A5017744726- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- Plant Disease Resistance and Genetics
- Fractal and DNA sequence analysis
- Bioinformatics and Genomic Networks
- Plant and Fungal Interactions Research
- Chromosomal and Genetic Variations
- Plant Reproductive Biology
- Complex Systems and Time Series Analysis
- Cancer-related molecular mechanisms research
- Bayesian Modeling and Causal Inference
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- RNA Research and Splicing
- Plant and animal studies
- Insect and Arachnid Ecology and Behavior
- Computational Drug Discovery Methods
- Protein Degradation and Inhibitors
- Chromatin Remodeling and Cancer
- Insect and Pesticide Research
- Plant nutrient uptake and metabolism
German Centre for Integrative Biodiversity Research
2014-2024
Martin Luther University Halle-Wittenberg
2014-2024
Luther University
2014-2021
Supply Chain Competence Center (Germany)
2021
Novosibirsk State University
2017-2019
Czech Academy of Sciences, Institute of Computer Science
2019
California Institute of Technology
2018
Helmholtz Centre for Environmental Research
2017
Leibniz Institute of Plant Genetics and Crop Plant Research
2004-2014
Julius Kühn-Institut
2013
Abstract Motivation: Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression. Results: Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The is performed independently for the CDS 3′-untranslated regions (3′-UTRs) reveals different sets models two regions....
Precision-recall (PR) and receiver operating characteristic (ROC) curves are valuable measures of classifier performance. Here, we present the R-package PRROC, which allows for computing visualizing both PR ROC curves. In contrast to available R-packages, PRROC areas under these soft-labeled data using a continuous interpolation between points addition, provides generic plot function generating publication-quality graphics
Abstract Urbanisation is an important global driver of biodiversity change, negatively impacting some species groups whilst providing opportunities for others. Yet its impact on ecosystem services poorly investigated. Here, using a replicated experimental design, we test how Central European cities flying insects and the service pollination. City sites have lower insect richness, particularly Diptera Lepidoptera, than neighbouring rural sites. In contrast, Hymenoptera, especially bees, show...
We study statistical properties of the Jensen-Shannon divergence D, which quantifies difference between probability distributions, and has been widely applied to analyses symbolic sequences. present three interpretations D in framework physics, information theory, mathematical statistics, obtain approximations mean, variance, distribution random, uncorrelated a segmentation method based on that is able segment nonstationary sequence into stationary subsequences, apply this DNA sequences, are...
Describes data exploration techniques designed to classify DNA sequences. Several visualization and mining were used validate attempt discover new methods for distinguishing coding sequences (exons) from non-coding (introns). The goal of the was see whether some other, possibly non-linear combination fundamental position-dependent nucleotide frequency values could be a better predictor than AMI (average mutual information). We tried many different classification including rule-based...
We study long-range magnitude cross-correlations in collective modes of real-world data from finance, physiology, and genomics using time-lag random matrix theory. find i) time series price fluctuations, ii) physiological series, both healthy pathological, indicating scale-invariant interactions between different iii) ChIP-seq the mouse genome, where we uncover a complex interplay DNA-binding proteins, resulting power-law xij, probability that protein i binds to gene j, ranging up 10 million...
Abstract Seed germination is a critical stage in the plant life cycle and first step toward successful establishment. Therefore, understanding of important ecological agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, embryo) control germination, but little known about underlying spatial temporal transcriptome changes lead to germination. We analyzed genome-wide expression germinating Arabidopsis (Arabidopsis thaliana) seeds with both detail...
Motivation: We propose a new class of variable-order Bayesian network (VOBN) models for the identification transcription factor binding sites (TFBSs). The proposed generalize widely used position weight matrix (PWM) models, Markov and models. In contrast to these where each fixed subset remaining positions is model dependencies, in VOBN subsets may vary based on specific nucleotides observed, which are called context. This flexibility turns out be advantage classification analysis TFBSs, as...
Precision-recall curves are highly informative about the performance of binary classifiers, and area under these is a popular scalar measure for comparing different classifiers. However, many applications class labels not provided with absolute certainty, but some degree confidence, often reflected by weights or soft assigned to data points. Computing precision-recall curve requires interpolating between adjacent supporting points, previous interpolation schemes directly applicable weighted...
The plant-specific, B3 domain-containing transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is an essential component of the regulatory network controlling development and maturation Arabidopsis thaliana seed. Genome-wide chromatin immunoprecipitation (ChIP-chip), transcriptome analysis, quantitative reverse transcriptase–polymerase chain reaction a transient promoter activation assay have been combined to identify set 98 ABI3 target genes. Most these presumptive targets require presence...
Significance Plant grafting is an ancient and agriculturally important technique. Despite its widespread use, little known about how plants graft. Here, we perform a genome-wide transcriptome analysis of tissues above below graft junctions. We observed sequential activation genes for vascular development including cambium-, phloem-, xylem-related genes. Massive changes in gene expression that rapidly differentiate the top from bottom occur. These disappear as heals vasculature reconnects....
MicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding 3'UTR region mRNAs. produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims provide comprehensive information about position human and mouse microRNA their regulation transcription factors, including unique compilation both predicted experimentally supported data. Expression profiles microRNAs in several tissues cell lines,...
Organisms typically face infection by diverse pathogens, and hosts are thought to have developed specific responses each type of pathogen they encounter. The advent transcriptomics now makes it possible test this hypothesis compare host gene expression multiple pathogens at a genome-wide scale. Here, we performed meta-analysis published new transcriptomes using newly bioinformatics approach that filters genes based on their profile across datasets. Thereby, identified common unique molecular...
The developmental hourglass model has been used to describe the morphological transitions of related species throughout embryogenesis. Recently, quantifiable approaches combining transcriptomic and evolutionary information provided novel evidence for presence a phylotranscriptomic pattern across kingdoms. As its biological function is unknown it remains speculative whether this functional or merely represents nonfunctional relic. latter would seriously hamper future experimental designed...
Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view their vivo binding targets landscapes represents gap understanding mode action proteins. Here, we adapt individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) to determine repertoire circadian clock-regulated Arabidopsis thaliana glycine-rich protein AtGRP7.iCLIP identifies 858 transcripts with significantly...
Rhizobacteria are known to induce defense responses in plants without causing disease symptoms, resulting increased resistance plant pathogens. This study investigated how Streptomyces sp. strain AcH 505 suppressed oak powdery mildew infection pedunculate oak, by analyzing RNA-Seq data from singly- and co-inoculated oaks. We found that this elicited a systemic response was, part, enhanced upon pathogen challenge. In addition induction of the jasmonic acid/ethylene-dependent pathway, suggests...
Describes data exploration techniques designed to classify DNA sequences. Several visualization and mining were used validate attempt discover new methods for distinguishing coding sequences (exons) from non-coding (introns). The goal of the was see whether some other, possibly non-linear combination fundamental position-dependent nucleotide frequency values could be a better predictor than AMI (average mutual information). We tried many different classification including rule-based...
We present a new computational approach to finding borders between coding and noncoding DNA. This has two features: (i) DNA sequences are described by 12-letter alphabet that captures the differential base composition at each codon position, (ii) search for is carried out means of an entropic segmentation method which uses only general statistical properties find this highly accurate in regions requires no "prior training" on known data sets. Our results appear be more than those obtained...
We explore if there exist universal statistical patterns that are different in coding and noncoding DNA can be found all living organisms, regardless of their phylogenetic origin. find (i) the mutual information function [symbol: see text] has a significantly functional form DNA. further (ii) probability distributions average DNA, while (iii) they almost same for organisms taxonomic classes. Surprisingly, we is capable predicting regions as accurately organism-specific measures.