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Article
rhizoTrak: a flexible open source Fiji plugin for user-friendly manual annotation of time-series images from minirhizotrons
Minirhizotrons are commonly used to study root turnover which is essential for understanding ecosystem carbon and nutrient cycling. Yet, extracting data from minirhizotron images requires extensive annotation ...
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Article
Open AccessImproving MetFrag with statistical learning of fragment annotations
Molecule identification is a crucial step in metabolomics and environmental sciences. Besides in silico fragmentation, as performed by MetFrag, also machine learning and statistical methods evolved, showing an...
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Article
Aus Fehlern lernen — Wo binden Transkriptionsfaktoren an die DNA?
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Article
Open AccessAccurate prediction of cell type-specific transcription factor binding
Prediction of cell type-specific, in vivo transcription factor binding sites is one of the central challenges in regulatory genomics. Here, we present our approach that earned a shared first rank in the “ENCOD...
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Article
Open AccessDiffLogo: a comparative visualization of sequence motifs
For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of i...
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Chapter and Conference Paper
Vision-Based 3D-Reconstruction of Barley Plants
For multi-view 3D reconstruction robust standard procedures have been established and can directly be applied to many scenarios. However, the extraction of point correspondences as a prerequisite for reconstru...
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Chapter
Model Dependency of RBMCDA for Tracking Multiple Targets in Fluorescence Microscopy
The analysis of the dynamics of sub-cellular structures is of great interest to bio-medical research. We propose to use probabilistic tracking techniques to analyze the dynamics of stress granules (SGs) to avo...
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Article
Sequence and expression of the chicken membrane-associated phospholipases A1 alpha (LIPH) and beta (LIPI)
Cancer/testis antigens (CTA) are a heterogeneous group of antigens that are expressed preferentially in tumor cells and testis. Based on this definition the human membrane-associated phospholipase A1 beta (lip...
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Chapter and Conference Paper
Knowing What Happened - Automatic Documentation of Image Analysis Processes
Proper archiving or later reconstruction and verification of results in data analysis requires thorough logging of all manipulative actions on the data and corresponding parameter settings. Unfortunately such ...
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Chapter and Conference Paper
Scratch Assay Analysis with Topology-Preserving Level Sets and Texture Measures
Scratch assays are widely used for cell motility and migration assessment in biomedical research. However, quantitative data is very often extracted manually. Here, we present a fully automated analysis pipeli...
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Chapter and Conference Paper
Adaptive Segmentation of Particles and Cells for Fluorescent Microscope Imaging
Analysis of biomolecules in cells essentially relies on fluorescence microscopy. In combination with fully automatic image analysis it allows for insights into biological processes on the sub-cellular level an...
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Article
Open AccessApples and oranges: avoiding different priors in Bayesian DNA sequence analysis
One of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, t...
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Article
Open AccessUnifying generative and discriminative learning principles
The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been develo...
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Protocol
Probabilistic Approaches to Transcription Factor Binding Site Prediction
Many different computer programs for the prediction of transcription factor binding sites have been developed over the last decades. These programs differ from each other by pursuing different objectives and b...
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Chapter and Conference Paper
Joint Analysis of In-situ Hybridization and Gene Expression Data
To understand transcriptional regulation during development a detailed analysis of gene expression is needed. In-situ hybridization experiments measure the spatial distribution of mRNA-molecules and thus compl...
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Chapter and Conference Paper
Robust Image Sequence Mosaicing
Mosaicing is a technique to efficiently condense the static information of an image sequence within one extended mosaic image. The core of mosaicing is to estimate a global transformation between images due to...
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Chapter and Conference Paper
A Region Based Seed Detection for Root Detection in Minirhizotron Images
Automatic analysis of plant root images is very important for the analysis of root architecture and morphology as requested by ecological, agronomic and biological studies. Extending the approach in [1] we imp...
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Chapter and Conference Paper
Analysis of Object Interactions in Dynamic Scenes
One important source of information in scene understanding is given by actions performed either by human actors or robots. In this paper an approach to recognition and low-level interpretation of actions is pr...
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Chapter and Conference Paper
Analysis of Amperometric Biosensor Curves Using Hidden-Markov-Models
In this paper a HMM based method for analysing curves of amperometric biosensors is presented. In addition to our multi-HMM approach, we propose an enhanced single-HMM approach, which is used to detect the cur...
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Chapter and Conference Paper
Detection and Tracking of Moving Objects for Mosaic Image Generation
Mosaic images provide an efficient representation of image sequences and simplify scene exploration and analysis. However, the application of conventional methods to generate mosaics of scenes with moving obje...
