The current rate at which new DNA and protein sequences are being generated is too fast to experimentally discover the functions of those sequences, emphasizing the need for accurate Automatic Function Prediction (AFP) methods. AFP has been an active...
A large data array on plant gene expression accumulated thanks to comparative omic studies directs the efforts of researchers to the specific or fine effects of the target gene functions and, as a consequence, elaboration of relatively simple and con...
Gene function prediction is a complicated and challenging hierarchical multi-label classification (HMC) task, in which genes may have many functions at the same time and these functions are organized in a hierarchy. This paper proposed a novel HMC al...
Brassica napus L. provides high-quality edible oil and clean energy for humans. For a long time, rapeseed breeders have tried to breed improved varieties through traditional breeding strategies. However, B. napus is an allotetraploid species containi...
Gene duplication played a fundamental role in eukaryote evolution and different copies of a given gene can be present in extant species, often with expressions and functions differentiated during evolution. We assume that, when such differentiation o...
In previous research, the pine wood nematode Bxadh2 gene significantly increased its expression in pine seedlings inoculated with endophytic Bacillus cereus GD2 and pine wood nematode. To explore pine wood nematode Bxadh2 gene function, we cloned and...
Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive gen...
With the continuous accumulation of biological data, more and more machine learning algorithms have been introduced into the field of gene function prediction, which has great significance in decoding the secret of life. Recently, a multi-label super...
WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and t...
Protein function prediction plays a crucial role in uncovering the molecular mechanisms underlying life processes in the post-genomic era. However, with the widespread adoption of high-throughput sequencing technologies, the pace of protein function...
In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae spec...
Gene function verification is a crucial step in studying the molecular mechanisms regulating various plant life activities. However, a stable and efficient homologous genetic transgenic system for herbaceous peonies has not been established. In this...
Oxidative stress is known to modulate insulin secretion and initiate gene alterations resulting in impairment of β-cell function and type 2 diabetes mellitus (T2DM). Rice bran (RB) phenolic extracts contain bioactive properties that may target m...
Polycystic ovary syndrome (PCOS) is a complex disorder characterized by reproductive abnormalities such as hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology, and is frequently accompanied by metabolic disturbances such as ins...
Protein Language Models (PLMs) are shown to be capable of learning sequence representations useful for various prediction tasks, from subcellular localization, evolutionary relationships, family membership, and more. They have yet to be demonstrated...
Lateral root initiation is a post-embryonic process that requires the specification of a subset of pericycle cells adjacent to the xylem pole in the primary root into lateral root founder cells. The first visible event of lateral root initiation in A...
Nonalcoholic fatty liver disease (NAFLD) is associated with an increased risk of kidney disease in adults and children. However, it is uncertain whether this association is influenced by major NAFLD susceptibility genes. In a sample of 230 overweight...
Silver nanoparticles (AgNPs) have been widely used in industry due to their unique physical and chemical properties. However, AgNPs have caused environmental concerns. To understand the risks of AgNPs, Arabidopsis microarray data for AgNP, Ag+, cold,...
As one of the most prominent gene families, R2R3-MYB transcription factors significantly regulate biochemical and physiological processes under salt stress. However, in Sophora alopecuroides, a perennial herb known for its exceptional saline alkali r...
The HNF1A transcription factor, implicated in the regulation of pancreatic beta cells, as well as in glucose and lipid metabolism, is responsible for type 3 maturity-onset diabetes of the young (MODY3). HNF1A is also involved in increased susceptibil...
The functional gene is a product of functional information expression methods inspired by biological genes. Product innovation design is essentially a process of functional problem-solving, which has an intrinsic connection with biological gene expre...
Background: Our previous comparison of peripheral blood mononuclear cells (PBMCs) from long-term Transcendental Meditation® (TM®) practitioners and matched non-practitioner controls found 200 differentially expressed (DE) genes. Bioinformatic...
Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similar...
Epidemiological studies support an independent inverse association between high-density lipoprotein (HDL) cholesterol levels and heart failure incidence. The effect of selective HDL-raising adeno-associated viral serotype 8-human apolipoprotein (apo)...
There is evidence to suggest that hormonal migraine is associated with altered cerebrovascular function. We aimed to investigate whether the expression of genes related to endothelial function in venous blood (1) might influence cerebrovascular funct...
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplicat...
Straw returning is a critical practice with profound strategic importance for sustainable agricultural development. However, within a comprehensive soil health evaluation framework, research analyzing the impact of tobacco straw returning on soil eco...
The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence...
Clustering techniques can group genes based on similarity in biological functions. However, the drawback of using clustering techniques is the inability to identify an optimal number of potential clusters beforehand. Several existing optimization tec...
The proper balance of gene expression is essential for cellular health, organismal development, and maintaining homeostasis. In response to complex internal and external signals, the cell needs to modulate gene expression to maintain proteostasis and...
Potassium, an essential inorganic cation, is crucial for the growth of oil crops like Brassica napus L. Given the scarcity of potassium in soil, enhancing rapeseed’s potassium utilization efficiency is of significant importance. This study iden...
The HD-Zip gene family plays a vital regulatory role in plant growth and development, but its function in plant secondary metabolism remains to be further elucidated. This study therefore investigated the involvement of the HD-Zip gene family in gins...
The aluminium activated malate transporter (ALMT) gene family is named after the first member of the family identified in wheat (Triticum aestivum L.). The product of this gene controls resistance to aluminium (Al) toxicity. ALMT genes encode transme...
Gene therapy is manipulation in/of gene expression in specific cells/tissue to treat diseases. This manipulation is carried out by introducing exogenous nucleic acids, such as DNA or RNA, into the cell. Because of their negative charge and considerab...
Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in...
The development of severe COVID-19, which is a complex multisystem disease, is thought to be associated with many genes whose action is modulated by numerous environmental and genetic factors. In this study, we focused on the ideas of the omnigenic m...
Tellurite is highly toxic to bacteria and commonly used in the clinical screening for pathogens; it is speculated that there is a potential relationship between tellurite resistance and bacterial pathogenicity. Until now, the core function genes of t...
Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different gene...
As one of the most diverse habitats of microorganisms, soil has been recognised as a reservoir of both antibiotics and the antibiotic resistance genes (ARGs). Bacteria naturally inhabiting soil or water often possess innate ARGs to counteract the che...
Different revegetatiom types can affect the chemical composition of soil organic carbon (SOC), soil microbial community and the functional genes related to carbon cycle. However, the relationships between SOC chemical functional groups and soil micro...
The OVATE gene family is a class of conserved transcription factors that play significant roles in plant growth, development, and abiotic stress, and also affect fruit shape in vegetable crops. Bottle gourd (Lagenaria siceraria), commonly known as ca...
Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamil...
The product innovation design is an innovation-intensive process that requires abundant knowledge and design experience, even across industries and disciplines, as a resource for problem solving. Therefore, designers need to have a good command of mo...
Food security and hidden hunger are two worldwide serious and complex challenges nowadays. As one of the newly emerged technologies, gene editing technology and its application to crop improvement offers the possibility to relieve the pressure of foo...
Genome-wide association analysis is an important approach to identify genetic variants associated with complex traits. Complex traits are not only affected by single gene loci, but also by the interaction of multiple gene loci. Studies of association...
Soil pH critically regulates microbial community structure and activity, thereby influencing carbon transformation processes in terrestrial ecosystems. However, the mechanisms underlying pH-mediated shifts in microbial metabolic functions and cellulo...
Improved reproductive efficiency could lead to economic benefits for the beef industry, once the intensive selection pressure has led to a decreased fertility. However, several factors limit our understanding of fertility traits, including genetic di...
The microorganisms of mariculture sediments are key to regulating and maintaining their ecosystem balance and have garnered research interest. Although the microbial composition and functional potential of mariculture sediments have been extensively...
Catalase (CAT) is an important antioxidant enzyme in plants that plays a key role in plant growth and stress responses. CAT is usually encoded by a small gene family that has been cloned and functionally studied in some species, such as Arabidopsis,...
Although great progress has been made in transgenic technology, increasing the expression level and thus promising the expected phenotypes of exogenous genes in transgenic plants is still a crucial task for genetic transformation and crop engineering...
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