Die chronologische Liste zeigt aktuelle Veröffentlichungen aus dem Forschungsbetrieb der Hochschule Weihenstephan-Triesdorf. Zuständig ist das Zentrum für Forschung und Wissenstransfer (ZFW).
In this chapter, we introduce the concept of RNA-Seq analyses. First, we start to provide an overview of a typical RNA-Seq experiment that includes extraction of sample RNA, enrichment, and cDNA library preparation. Next, we review tools for quality control and data pre-processing followed by a standard workflow to perform RNA-Seq analyses. For this purpose, we discuss two common RNA-Seq strategies, that is a reference-based alignment and a de novo assembly approach. We learn how to do basic downstream analyses of RNA-Seq data, including quantification of expressed genes, differential gene expression (DE) between different groups as well as functional gene analysis. Eventually, we provide a best-practice example for a reference-based RNA-Seq analysis from beginning to end, including all necessary tools and steps on GitHub: https://github.com/grimmlab/BookChapter-RNA-Seq-Analyses.
Mehr
Quirin Göttl,
Prof. Dr. Dominik Grimm,
Prof. Dr.-Ing. Jakob Burger
Automated flowsheet synthesis is an important field in computer-aided process engineering. The present work demonstrates how reinforcement learning can be used for automated flowsheet synthesis without any heuristics of prior knowledge of conceptual design. The environment consists of a steady-state flowsheet simulator that contains all physical knowledge. An agent is trained to take discrete actions and sequentially built up flowsheets that solve a given process problem. A novel method named SynGameZero is developed to ensure good exploration schemes in the complex problem. Therein, flowsheet synthesis is modelled as a game of two competing players. The agent plays this game against itself during training and consists of an artificial neural network and a tree search for forward planning. The method is applied successfully to a reaction-distillation process in a quaternary system.
Mehr
Prof. Dr. Klaus Menrad,
Prof. Dr. Florian Haselbeck,
M.Sc. Daniel Berki-Kiss,
Dr. Thomas Decker,
Prof. Dr. Dominik Grimm,
Prof. Dr. Thomas Hannus,
Dr. rer. pol. Kai Sparke,
M. Lehberger,
M. Drechsler,
Prof. Dr. Andreas Holzapfel,
S. Schröder,
Gerald Neu,
F. Bertlich
Automated flowsheet synthesis is an important field in computer-aided process engineering. The present work demonstrates how reinforcement learning can be used for automated flowsheet synthesis without any heuristics of prior knowledge of conceptual design. The environment consists of a steady-state flowsheet simulator that contains all physical knowledge. An agent is trained to take discrete actions and sequentially built up flowsheets that solve a given process problem. A novel method named SynGameZero is developed to ensure good exploration schemes in the complex problem. Therein, flowsheet synthesis is modelled as a game of two competing players. The agent plays this game against itself during training and consists of an artificial neural network and a tree search for forward planning. The method is applied successfully to a reaction-distillation process in a quaternary system.
Mehr
Nikita Genze,
Richa Bharti,
Michael Grieb,
Dr. Sebastian J. Schultheiss,
Prof. Dr. Dominik Grimm
BackgroundAssessment of seed germination is an essential task for seed researchers to measure the quality and performance of seeds. Usually, seed assessments are done manually, which is a cumbersome, time consuming and error-prone process. Classical image analyses methods are not well suited for large-scale germination experiments, because they often rely on manual adjustments of color-based thresholds. We here propose a machine learning approach using modern artificial neural networks with region proposals for accurate seed germination detection and high-throughput seed germination experiments.ResultsWe generated labeled imaging data of the germination process of more than 2400 seeds for three different crops, Zea mays (maize), Secale cereale (rye) and Pennisetum glaucum (pearl millet), with a total of more than 23,000 images. Different state-of-the-art convolutional neural network (CNN) architectures with region proposals have been trained using transfer learning to automatically identify seeds within petri dishes and to predict whether the seeds germinated or not. Our proposed models achieved a high mean average precision (mAP) on a hold-out test data set of approximately 97.9%, 94.2% and 94.3% for Zea mays, Secale cerealeand Pennisetum glaucum respectively. Further, various single-value germination indices, such as Mean Germination Time and Germination Uncertainty, can be computed more accurately with the predictions of our proposed model compared to manual countings.ConclusionOur proposed machine learning-based method can help to speed up the assessment of seed germination experiments for different seed cultivars. It has lower error rates and a higher performance compared to conventional and manual methods, leading to more accurate germination indices and quality assessments of seeds.
Mehr
Anja Gumpinger,
Bastian Rieck,
Prof. Dr. Dominik Grimm,
Headache Genetics Consortium International,
Karsten Borgwardt
Matteo Togninalli,
Ümit Seren,
Jan A Freudenthal,
J Grey Monroe,
Dazhe Meng,
Magnus Nordborg,
Detlef Weigel,
Karsten Borgwardt,
Arthur Korte,
Prof. Dr. Dominik Grimm
AbstractGenome-wide association studies (GWAS) are integral for studying genotype-phenotype relationships and gaining a deeper understanding of the genetic architecture underlying trait variation. A plethora of genetic associations between distinct loci and various traits have been successfully discovered and published for the model plant Arabidopsis thaliana. This success and the free availability of full genomes and phenotypic data for more than 1,000 different natural inbred lines led to the development of several data repositories. AraPheno (https://arapheno.1001genomes.org) serves as a central repository of population-scale phenotypes in A. thaliana, while the AraGWAS Catalog (https://aragwas.1001genomes.org) provides a publicly available, manually curated and standardized collection of marker-trait associations for all available phenotypes from AraPheno. In this major update, we introduce the next generation of both platforms, including new data, features and tools. We included novel results on associations between knockout-mutations and all AraPheno traits. Furthermore, AraPheno has been extended to display RNA-Seq data for hundreds of accessions, providing expression information for over 28 000 genes for these accessions. All data, including the imputed genotype matrix used for GWAS, are easily downloadable via the respective databases.
Mehr
Richa Bharti,
Prof. Dr. Dominik Grimm
Berechtigungen: Open Access
Berechtigungen: Peer Reviewed
Current challenges and best-practice protocols for microbiome analysis (2019) Briefings in Bioinformatics 22 (1), S. 178-193.
DOI: 10.1093/bib/bbz155
AbstractAnalyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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