Related papers: M3D: a kernel-based test for shape changes in meth…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
Domain shift presents a significant challenge in applying Deep Learning to the segmentation of 3D medical images from sources like Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Although numerous Domain Adaptation methods…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
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…
We present a new method for assessing the intrinsic 3D shape of prestellar cores from molecular column densities. We have employed hydrodynamic simulations of contracting, isothermal cores considering three intrinsic geometries: spherical,…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
Face recognition is a widely accepted biometric verification tool, as the face contains a lot of information about the identity of a person. In this study, a 2-step neural-based pipeline is presented for matching 3D facial shape to multiple…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates, and changes in CpG methylation are essential to cellular differentiation. Genome-wide DNA methylation assays…
Identifying disease-associated changes in DNA methylation can help to gain a better understanding of disease etiology. Bisulfite sequencing technology allows the generation of methylation profiles at single base of DNA. We previously…
Large kernel convolutions offer a scalable alternative to vision transformers for high-resolution 3D volumetric analysis, yet naively increasing kernel size often leads to optimization instability. Motivated by the spatial bias inherent in…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…