Related papers: CHERRY: a Computational metHod for accuratE pRedic…
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct…
Background: Prokaryotic viruses, which infect bacteria and archaea, are the most abundant and diverse biological entities in the biosphere. To understand their regulatory roles in various ecosystems and to harness the potential of…
Link prediction in heterogeneous networks is crucial for understanding the intricacies of network structures and forecasting their future developments. Traditional methodologies often face significant obstacles, including…
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
This paper develops and analyzes optimization models for rapid detection of viruses in large contact networks. In the model, a virus spreads in a stochastic manner over an undirected connected graph, under various assumptions on the spread…
Viruses are submicroscopic agents that can infect all kinds of lifeforms and use their hosts' living cells to replicate themselves. Despite having some of the simplest genetic structures among all living beings, viruses are highly…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Groups with complex set intersection relations are a natural way to model a wide array of data, from the formation of social groups to the complex protein interactions which form the basis of biological life. One approach to representing…
Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
Coronaviruses are membrane-enveloped, non-segmented positive-strand RNA viruses belonging to the Coronaviridae family. Various animal species, mainly mammalian and avian, are severely infected by various coronaviruses, causing serious…
Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…
Computational prediction of origin of replication (ORI) has been of great interest in bioinformatics and several methods including GC-skew, auto-correlation etc. have been explored in the past. In this paper, we have extended the…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
Click-Through Rate (CTR) prediction, which aims to estimate the probability that a user will click an item, is an essential component of online advertising. Existing methods mainly attempt to mine user interests from users' historical…