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Genomic variants, including copy number variants (CNVs) and genome-wide associa-tion study (GWAS) single nucleotide polymorphisms (SNPs), represent structural alterations that influence genomic diversity and disease susceptibility. While…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
Combination pharmacotherapy offers substantial therapeutic advantages but also poses substantial risks of adverse drug reactions (ADRs). The accurate prediction of ADRs with interpretable computational methods is crucial for clinical safety…
Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its faithful transmission through disruptive events of cell-cycle,…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
Chromosome capture techniques like Hi-C have expanded our understanding of mammalian genome 3D architecture and how it influences gene activity. To analyze Hi-C data sets, researchers increasingly treat them as DNA-contact networks and use…
Enhancing the precision of segmenting coronary atherosclerotic plaques from CT Angiography (CTA) images is pivotal for advanced Coronary Atherosclerosis Analysis (CAA), which distinctively relies on the analysis of vessel cross-section…
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…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
The goal of cross-domain object matching (CDOM) is to find correspondence between two sets of objects in different domains in an unsupervised way. Photo album summarization is a typical application of CDOM, where photos are automatically…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
Chromatin is a complex of DNA, RNA and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
Graph clustering is a fundamental technique in data analysis with applications in many different fields. While there is a large body of work on clustering undirected graphs, the problem of clustering directed graphs is much less understood.…
Spatial relationships in multi-species data can indicate and affect system outcomes and behaviors, ranging from disease progression in cancer to coral reef resilience in ecology; therefore, quantifying these relationships is an important…
Histopathology image synthesis aims to address the data shortage issue in training deep learning approaches for accurate cancer detection. However, existing methods struggle to produce realistic images that have accurate nuclei boundaries…
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional…
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop…
Representational similarity in neural networks is inherently scale-dependent, yet widely used metrics such as Centered Kernel Alignment (CKA) and Procrustes analysis provide only global scalar estimates. These scalars often fail to…