Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of...
With estrus confined to three winter months, early pregnancy detection is essential for reproductive management in farmed sika deer. However, the development of reliable non-invasive early pregnancy detection techniques has been hindered by limited u...
Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in t...
Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud dev...
Transition to flowering is a crucial part of plant life directly affecting the fitness of a plant. Time series of transcriptomes is a useful tool for the investigation of process dynamics and can be used for the identification of novel genes and gene...
Inferring time-varying gene regulatory networks from time-series single-cell RNA sequencing (scRNA-seq) data remains a challenging task. The existing methods have notable limitations as most are either designed for reconstructing time-varying network...
We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut grow...
Embryonic diapause is a reversible arrest of embryonic development that enables insects to survive adverse environmental conditions. In the silkworm (Bombyx mori), diapause is established during early egg development and can be efficiently terminated...
Background: Jerusalem artichoke (Helianthus tuberosus L.) is moderately tolerant to salinity stress and has high economic value. The salt tolerance mechanisms of Jerusalem artichoke are still unclear. Especially in the early stage of Jerusalem artich...
Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. The wheat grain expanding phase is the early process involving the rapid morphological changes and initiation of grain filling. H...
Hypertension threatens the health of aging captive giant pandas, yet its molecular signatures remain poorly characterized. Here, multi-omics sequencing was applied to explore the molecular regulatory process of hypertension and the pharmacodynamic ef...
Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying...
Root flavones, especially baicalin, baicalein, wogonoside, and wogonin, contribute substantially to the medicinal quality of Scutellaria baicalensis Georgi. In the arid and semi-arid regions where this crop is grown, salinized soils constrain establi...
Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by...
Background: There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. Me...
Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, l...
Liver regeneration induced by partial hepatectomy (PHx) has attracted intensive research interests due to the great significance for liver resection and transplantation. The zebrafish (Danio rerio) is an excellent model to study liver regeneration. I...
Skeletal muscle satellite cells (SMSCs), which are multifunctional muscle-derived stem cells, can differentiate into adipocytes. Long-chain non-coding RNA (lncRNA) has diverse biological functions, including the regulation of gene expression, chromos...
Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene expression, offerin...
Heterogeneity exists inter- and intratumorally, which might lead to different drug responses. Therefore, it is extremely important to clarify the drug response at single-cell resolution. Here, we propose a precise single-cell drug response (scDR) pre...
Genome-wide gene expression analysis are routinely used to gain a systems-level understanding of complex processes, including network connectivity. Network connectivity tends to be built on a small subset of extremely high co-expression signals that...
Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of c...
Drought stress severely restricts the growth of pear trees. As a widely used drought-tolerant rootstock, Pyrus betulifolia exhibits stable growth performance; however, the molecular mechanisms underlying its drought tolerance remain to be elucidated....
Transcriptional profiling of muscle-invasive bladder cancer (MIBC) using RNA sequencing (RNA-seq) technology has demonstrated the existence of intrinsic basal and luminal molecular subtypes that vary in their prognosis and response to therapy. Howeve...
The abscisic acid (ABA) increase and auxin decline are both indicators of ripening initiation in grape berry, and norisoprenoid accumulation also starts at around the onset of ripening. However, the relationship between ABA, auxin, and norisoprenoids...
The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing d...
Fat deposition in pigs, which significantly contributes to meat quality, fattening efficiency, reproductive performance, and immunity, is critically affected by preadipocyte adipogenic differentiation. We elucidated adipogenesis in pigs using transcr...
Salt stress severely constrains wheat growth and yield by inducing osmotic imbalance, ion toxicity, and excessive accumulation of reactive oxygen species (ROS). Although salt-tolerant cultivars can adapt through rapid signaling transduction and maint...
The absence of a conventional association between the cell–cell cohabitation and its emergent dynamics into cliques during development has hindered our understanding of how cell populations proliferate, differentiate, and compete (i.e., the cel...
The angiosperm seed represents a critical evolutionary breakthrough that has been shown to propel the reproductive success and radiation of flowering plants. Seeds promote the rapid diversification of angiosperms by establishing postzygotic reproduct...
Trajectory inference (TI) or pseudotime analysis has dramatically extended the analytical framework of single-cell RNA-seq data, allowing regulatory genes contributing to cell differentiation and those involved in various dynamic cellular processes t...
Comparative omics analysis offers one of the most direct and effective approaches to gain novel insights into crop traits, facilitating candidate gene identification and crop improvement. Verticillium dahliae causes one of the most globally devastati...
Somatic in situ regeneration (SISR) is a unique reproductive mode of the green-tide-forming alga Ulva prolifera. Based on reproductive and developmental characteristics, a previous study has speculated that SISR represents an early evolutionary form...
Single-cell RNA-sequencing (scRNA-seq) technology has provided significant insights into cancer drug resistance at the single-cell level. However, understanding dynamic cell transitions at the molecular systems level remains limited, requiring a syst...
Smut disease is a major constraint on proso millet (Panicum miliaceum L.) production. Our previous metabolomic work in the cultivar ‘Chishu 13’ outlined a two-stage defense strategy involving energy metabolism at jointing and phenylpropan...
Injuries and subclinical effects from exposure to blasts are of significant concern in military operational settings, including tactical training, and are associated with self-reported concussion-like symptomology and physiological changes such as in...
Caprine herpesvirus 1 (CpHV-1) is a member of the alpha subfamily of herpesviruses, which is responsible for genital lesions and latent infections in goat populations worldwide. In this study, for the first time, the transcriptome and proteomics of C...
Low temperature stress represents a major threat to the lives of both farmed and wild fish species. However, biological pathways determining the development of cold resistance in fish remain largely unknown. Zebrafish larvae at 96 hpf were exposed to...
The Sichuan taimen (Hucho bleekeri) is a flagship species for the Yangtze River and is classified as critically endangered by the IUCN. Successful artificial breeding and conservation efforts are therefore essential for maintaining population stabili...
Background: Sound vibration is an emerging physical signal that influences plant growth and secondary metabolism; however, the genome-wide transcriptional responses of valuable medicinal orchids to complex acoustic stimuli remain largely uncharacteri...
Background: Early studies indicated that the high content of tanshinone IIA (T−IIA) and rosmarinic acid (RA) in Salvia castanea Diels f. Tomentosa Stib (SCT) gives them significant potential for development as therapeutic agents for ischemic st...
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying...
From time course gene expression data, we may identify genes that modulate in a certain pattern across time. Such patterns are advantageous to investigate the transcriptomic response to a certain condition. Especially, it is of interest to compare tw...
Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological st...
The red imported fire ant (Solenopsis invicta Buren, 1972) is a globally significant invasive species, causing extensive agricultural, human health, and biodiversity damage amounting to billions of dollars worldwide. The pathogenic fungus Metarhizium...
Trachinotus ovatus is a euryhaline, warm-water pelagic fish species with strong adaptability, rapid growth, and a high survival rate, making it one of the most important marine aquaculture species in China. In recent years, extensive experience has b...
A systematic evaluation of salt tolerance at the seedling stage was conducted using 143 maize inbred lines under a 150 mM mixed-salt solution (NaCl:Na2SO4 = 9:1, EC = 16.78 dS/m) that mirrors the ionic composition of saline groundwater in the Yellow...
Background/Objectives: Floral bud morphogenesis is a critical developmental process determining yield potential in blueberry, yet the molecular regulatory mechanisms in leaves during this phase remain poorly understood. Methods: In this study, we emp...
Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanism...
Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, in which Ca2+ also plays a significant role. There is diversity in the regulation of different gene expressions by cytosolic Ca2+ ([Ca2+]cyt) and nucleosolic Ca...
of 2