Jiaojiao Guan
YOU?
Author Swipe
View article: GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search
GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search Open
Motivation Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their widespread environmental presence and critical roles in processes such as host metabolic …
View article: PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment
PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment Open
Plasmids play a pivotal role in the emergence of multidrug-resistant and pathogenic bacteria, posing significant clinical challenges. The integration of metagenomic sequencing with advanced bioinformatics tools surpasses traditional wet la…
View article: Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong
Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong Open
Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders fo…
View article: MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction
MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction Open
Motivation Plasmids play an essential role in horizontal gene transfer, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. There exist some plasmids that can transfer, replicate, or persist in m…
View article: GiantHunter: Accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search
GiantHunter: Accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search Open
Motivation: Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their widespread environmental presence and critical roles in processes such as host metabolic…
View article: GOPhage: protein function annotation for bacteriophages by integrating the genomic context
GOPhage: protein function annotation for bacteriophages by integrating the genomic context Open
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new …
View article: ViraLM: empowering virus discovery through the genome foundation model
ViraLM: empowering virus discovery through the genome foundation model Open
Motivation Viruses, with their ubiquitous presence and high diversity, play pivotal roles in ecological systems and public health. Accurate identification of viruses in various ecosystems is essential for comprehending their variety and as…
View article: Accurate and efficient protein embedding using multi-teacher distillation learning
Accurate and efficient protein embedding using multi-teacher distillation learning Open
Motivation Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein–protein interaction predictio…
View article: PhaGO: Protein function annotation for bacteriophages by integrating the genomic context
PhaGO: Protein function annotation for bacteriophages by integrating the genomic context Open
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new …
View article: MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction
MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction Open
Plasmids play an essential role in horizontal gene transfer among diverse microorganisms, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. Identifying the host bacteria where a plasmid can tra…
View article: PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure Open
Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO)…
View article: Accurate and efficient protein embedding using multi-teacher distillation learning
Accurate and efficient protein embedding using multi-teacher distillation learning Open
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction predicti…
View article: ViraLM: Empowering Virus Discovery through the Genome Foundation Model
ViraLM: Empowering Virus Discovery through the Genome Foundation Model Open
Motivation Viruses, with their ubiquitous presence and high diversity, play pivotal roles in ecological systems and have significant implications for public health. Accurately identifying these viruses in various ecosystems is essential fo…
View article: PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure Open
Background Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene On…
View article: Predicting the Disease Genes of Multiple Sclerosis Based on Network Representation Learning
Predicting the Disease Genes of Multiple Sclerosis Based on Network Representation Learning Open
Multiple sclerosis (MS) is an autoimmune disease for which it is difficult to find exact disease-related genes. Effectively identifying disease-related genes would contribute to improving the treatment and diagnosis of multiple sclerosis. …
View article: Predicting Parkinson's Disease Genes Based on Node2vec and Autoencoder
Predicting Parkinson's Disease Genes Based on Node2vec and Autoencoder Open
Identifying genes associated with Parkinson's disease plays an extremely important role in the diagnosis and treatment of Parkinson's disease. In recent years, based on the guilt-by-association hypothesis, many methods have been proposed t…