Next-generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining the nucleotide sequences of target...
Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide th...
Although RNA sequencing (RNA-seq) enables rapid transcriptome profiling, functional annotation of fungal transcriptomes remains challenging. Existing tools prioritize broad taxonomic coverage, and reference genomes are scarce for non-model species. T...
Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for proofreading and improving...
Background/Objectives: Transcriptome assembly and functional annotation are essential in understanding gene expression and biological function. Nevertheless, many existing pipelines lack the flexibility to integrate both short- and long-read sequenci...
Nipah henipavirus is an emerging RNA virus that poses a danger to world safety due to its high fatality rate. The Nipah virus has caused several illness epidemics in South and Southeast Asia. The matrix protein of Nipah henipavirus plays a crucial fu...
The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred...
Microsporidia are spore-forming eukaryotes that are related to fungi but have unique traits that set them apart. They have compact genomes as a result of evolutionary gene loss associated with their complete dependency on hosts for survival. Despite...
An aquatic gastropod belonging to the family Neritidae, Clithon retropictus is listed as an endangered class II species in South Korea. The lack of information on its genomic background limits the ability to obtain functional data resources and inhib...
We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological...
The important role of Lactiplantibacillus plantarum strains in improving the human mucosal and systemic immunity, preventing non-steroidal anti-provocative drug-induced reduction in T-regulatory cells, and as probiotic starter cultures in food proces...
The process of domestication, despite its short duration as it compared with the time scale of the natural evolutionary process, has caused rapid and substantial changes in the phenotype of domestic animal species. Nonetheless, the genetic mechanisms...
Fusarium wilt is considered the most devastating banana disease incited by Fusarium oxysporum f. sp. cubense (FOC). The present study addresses suppressive subtraction hybridization (SSH) analysis for differential gene expression in banana plant, med...
FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbio...
Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper underst...
Functional annotation of unknown function genes reveals unidentified functions that can enhance our understanding of complex genome communications. A common approach for inferring gene function involves the ortholog-based method. However, genetic dat...
Within the Human Proteome Project initiative framework for creating functional annotations of uPE1 proteins, the neXt-CP50 Challenge was launched in 2018. In analogy with the missing-protein challenge, each command deciphers the functional features o...
Transcription factors are an integral component of the cellular machinery responsible for regulating many biological processes, and they recognize distinct DNA sequence patterns as well as internal/external signals to mediate target gene expression....
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated i...
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the fi...
Background: Prioritizing tag-SNPs carried on extended risk haplotypes at susceptibility loci for common disease is a challenge. Methods: We utilized trans-ancestral exclusion mapping to reduce risk haplotypes at IKZF1 and IKZF3 identified in multiple...
Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through s...
Background/Objectives: The prevalence of dementia among South Asians across India is high among those who are 65 years and older, yet little is known about genetic risk factors for dementia in this population. Methods: Using whole-genome sequence dat...
With inadequate water purification and sewage disposal systems, cholera poses a significant health threat in developing nations. Vibrio cholerae (V. cholerae) is one of the main microscopic organisms associated with cholera illness. If cholera is not...
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to...
Cytochrome P450 monooxygenases (P450s) are one of the most widespread enzyme superfamilies in the biological world. In insects, P450 proteins play a crucial role in the synthesis of endogenous substances and the metabolism of xenobiotics. To date, ex...
With the expanding applications of carbon nanotubes (CNT) in biomedicine and agriculture, questions about the toxicity and biocompatibility of CNT in humans and domestic animals are becoming matters of serious concern. This study used proteomic metho...
Human genetic studies have implicated more than a hundred genes in Autism Spectrum Disorder (ASD). Understanding how variation in implicated genes influence expression of co-occurring conditions and drug response can inform more effective, personaliz...
Members of the DUF34 (domain of unknown function 34) family, also known as the NIF3 protein superfamily, are ubiquitous across superkingdoms. Proteins of this family have been widely annotated as “GTP cyclohydrolase I type 2” through electronic propa...
Lipases play essential roles in digestion, transport, and processing of dietary lipids in insects. For parasitoid wasps with a unique life cycle, lipase functions could be multitudinous in particular. Pteromalus puparum is a pupal endoparasitoid of b...
Long non-coding RNAs (lncRNAs), comprising a significant portion of the human transcriptome, serve as vital regulators of cellular processes and potential disease biomarkers. However, the function of most lncRNAs remains unknown, and furthermore, exi...
The study of molecular interactions, especially the inter-species protein-protein interactions, is crucial for understanding the disease infection mechanism in plants. These interactions play an important role in disease infection and host immune res...
The genome of Geobacillus sp. G4, a thermophilic bacterium isolated from a geothermal field in Peru, was sequenced and analyzed to evaluate its taxonomic and biotechnological potential. This strain exhibits optimal growth at temperatures between 50 a...
Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. The main reservoirs are found in poultry farms, but they are also found in wild birds. The development of ant...
Shigella flexneri is the principal cause of bacillary dysentery, contributing significantly to the global burden of diarrheal disease. The appearance and increase in the multi-drug resistance among Shigella strains, necessitates further genetic studi...
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the stud...
Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interp...
The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major func...
Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance g...
Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-fam...
Imaging sonar is a crucial tool for underwater visual perception. Compared to 2D sonar images, 3D sonar images offer superior spatial positioning capabilities, although the data acquisition cost is higher and lacks open source references for data ann...
Soda lakes are extreme saline–alkaline environments that harbor metabolically versatile microbial communities with significant biotechnological potential. This study employed shotgun metagenomics (NovaSeq PE150) to investigate the functional di...
From inadequate prior antidepressants that targeted monoamine neurotransmitter systems emerged the discovery of alternative drugs for depression. For instance, drugs targeted interleukin 6 receptor (IL6R) in inflammatory system. Genomic analysis-base...
In order to shed light on the usage of protein language model-based alignment procedures, we attempted the classification of Glutathione S-transferases (GST; EC 2.5.1.18) and compared our results with the ARBA/UNI rule-based annotation in UniProt. GS...
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresse...
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle,...
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional...
Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) is an important forest pest in China that mainly infests timber and economic forests. This pest primarily causes plant tissue to necrotize, rot, and eventually die by feeding on the woody parts of...
Classifying citations according to function has many benefits when it comes to information retrieval tasks, scholarly communication studies, and ranking metric developments. Many citation function classification schemes have been proposed, but most o...
Envenomation resulted from sea snake bite is a highly lethal health hazard in Southeast Asia. Although commonly caused by sea snakes of Hydrophiinae, each species is evolutionarily distinct and thus, unveiling the toxin gene diversity within individu...
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