Related papers: BHiCect 2.0: Multi-resolution clustering of Hi-C d…

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…

Motivation: Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin…

Graph-based multi-view clustering has achieved better performance than most non-graph approaches. However, in many real-world scenarios, the graph structure of data is not given or the quality of initial graph is poor. Additionally,…

Recently, the field of machine learning has undergone a transition from model-centric to data-centric. The advancements in diverse learning tasks have been propelled by the accumulation of more extensive datasets, subsequently facilitating…

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,…

Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized…

The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…

While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…

Motivation: Histone modifications are among the most important factors that control gene regulation. Computational methods that predict gene expression from histone modification signals are highly desirable for understanding their…

In natural images, the scales (thickness) of object skeletons may dramatically vary among objects and object parts, making object skeleton detection a challenging problem. We present a new convolutional neural network (CNN) architecture by…

Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated…

Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…

High-dimensional single-cell data poses significant challenges in identifying underlying biological patterns due to the complexity and heterogeneity of cellular states. We propose a comprehensive gene-cell dependency visualization via…

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex…

In this paper, we present novel variations of an earlier approach called homogeneous clustering algorithm for reducing dataset size. The intuition behind the approaches proposed in this paper is to partition the dataset into homogeneous…

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…

We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics…

Gene annotation addresses the problem of predicting unknown associations between gene and functions (e.g., biological processes) of a specific organism. Despite recent advances, the cost and time demanded by annotation procedures that rely…

Motivation: The application of PacBio HiFi and ultra-long ONT reads have achieved huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding software,…

The complexity of clouds, particularly in terms of texture detail at high resolutions, has not been well explored by most existing cloud detection networks. This paper introduces the High-Resolution Cloud Detection Network (HR-cloud-Net),…