Related papers: CHERRY: a Computational metHod for accuratE pRedic…
The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The…
Predicting interspecies interactions is a key challenge in microbial ecology, as these interactions are critical to determining the structure and activity of microbial communities. In this work, we used data on monoculture growth…
Many microbes associate with higher eukaryotes and impact their vitality. In order to engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenence, which in large part, demands an understanding…
Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…
Computational prediction of origin of replication (ORI) has been of great interest in bioinformatics and several methods including GC Skew, Z curve, auto-correlation etc. have been explored in the past. In this paper, we have extended the…
Motivation: Peptide-protein interactions (PepPIs) are central to cellular regulation and peptide therapeutics, but experimental characterization remains too slow for large-scale screening. Existing methods usually emphasize either…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…
Higher-order interactions (HOIs) in complex systems, such as scientific collaborations, multi-protein complexes, and multi-user communications, are commonly modeled as hypergraphs, where each hyperedge (i.e., a subset of nodes) represents…
Computer viruses have many similarities to biological viruses, and their association may offer new perspectives and new opportunities in the effort to tackle and even eradicate them. Evolutionary game theory has been established as a useful…
Using runtime execution artifacts to identify malware and its associated family is an established technique in the security domain. Many papers in the literature rely on explicit features derived from network, file system, or registry…
Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and…
Understanding the host-specificity of different families of viruses sheds light on the origin of, e.g., SARS-CoV-2, rabies, and other such zoonotic pathogens in humans. It enables epidemiologists, medical professionals, and policymakers to…
Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg.…
Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction…
Most causal discovery methods recover a completed partially directed acyclic graph representing a Markov equivalence class from observational data. Recent work has extended these methods to federated settings to address data…
There is an influx of heterogeneous information network (HIN) based recommender systems in recent years since HIN is capable of characterizing complex graphs and contains rich semantics. Although the existing approaches have achieved…
Because of its relevance to everyday life, the spreading of viral infections has been of central interest in a variety of scientific communities involved in fighting, preventing and theoretically interpreting epidemic processes. Recent…
Detecting the origin of information or infection spread in networks is a fundamental challenge with applications in misinformation tracking, epidemiology, and beyond. We study the multi-source detection problem: given snapshot observations…