Bioinformatics
The bioinformatics lab at the Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability is led by Prof. Dr. Dominik Grimm from the University of Applied Sciences Weihenstephan-Triesdorf.
Bioinformatics is a young interdisciplinary research area that develops computational and statistical tools to analyze, store, integrate and visualize biological and biomedical data. One of the main research areas of our group is the development and usage of novel computational tools and machine learning methods to gain a deeper understanding of the underlying genetic architecture of complex biological processes and phenotypes. In addition, we are interested in developing efficient pipelines and applications to process and analyze Next Generation Sequencing (NGS) data. Further, we develop modern cloud-based applications and databases to simplify the analysis, storage, retrieval and visualization of diverse and complex biological and biomedical data.
Software & Resources
easyGWAS
easyGWAS is a novel web- and cloud platform for performing, analysing and comparing genome-wide association studies (GWAS).
The AraGWAS Catalog
The AraGWAS Catalog is a public and manually curated database for standardised GWAS results for Arabidopsis thaliana.
Software and Methods developed by the group can be found and downloaded at our Lab News
New Paper: HeliantHOME, a public and centralized database of phenotypic sunflower data
New paper in Scientific Data: “HeliantHOME, a public and centralized database of phenotypic sunflower data”. We have created HeliantHOME (http://www.helianthome.org), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals.
New Paper: A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species
New paper: “A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species”. In this work, our aim is to systematically compare 12 different phenotype prediction models, including basic genomic selection methods to more advanced deep learning-based techniques. More importantly, we assess the performance of these models on simulated phenotype data as well as on real-world data from Arabidopsis thaliana and two breeding datasets from soy and corn. The synthetic phenotypic data allow us to analyze all prediction models and especially the selected markers under controlled and predefined settings. We show that Bayes B and linear regression models with sparsity constraints perform best under different simulation settings with respect to explained variance. Further, we can confirm results from other studies that there is no superiority of more complex neural network-based architectures for phenotype prediction compared to well-established methods. However, on real-world data, for which several prediction models yield comparable results with slight advantages for Elastic Net, this picture is less clear, suggesting that there is a lot of room for future research.
New Paper: Deep learning-based early weed segmentation using motion blurred UAV images of sorghum fields
New paper about “Deep learning-based early weed segmentation using motion blurred UAV images of sorghum fields”. In this work, we developed and analysed different deep learning-based architectures to accurately segment crop and weed species in UAV images of agricultural fields under challenging capturing conditions. For this propose, we created an expert-curated fully-annotated weed segmentation UAV dataset in sorghum fields. We show that our trained models have high precision in detecting general plant shapes with minor weaknesses at borders of the plants. More importantly, our method is capable in segmenting intra-row and partly occluded weeds on an individual plant basis. All code and data are publicly available on GitHub and Mendeley Data.
