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The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Background: While the importance of gene-gene interactions in human diseases has been well recognized, identifying them has been a great challenge, especially through association studies with millions of genetic markers and thousands of…
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and…
The spatial organization of the DNA in the cell nucleus plays an important role for gene regulation, DNA replication, and genomic integrity. Through the development of chromosome conformation capture experiments (such as 3C, 4C, Hi-C) it is…
Summary: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data…
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
Chromatin conformation capture technologies such as Hi-C have revealed that the genome is organized in a hierarchy of structures spanning multiple scales observed at different resolutions. Current algorithms often focus on specific…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
The increasing quantity of multi-omics data, such as methylomic and transcriptomic profiles, collected on the same specimen, or even on the same cell, provide a unique opportunity to explore the complex interactions that define cell…
The task of data integration for multi-omics data has emerged as a powerful strategy to unravel the complex biological underpinnings of cancer. Recent advancements in graph neural networks (GNNs) offer an effective framework to model…
To enhance the precision of cancer prognosis, recent research has increasingly focused on multimodal survival methods by integrating genomic data and histology images. However, current approaches overlook the fact that the proteome serves…
Background: It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver" mutations that are…
Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as…