Related papers: Methylator: A Modular Framework for DNA Methylatio…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters…
Galaxy morphology classification plays a crucial role in understanding the structure and evolution of the universe. With galaxy observation data growing exponentially, machine learning has become a core technology for this classification…
Background: The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M =…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In…
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to…
Gene expression and DNA methylation are two interconnected biological processes and understanding their relationship is important in advancing understanding in diverse areas, including disease pathogenesis, environmental adaptation,…
Recent evidence highlights the usefulness of DNA methylation (DNAm) biomarkers as surrogates for exposure to risk factors for non-communicable diseases in epidemiological studies and randomized trials. DNAm variability has been demonstrated…
The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…
Bioinformatics platforms have significantly changed clinical diagnostics by facilitating the analysis of genomic data, thereby advancing personalized medicine and improving patient care. This study examines the integration, usage patterns,…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
In many applications, Neural Nets (NNs) have classification performance on par or even exceeding human capacity. Moreover, it is likely that NNs leverage underlying features that might differ from those humans perceive to classify. Can we…
Accurately predicting chronological age from DNA methylation patterns is crucial for advancing biological age estimation. However, this task is made challenging by Epigenetic Correlation Drift (ECD) and Heterogeneity Among CpGs (HAC), which…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
Nucleic acid sensing is crucial for advancing diagnostics, therapeutic monitoring and molecu-lar biology research, by enabling the precise identification of DNA and RNA interactions. Here, we present an innovative sensing platform based on…
Bone metastasis analysis is a significant challenge in pathology and plays a critical role in determining patient quality of life and treatment strategies. The microenvironment and specific tissue structures are essential for pathologists…
Major Depressive Disorder (MDD) is a clinically heterogeneous syndrome with diverse etiological pathways. Traditional Epigenome-Wide Association Studies (EWAS) have successfully identified risk loci based on differential methylation…
The rapid expansion of spaceborne methane observing capabilities at the facility-scale (fostered both by public missions and commercial constellations) has created a need for harmonised, reproducible, and uncertainty-aware processing chains…
The distribution and interactions of cellular organelles play a critical role in mediating cellular physiology and pathology. Large-scale electron microscopy enables visualization of organelle distribution and interactions at the tissue…