Related papers: bioSBM: a random graph model to integrate epigenom…
Biomedical information graphs are crucial for interaction discovering of biomedical information in modern age, such as identification of multifarious molecular interactions and drug discovery, which attracts increasing interests in…
Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior…
$n$-gram profiles have been successfully and widely used to analyse long sequences of potentially differing lengths for clustering or classification. Mainly, machine learning algorithms have been used for this purpose but, despite their…
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…
In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones…
Molecular activity prediction is critical in drug design. Machine learning techniques such as kernel methods and random forests have been successful for this task. These models require fixed-size feature vectors as input while the molecules…
A structural genetic model incorporating a modern understanding of the genome and common practice in genome-wide association studies is derived mathematically. The model shows the Haldane map distance as a direct consequence of the…
Isocitrate DeHydrogenase (IDH) mutation status is a crucial biomarker for glioma prognosis. However, current prediction methods are limited by the low availability and noise of functional MRI. Structural and morphological connectomes offer…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with…
Hi-C technology measures genome-wide interaction frequencies, providing a powerful tool for studying the 3D genomic structure within the nucleus. However, high sequencing costs and technical challenges often result in Hi-C data with limited…
More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…
In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models…
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes,…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…
A deep understanding of the intricate interactions between particles within a system is a key approach to revealing the essential characteristics of the system, whether it is an in-depth analysis of molecular properties in the field of…