Single-Cell Bioinformatics (WS 2024/2025)

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 16th, 2024 and February 5th, 2025 (in presence).
• First lecture: October 16th, 2024
• First tutorial: October 22nd, 2024

Lecturers and TAs

• Jun.-Prof. Dr. Fabian Müller
• Dr. Thomas Hentrich
• Dr. Fabian Kern
• Irem Gündüz
• Midhuna Maran

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

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

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 007
• Programming assignments:
  • Assignment 1 deadline: November 15th, 2024
  • Assignment 2 deadline: December 13th, 2024
  • Assignment 3 deadline: January 17th, 2025
• Exam: February 5th, 2025

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/

TO: irgu00001@stud.uni-saarland.de, fabian.mueller@uni-saarland.de
SUBJECT: SCB (WiSe2024)
BODY: John Snow, jsnow@uni-saarland.de, Bioinformatics Master, 3, 999999

Lecture materials

Lecture slides, programming assignments and current research papers on single-cell technology and bioinformatics methods can be found on the lecture materials page (password protected)