (YouTube).
:*[https://teaching.healthtech.dtu.dk/material/22111/GeneStructure.pdf Overview of eukaryotic gene structure] (PDF).


:'''Extra material:'''  
:'''Lecture:''' ''MHC binding prediction, Part 2'' — Morten Nielsen.
:*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)
:'''Slides:''' Available on DTU Learn.
:*[https://doi.org/10.1093/nar/gkac1012 "GenBank 2023 update"] — article from the annual database issue of Nucleic Acids Research, 2023.
:'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_MHC_bind/exercise_2023_part2.php MHC Binding Prediction 2]'''
<!--
:'''Curriculum:''' Pages 35–55 of ''Immunological Bioinformatics'' (PDF available on DTU Learn under General information and files → Textbook excerpt).
:'''Handout:''' [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores].
-->
-->


=== Wednesday, Sep 17 — MHC binding predictions part 1 ===
=== Wednesday, 23 September 2026 — Antigen processing and presentation ===
:'''Lecture:''' ''MHC binding predictions Part 1'' — Morten Nielsen
 
:'''Slides:''' on DTU Learn.
:'''Lecture:''' ''Antigen processing and presentation'' — Carolina Barra Quaglia.
:'''Slides:''' Available on DTU Learn.
:'''Exercise: To be updated'''
 
=== Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction ===


:'''Exercises:'''
:'''Lectures:'''
:* ''Allergenicity prediction'' — Carolina Barra Quaglia.
:* ''Immunogenicity prediction'' — Carolina Barra Quaglia.
:'''Slides:''' Available on DTU Learn.
:'''Exercises: To be updated'''


=== Wednesday, Sep 24 — MHC binding predictions part 2 ===
=== Wednesday, 7 October 2026 — Vaccine design ===
:'''Lecture:''' ''MHC binding predictions part 2'' — Morten Nielsen.
<!--:'''Curriculum:''' Page 35-55 in Immunological Bioinformatics (PDF: on DTU Learn → General information and files → Textbook excerpt).
:'''Handout''' for the
lecture: [https://teaching.healthtech.dtu.dk/material/22111/New_handout_alignscores.pdf Alignment scores]
-->
:'''Slides:''' on DTU Learn.
:'''Exercise:'''
<!--[[ExPairwiseAlignment|Pairwise alignment]]
-->


=== Wednesday, Oct 1 — Vaccine design ===
:'''Lecture:''' ''Vaccine design'' — Morten Nielsen.
:'''Lecture:''' ''Vaccine design'' — Morten Nielsen.
<!--:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).
:'''Slides:''' Available on DTU Learn.
-->
:'''Exercise:[https://teaching.healthtech.dtu.dk/morten_teaching/27485.imm/exercise_HCVVaccine/exercise_HCVVaccine_2023.php HCV Vaccine development]'''
:'''Slides:''' on DTU Learn.
 
:'''Exercise:
=== Wednesday, 14 October 2026 — Autumn break ===
<!--
:'''Exercise: [[Exercise:_BLAST2|BLAST]]'''  
:'''Extra material:'''
::[[File:Phone_34.gif‎]] '''Videos about BLAST from NCBI:''' (Video introduction to NCBI's web interface and Expect Values)  [http://www.youtube.com/playlist?list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq NCBI's YouTube channel]
-->


=== Wednesday, Oct 8 — Allergenicity prediction ===
=== Wednesday, 21 October 2026 — BCR and TCR structure prediction ===


:'''Lecture:''' ''Allergenicity prediction'' — Carolina Barra Quaglia
:'''Workshop:''' ''BCR and TCR structure prediction'' — Carolina Barra Quaglia.
:'''Lecture:''' ''Immunogenicity prediction'' — Carolina Barra Quaglia
:'''Slides:''' Available on DTU Learn.
<!--:'''Curriculum:''' [http://en.wikipedia.org/wiki/Protein_structure Protein Structure (Wikipedia)]
:'''Exercise:'''
-->
 
:'''Slides:''' on DTU Learn.
=== Wednesday, 28 October 2026 — B-cell epitope prediction ===
<!--:'''Link to advanced course:'''  
::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]
-->
<!--:'''Software''' for installation: [https://pymol.org/2/ PyMOL]
::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.
-->
:'''Exercises:'''
<!--:#[https://teaching.healthtech.dtu.dk/material/22111/PyMol_tutorial2017_v4.pdf PyMol tutorial] (PDF) — basic usage of PyMOL.
:#[[Protein Structure and Visualization]]
-->


<!--:'''Extra material:'''
:*[https://doi.org/10.1093/nar/gkac1077 "RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning"] — article from the annual database issue of Nucleic Acids Research, 2023.
:*[[PyMOL]] — some tips and tricks.
:*[https://teaching.healthtech.dtu.dk/material/22111/PDF/PyMOL_structure_navigation.pdf PyMOL basics — a small example] (optional extra exercise)
-->


------
:'''Lecture:''' ''B-cell epitope prediction'' — TBD.
<div align="center">
:'''Slides:''' Available on DTU Learn.
'''Autumn holiday'''  
:'''Exercise:'''
</div>
------


=== Wednesday, Oct 22 — BCR and TCR structure predictions ===
=== Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions ===
:'''Workshop:''' ''BCR and TCR structure predictions'' — Carolina Barra Quaglia
:'''Slides:''' on DTU Learn.
:''' GitHub link:'''
<!--
:'''Curriculum:'''
'''Mid-term evaluation:''' Go to https://evaluering.dtu.dk/ and click "Mid-term evaluation" under 22111 [[Image:Emblem-important_tiny.png‎]]
:'''Exercise:'''
-->


=== Wednesday, Oct 29 — B Cell epitope predictions ===
:'''Lecture:''' ''B Cell epitope predictions'' — Paolo Marcatili
:'''Slides:''' on DTU Learn.
:'''Exercise:'''
<!--:'''Curriculum:'''
:# Pages 68-80 in Immunological Bioinformatics (PDF: on DTU Learn).
:# Pages 1-8 of "''Information theory primer''" ([https://teaching.healthtech.dtu.dk/material/22111/PDF/informationtheory_primer.pdf PDF])
:#* Read also the appendix on logarithms (especially log<sub>2</sub>) if needed!
:'''Handout''' for the lecture: [https://teaching.healthtech.dtu.dk/material/22111/Logo_exercise.pdf How to construct sequence logos] (PDF)
:'''Exercise:''' [[ExSeqLogos|DNA and Peptide Logos]]
-->


=== Wednesday, Nov 5 — TCR interaction models ===
:'''Lecture:''' ''TCR interaction models'' — Morten Nielsen
:'''Lecture:''' ''TCR interaction models'' — TBD
:'''Slides:''' Available on DTU Learn.
: ''Short introduction to project work'' — Carolina Barra
:'''Exercises:'''
:'''Slides:''' on DTU Learn.
<!--
:'''Handouts:'''
:'''Exercises:'''
:'''Exercises:'''
 
:# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudofrequencies]. '''Note:''' If you solve this manually, select only a few amino acids from the table. If you solve it programmatically using Python, Excel, or another tool, complete the entire table.
<!--:'''Handouts''' for the lecture:
:# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]].
:'''Exercises:'''
:'''Related advanced course:'''
:# [https://teaching.healthtech.dtu.dk/material/22111/Estimationofpseudocounts_new+examples.pdf How to estimate pseudo frequencies] '''Note''': If you solve this manually, just select a couple of amino acids from the table. But if you solve it programmatically (python, Excel, other...), fill out the entire table.
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in Bioinformatics].
:# [[Exercise: Construction of sequence logos and weight matrices|Construction of weight matrices]]  
:'''Link to advanced course: '''
:: [http://teaching.healthtech.dtu.dk/22125/ 22125: Algorithms in bioinformatics]
-->
-->


=== Wednesday, Nov 12 — Project work ===
=== Wednesday, 11 November 2026 — Written EXAM ===
:'''Lecture:''' No LECTURE


=== Wednesday, Nov 19 — Project work ===
: 9-11 '''EXAM'''
:'''Lecture:''' No LECTURE
: 11-12 '''Introduction:''' ''Short introduction to project work'' — Carolina Barra Quaglia.
<!--:'''Curriculum:''' RevTrans ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169015/ article])
:'''Exercise:''' [[Exercise: Multiple Alignments (Seaview version)|Multiple Alignments]]
-->


=== Wednesday, Nov 26 — Project work ===
=== Wednesday, 18 November 2026 — Project work ===
:'''Lecture:''' No LECTURE
<!-- :'''Extra lecture:''' ''Bioinformatics and Systems Biology in precision medicine'' — Rasmus Wernersson -->


:'''Lecture:''' No lecture.


=== Wednesday, Dec 3 — Poster session ===  
=== Wednesday, 25 November 2026 — Project work ===


:Poster presentations will be '''starting at 8:00am'''
:'''Lecture:''' No lecture.


:'''Agenda for the poster presentations:''' TBD
=== Wednesday, 2 December 2026 — Poster session ===


== Exam ==
:Poster presentations will begin at '''08:00'''.


=== Wednesday, Dec 18 ===
:'''Poster presentation agenda:''' To be announced.
'''Winter exam E5-A 2024:''' Go to https://eksamen.dtu.dk/ and find 22145.  


== Exam ==


<!-- === Link collection ===
In order to get access to the written exam you should submit first all the exercises
A quick overview of the websites we have used in the course: [[Link collection]]


=== FAQ ===
The exam has two parts: A 2hs written exam on '''November 11th''' and an oral presentation of the group project on '''December 2nd'''. Failure to pass one of the two will correspond to the No Pass grade
Questions we have received and answered: [[FAQ]]
-->

Latest revision as of 14:37, 27 August 2026

General information

Where and when

Classes are held on Wednesdays from 8:00 to 12:00 in Building 208, Holdlokale 3/065, beginning on Wednesday, 2 September 2026, at 09:00.

The first hour of each class 8-9 is dedicated to course preparation, including videos, papers, or other reading material provided on DTU Learn. Unless otherwise specified, we meet at the classroom at 09:00.

Teachers

Teaching assistant

Course content

The course introduces students to state-of-the-art methods in computational immunology.

The methods are presented in the context of immunology as a domain-specific field. Introductions to the underlying theory are followed by practical exercises, enabling students to perform analyses independently. The course covers immunological bioinformatics and computational vaccinology, with perspectives on infectious diseases, cancer immunotherapy, and autoimmunity.

The course is taught in two parts:

  • Part 1 consists of lectures and group-based exercises. Part 1 ends with a "in class" written exam on November 11th.
  • Part 2 consists of a group research project, culminating in a poster presentation on the final day of the course. December 2nd.

See also the DTU course description for course 22145.

Curriculum

There is no required textbook. The curriculum consists of lectures and exercises completed in class, supplemented by papers and book chapters made available on DTU Learn. Please note that all exercise guides are part of the mandatory curriculum, including the answers, which will be made available on DTU Learn after each exercise.

Hand-ins

Regardless of the software used to prepare your work, all submissions must be handed in as PDF files.

Group submissions are permitted and recommended.

The hand-ins are mandatory however, they do not affect your grade. Their main purpose is to help you prepare for the exam and to help the teaching team assess students' understanding. If several participants make the same mistake, the issue will be clarified at the beginning of the following lecture.

Exam

The assessment consists of two parts: a written two-hour written exam in week 10, and a group oral project presentation with individual questions at the end of the course. The final grade is based on an overall assessment of both parts. To pass the course, you must complete the oral presentation and pass the written exam.


All aids are permitted during the written exam, including books, papers, and notes. Internet is not allowed in the written exam You are not permitted to communicate with other people through email, social media, chat services, or any file-sharing platforms. Internet traffic may be logged during the exam to ensure compliance with these restrictions.

The use of generative AI is permitted during the project work, but you must clearly state where and how you used them as stated in DTU guidelines.

Please beware that content, results, links etc. that you discover via generative AI may be incorrect - simply because of the way generative AI models are built.

Generative AI produces content from huge amounts of data collected from the internet. The data that the AI system is based on is not necessarily publicly available and it may be copyright protected.

You are solely responsible to adhere to the academic standards of honesty, transparency and accountability as outlined in DTU's code of honour and Principles for good scientific conduct.

DTU Learn link

Lecture and exercise plan

Note: This is a preliminary plan and may be subject to changes. Check the page regularly for updates.

Wednesday, 2 September 2026 — Introduction and databases

Preparation material:
  • Video: Immunology Recap
  • Video: Adaptive Immunity
  • Book chapter: The adaptive Immune system
Lectures: We start at 9am
  • Introduction to immunological bioinformatics — Carolina Barra Quaglia.
  • Databases — Carolina Barra Quaglia.
Slides: All slides will be made available on DTU Learn.
Exercise:IEDB

Wednesday, 9 September 2026 — MHC binding prediction, Part 1

Lecture: MHC binding prediction, Part 1 — Morten Nielsen.
Slides: Available on DTU Learn.
Exercise: MHC binding prediction

Wednesday, 16 September 2026 — MHC binding prediction, Part 2

Lecture: MHC binding prediction, Part 2 — Morten Nielsen.
Slides: Available on DTU Learn.
Exercise:MHC Binding Prediction 2

Wednesday, 23 September 2026 — Antigen processing and presentation

Lecture: Antigen processing and presentation — Carolina Barra Quaglia.
Slides: Available on DTU Learn.
Exercise: To be updated

Wednesday, 30 September 2026 — Allergenicity and immunogenicity prediction

Lectures:
  • Allergenicity prediction — Carolina Barra Quaglia.
  • Immunogenicity prediction — Carolina Barra Quaglia.
Slides: Available on DTU Learn.
Exercises: To be updated

Wednesday, 7 October 2026 — Vaccine design

Lecture: Vaccine design — Morten Nielsen.
Slides: Available on DTU Learn.
Exercise:HCV Vaccine development

Wednesday, 14 October 2026 — Autumn break

Wednesday, 21 October 2026 — BCR and TCR structure prediction

Workshop: BCR and TCR structure prediction — Carolina Barra Quaglia.
Slides: Available on DTU Learn.
Exercise:

Wednesday, 28 October 2026 — B-cell epitope prediction

Lecture: B-cell epitope prediction — TBD.
Slides: Available on DTU Learn.
Exercise:

Wednesday, 4 November 2026 — T-Cell Receptor interaction predictions

Lecture: TCR interaction models — Morten Nielsen
Slides: Available on DTU Learn.
Exercises:

Wednesday, 11 November 2026 — Written EXAM

9-11 EXAM
11-12 Introduction: Short introduction to project work — Carolina Barra Quaglia.

Wednesday, 18 November 2026 — Project work

Lecture: No lecture.

Wednesday, 25 November 2026 — Project work

Lecture: No lecture.

Wednesday, 2 December 2026 — Poster session

Poster presentations will begin at 08:00.
Poster presentation agenda: To be announced.

Exam

In order to get access to the written exam you should submit first all the exercises

The exam has two parts: A 2hs written exam on November 11th and an oral presentation of the group project on December 2nd. Failure to pass one of the two will correspond to the No Pass grade

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