Research Project Computational Plant Genomics

What it is about

You work on an individual research project in the area of Computational Plant Genomics. You will learn to process NGS and other plant genomic data with current bioinformatics tools on Linux/HPC environments, independently carry out analyses, and document and present results scientifically.

What you will be able to do

Proficient handling of Linux and HPC clusters
Deepening knowledge of NGS and plant genomic data
Application of various bioinformatics tools and methods
Development and deployment of bioinformatics pipelines
Efficient use of scientific literature and data sources
Independent planning and execution of a research project
Critical interpretation of biological analysis results
Clear documentation and presentation of research results

What the module consists of

Research ProjectConducting an individual project with supervised research questions catalog
Presence/Feedback SessionsRegular feedback on project progress and methodological reflection
Presentations in the working groupPresentation of project progress and discussion of scientific literature

Teaching method

Individual Project SupervisionClose supervision to develop and implement own analyses
Hands-on Training on Linux/HPCPractical handling of data processing and compute-intensive workflows
Tutorials / How-to GuidesSupport in learning concrete tools and workflows
Benchmarking of ToolsEvaluation of speed, accuracy, and suitability of different software
Participation in Group SessionsPresentation and discussion to contextualize the results

What you should already know

Solid foundations in molecular biology
Basic knowledge in Computational Biology
WZ0637: Lab Course Methods for Analysis of Next Generation Sequencing Datarecommended
LS20039: Fundamentals of Computational Data Analysis and Bioinformatics for Plant Transcriptomics and RNA-seqrecommended

Assessment

Project reportPresentation

The module assessment consists of a project report (~5000 words / 15–20 pages, including figures and references) and a presentation. The report accounts for 65% of the final grade and should show the state of research, hypothesis, methods, analysis, evaluation, and critical reflection of the applied methods. The presentation (20-minute talk + 10-minute discussion) contributes 35% to the grade. Information on tools used is not listed separately.

Reading list

Bayer, P.E. et al. - Plant pan-genomes are the new reference. Nat. Plants (2020).
Schreiber, M. et al. - Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet (2024).
Pereira-Santana, A., Gamboa-Tuz, S. D., Rodríguez-Zapata, L. C. (Eds.) - Plant comparative genomics. Humana (2022).
Emms, D.M., Kelly, S. - OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol (2019).
Bioconductor workflow - rnaseqGene (Gene expression analyses).
Yang, Z., Nie, G., Feng, G. et al. - Genome-wide identification... of the NAC transcription factor family in orchardgrass. BMC Genomics (2021).

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Research Project Computational Plant Genomics

What it is about

What you will be able to do

What the module consists of

Teaching method

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