The aim of this workshop was to introduce phylogenetic and phylogenomic concepts and how to apply these analyses using the Linux command line. Students first learned about the history of phylogenetic methods and traditional molecular marker regions, which were used for decades to examine the relationships of organisms. We then continued the course by teaching basic but powerful Linux commands to manage folder structure, handle large files, and install and execute programs. This new knowledge about the Linux command line was then applied to bioinformatic methods to build alignments, run complex phylogenetic methods, assemble high throughput sequencing data into continuous genomes, verify the integrity of these genomes by sequence mapping, use search methods to identify gene regions, and use these regions for phylogenetic reconstruction. In addition, we introduced next-generation applications such as RADseq and target enrichment (HybSeq) with example datasets from former studies on lichen genomes. The course website offers students constant access to the course material and represents a great resource for interested autodidacts. We invite you to learn at home about the Linux command line, bioinformatics, and phylogenetic methods with our course material and example datasets. I tought this Bioinformatics Workshop together with Thorsten Lumbsch for interested students at the Ramkhamhaeng University in Thailand. We thank Kawinnat Buaruang from the Lichen Research Unit and Lichen Herbarium (RAMK) at the Ramkhamhaeng University for the invitation and great hospitality during our time in Thailand.
CBFM is a course based on the use of the Linux command line for computational biology applications. This course offers the novice both user tools and guidance to enter the world of Linux and computational biology. The course website offers constant access for students to the course material and represents a great resource for interested autodidacts.
The aim of this course was to sharpen the students' presentation skills, to encourage their involvement in scientific discussions, and to have fun with scientific communication. This course offered introductions in how to plan and organize a scientific presentation, how to prepare a PowerPoint presentation with well-designed, notable content, and information to consider when presenting work. The students then used their acquired knowledge to give short talks based on scientific publications. In subsequent discussions of their presentations, we gave feedback and focused on how the presenters could improve their performance.
PMEP is an introductory class taught to develop an evolutionary-based understanding of modern phylogenetics, taxonomy, and cladistics. Students used hands-on experiences to learn the basics of molecular biology and the methods of phylogenetic analyses in this 4-week all-day course. In this course, we used real-world examples from actual molecular biology research. These experiences offered students great insight into the work of a scientist—from the success to the disappointments that go along with research. I co-designed several student projects and taught this class together with my PhD advisor Dr. Volker Knoop. You can find more information about this class and the M.Sc. in Plant Sciences at the University of Bonn under the following links:
Please see my CV for a detailed list of all courses and guest lectures that I have taught.