22145 Immunological Bioinformatics Course Programme January 2021

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COURSE PLAN FOR 2021

EXAM

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs


Guidelines

  • The exam will be made available at the wiki at 13.00hs. Upload a pdf with your answers no later than 15.00hs on DTU inside written exam assignment.
  • You must connect at Zoom 5 minutes before the exam, and have the camera turned ON during the whole exam. Failing to meet this requirement will invalidate the exam.
  • This is an individual exam. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

Information for Course Participants

Course Format

  • NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
  • Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
  • This will be needed for the entire first day, the question and answer sessions, and the final exam
  • Classes will be a mixture of lectures, group work and individual exercises
  • Most of the group work will consist of computer exercises, where students are required to use their laptops
  • General Question and Answer will be live and uploaded after the session
  • Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
  • All learning resources will be available through DTU inside or this site
  • Expected time usage: 1 ECTS point equals approx. 28 hours, this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

Course Resources

Course Teachers


General Daily Schedule

  • 09.00 - 12.00 Lectures
  • 12.00 - 13.00 Lunch
  • 13.00 - 13.30 Live sessions Q&A
  • 13.30 - 17.00 Exercises

Location

  • NOTE: This edition of the course will be completely online

Profiles of Invited Speakers for Mini Symposium

2021 Course Schedule Overview

Teaching Day 1-8
Monday Jan. 4th Tuesday Jan. 5th Wednesday Jan. 6th Thursday Jan. 7th Friday Jan. 8th Monday Jan. 11th Tuesday Jan. 12th Wednesday Jan. 13th
Topic Introduction and Basic Immunology T-Cell Epitopes Antigen Processing and Presentation, HLA Clustering, and Vaccine Design Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes Immunopeptidomics, T-Cell Repertoires and the IEDB Antibody Humanization and T-Cell Interaction Models De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy Mini-symposium on Immunoinformatics by Invited Speakers
09.00 - 09.30 Course Introduction Live on Zoom Recording: MP4 [CB] Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: Slides [PDF]. Recording: [MP4], Logo handout: [PDF], Answer Logo handout Logo handout Recording [MP4]. Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: Slides [PDF]. Recording: [MP4]. Lecture: TCR and BCR structure. Recording: Antibody Modelling [PM]

Solution

Lecture: Immunopeptidomics Live on Zoom Recording: MP4 [CB] Lecture: Antibody Humanization Video [PM] Lecture: Protein Drug Deimmunization Live on Zoom pdf mp4 [BR] Talk 1: Cancer immunotherapy in the clinic. Marco Donia Live! video
09.30 - 10.15 Micro project group work Live on Zoom [CB] Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: Slides [PDF]. Recording: [MP4]. NN handout [PDF]. NN handout Recording [MP4]. Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: Slides [PDF]. Recording: [MP4]. Exercise: Antibody Structure Prediction and Analysis Recording: Exercise [PM] Exercise files: Peptides Alleles_list Answers: AnswersLive on Zoom [CB] Exercise: Antibody Humanization [PM] Exercise: Protein Drug Deimmunization [BR] Talk 2: SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection. Sunil Kumar Saini Live! video
10.15 - 10.30 Break Break Break Break Break Break Break Break
10.30 - 11.15 Micro project group work Live on Zoom [CB] Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: Slides [PDF]. Recording: [MP4]. Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: Slides [PDF]. Recording: [MP4]. Lecture: Linear B-cell epitope prediction. Recording: [1] [PM] Lecture: T-Cell Receptor Repertoires Live on Zoom Slides Recording: [[MP4] [MV] Lecture: Single cell technologies for T-cell epitopes Single Cell and NetTCR Project videoLive on Zoom [HP] Lecture: Humanization and deimmunization for cancer T cell therapy molecules video [PM] Talk 3: The utilization of bioinformatics to guide drug design. Monika Sekelja Live! video
11.15 - 12.00 Micro project group work Live on Zoom [CB] Lecture: Performance measures [MN]. Recording: [MP4]. Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont. Lecture: Conformational B-cell epitope prediction. Recording: [2][PM] Lecture: The Immune Epitope Database & Tools Live on Zoom PDF mp4 [BR] Lecture: Modelling TCRpMHC interactions videoLive on Zoom [AM] Lecture: Humanization and deimmunization for cancer T cell therapy molecules [PM] Talk 4: TBC Live!
12.00 - 13.00 Lunch Break Lunch Break Lunch Break Lunch Break Lunch Break Lunch Break Lunch Break Lunch Break
13.00 - 13.30 Live: Q&A Session [CB] Live: Quiz: MHC binding. Q&A Session [MN]. Recordings: R1 [MP4]. R2 [MP4]. R3 [MP4]. Live: Exercise recap [MN]. Quiz: MHC processing, epitope discovery and vaccine design. Q&A Session [MN]. Recordings: R1 [MP4]. Live: Exercise recap [MN] Recordings: R1 [MP4]. Live: Exercise recap Recordings: [MP4] [PM] Live: Exercise recap video [CB] and [BR] Live: Exercise recap video [HP] Live: Exercise recap [PM]
13.30 - 17.00 Micro project group work Live on Zoom Presentations_part1 Presentations_part2 [CB] Exercise:Prediction of MHC:peptide binding using PSSM and ANN

Answers: Prediction of MHC:peptide binding using PSSM and ANN

Exercise: Development of vaccines against HCV [MN] Answers Exercise: B cell epitope predictions [PM] Exercise: T-Cell Receptor Repertoires [MV] Suggested answers Exercise: IEDB [BR] Exercise: Single cell technologies for T-cell epitopes [HP] Exercise: CAR T-cell humanisation and de-immunisation [PM] Live on Zoom Introduction to project and exam [CB]
Learning Resources

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Optional

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  • None

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Project Period and Exam

Project

Wednesday January 13th - Wednesday January 20nd - Project Work

Please note the following (***time has been updated***):

  • The deadline for uploading the final project Poster presentation (i.e. not a report) to DTU inside will be Wednesday January 20nd at 11.59AM
  • It is a prerequisite for the exam to complete this assignment and as such, failure to meet the deadline will result in a failed exam
  • Furthermore and very important - Each group member is responsible for all aspects of the group work and subsequent presentation

Groups and Projects 2021

  • Groups will be preset based on educational diversity

Exam Schedule

 Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total) 
  Date: January 21st 2021 (specific times per group to be announced)

 Written exam ~20 questions 2hs, all conducted online on DTU Inside
  Date: January 22st 2021
  • Individual grades will be given after the finalization of the course
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