Single-Cell Bioinformatics (WiSe 2026/2027)

Format and Time

• Bioinformatics special lecture
• 9 ECTS credit points
• Lecture and programming projects (V4 Ü2)
• Course language: English
• The lecture will be held Wednesdays and Fridays 8:30 to 10:00 between October 14th, 2026 and February 3rd, 2027 (in presence).
• First lecture: October 14th, 2026
• First tutorial: October 20th, 2026

Lecturers and TAs

• Jun.-Prof. Dr. Fabian Müller
• Dr. Thomas Hentrich
• Nima Amini
• Irem Gündüz
• Adam Ashkar Masarwa

Course outline

The course reviews current technologies, laboratory techniques and bioinformatics methods for single-cell analysis. The lecture provides the theoretical background on single-cell *omics. Three programming projects will apply the learned bioinformatics methods to real-world single-cell datasets and will ensure that students have a working knowledge with practical experience on the material.

Content

Current technologies, laboratory techniques and bioinformatics methods for:

• Single-cell transcriptomics
• Single-cell epigenomics, including chromatin accessibility, DNA methylation and regulatory protein profiling
• Spatial transcriptomics
• Single-cell DNA sequencing
• Single-cell proteomics
• Single-cell multiomics
• Single-molecule sequencing
• Perturbation experiments with single-cell readout
• Emerging technologies
• Clinical Applications

Bioinformatics focus:

• Processing of single-cell sequencing data
• Data quality control
• Exploratory data analysis
• Differential data analysis
• Single-cell trajectory inference
• Data integration (multi-dataset and multi-omics)
• Inference of gene-regulation and gene regulatory networks
• Machine Learning & AI

Schedule

• Lectures:
  • Wednesdays, 8:30-10:00, building E1.3, HS 003
  • Fridays, 8:30-10:00, building E2.1, Room 001
• Tutorials:
  • Tuesdays, 10:00-12:00, building E2.1, Room 001
• Programming assignments:
  • Assignment 1 deadline: November 22nd, 2026
  • Assignment 2 deadline: December 20th, 2026
  • Assignment 3 deadline: January 24th, 2027
• Exam: February 3rd, 2027

All Lectures will be held in presence.

Entrance requirements

To enroll, students should have a basic knowledge in Next Generation Sequencing (NGS), modern genomics and epigenomics, sequence analysis, linear algebra and machine learning. They should have basic skills for script-based programming using the R language.  

Assessment/Exams

Final exam: written or oral, depending on participant numbers Participants need to score 50% on the three programming assignments to be admitted to the exam. The final grade will be based on the exam

What can you do to prepare for the lecture?

• Refresh your knowledge on Next-Generation Sequencing technology, genomics and epigenomics
• Refresh your knowledge on bioinformatics for sequence analysis, linear algebra and machine learning
• Familiarize yourself with the R programming language. You might find these tutorials useful:
  • http://swcarpentry.github.io/r-novice-inflammation/
  • https://adv-r.hadley.nz/

Lecture slides, programming assignments and current research papers on single-cell technology and bioinformatics methods can be found in the lecture MS Teams channel (after joining the lecture Teams, details given in the first lecture).