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

Lecturers and TAs

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?

Sign up

Deadline: October 20, 2024

If interested, sign up by submitting the following information via email to: irgu00001@stud.uni-saarland.de AND fabian.mueller@uni-saarland.de

  • Your name
  • Your UNIVERSITY email address
  • Your field of study (e.g. Bioinformatics)
  • Your current semester
  • Your immatriculation number

Example:

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)