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Simple changes of individual studies can improve the reproducibility of the biomedical scientific process as a whole

Initiative of the Federal Ministry of Food and Agriculture (BMEL) entitled `Minding animalsÐnew ways to improve animal welfare`. Author Contributions Conceptualization: Matthias Steinfath. Formal analysis ... : Matthias Steinfath, Norman Violet. Funding acquisition: Gilbert SchoÈnfelder. Investigation: Matthias Steinfath. Methodology: Matthias Steinfath, Norman Violet. Resources: Gilbert SchoÈnfelder

Network Structure and Biological Function: Reconstruction, Modeling, and Statistical Approaches

Matthias Steinfath 1 Dirk Repsilber 0 0 Genetics and Biometry unit, Research Institute for the Biology of Farm Animals (FBN) , 18196 Dummerstorf , Germany 1 University of Potsdam, Department of Biochemistry

Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers

A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of...

Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model...

Improved Heterosis Prediction by Combining Information on DNA- and Metabolic Markers

Background Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance...

QTL analysis of early stage heterosis for biomass in Arabidopsis

The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44% heterosis...

Xdigitise: visualization of hybridization experiments

Xdigitise is a software system for visualization of hybridization experiments giving the user facilities to analyze the corresponding images manually or automatically. Images of the high-density DNA arrays are displayed as well as the results of an external image analysis bundled with Xdigitise, e.g. the spot locations are marked and the duplicate correlations are shown by a...

Automated image analysis for array hybridization experiments

Motivation: Image analysis is a major part of data evaluation for array hybridization experiments in molecular biology. The program presented here is designed to analyze automatically images from hybridization experiments with various arrangements: different kinds of probes (oligonucleotides or complex probes), different supports (nylon filters or glass slides), different...

Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis

Background Gene expression analyses based on complex hybridization measurements have increased rapidly in recent years and have given rise to a huge amount of bioinformatic tools such as image analyses and cluster analyses. However, the amount of work done to integrate and evaluate these tools and the corresponding experimental procedures is not high. Although complex...

Information theoretical probe selection for hybridisation experiments

Motivation: The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on Shannon entropy as a quality criterion. The practical motivation for our algorithm is oligonucleotide fingerprinting, a method for the simultaneous identification of sequences (cDNA...