相关论文: Efficient network-guided multi-locus association m…

Genetic Network Programming (GNP) is an evolutionary algorithm that extends Genetic Programming (GP). It is typically used in agent control problems. In contrast to GP, which employs a tree structure, GNP utilizes a directed graph…

The aetiology of polygenic obesity is multifactorial, which indicates that life-style and environmental factors may influence multiples genes to aggravate this disorder. Several low-risk single nucleotide polymorphisms (SNPs) have been…

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially…

In this paper, association results from genome-wide association studies (GWAS) are combined with a deep learning framework to test the predictive capacity of statistically significant single nucleotide polymorphism (SNPs) associated with…

Mapping genotypes to phenotypes (G2P) is a fundamental goal in biology. So called PhyloG2P methods are a relatively new set of tools that leverage replicated evolution in phylogenetically independent lineages to identify genomic regions…

Counting the frequencies of 3-, 4-, and 5-node undirected motifs (also know as graphlets) is widely used for understanding complex networks such as social and biology networks. However, it is a great challenge to compute these metrics for a…

Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…

The \textit{Multi-Constraint Shortest Path (MCSP)} problem aims to find the shortest path between two nodes in a network subject to a given constraint set. It is typically processed as a \textit{skyline path} problem. However, the number of…

Skeleton-based action recognition is a hotspot in image processing. A key challenge of this task lies in its dependence on large, manually labeled datasets whose acquisition is costly and time-consuming. This paper devises a novel,…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…

Following the success of deep convolutional networks in various vision and speech related tasks, researchers have started investigating generalizations of the well-known technique for graph-structured data. A recently-proposed method called…

We propose AGS-GNN, a novel attribute-guided sampling algorithm for Graph Neural Networks (GNNs) that exploits node features and connectivity structure of a graph while simultaneously adapting for both homophily and heterophily in graphs.…

We propose a method for gene expression based analysis of cancer phenotypes incorporating network biology knowledge through unsupervised construction of computational graphs. The structural construction of the computational graphs is driven…

Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…

Computer vision-based methods have valuable use cases in precision medicine, and recognizing facial phenotypes of genetic disorders is one of them. Many genetic disorders are known to affect faces' visual appearance and geometry. Automated…

In this study, the concept of small worlds is investigated in the context of large-scale wireless ad hoc and sensor networks. Wireless networks are spatial graphs that are usually much more clustered than random networks and have much…

Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…