Xiaoyu Weng
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View article: Novel methods for temporally varying gene identification in longitudinal studies reveal bleeding and clotting pathway activation caused by blood draws
Novel methods for temporally varying gene identification in longitudinal studies reveal bleeding and clotting pathway activation caused by blood draws Open
Recent advances in sequencing technology enable the capture of gene expression dynamics through longitudinal study designs. However, the field lacks robust analytical tools for these high-dimensional datasets. To address this, we developed…
View article: Clinical relevance of inflammatory markers in the evaluation of severity of ulcerative colitis: A retrospective study
Clinical relevance of inflammatory markers in the evaluation of severity of ulcerative colitis: A retrospective study Open
This study aimed to investigate the clinical relevance of inflammatory markers in the severity assessment of ulcerative colitis (UC). The inflammatory markers included the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio …
View article: MYBBP1A‑mediated IGFBP4 promoter methylation promotes epithelial‑mesenchymal transition and metastasis through activation of NOTCH pathway in liver cancer
MYBBP1A‑mediated IGFBP4 promoter methylation promotes epithelial‑mesenchymal transition and metastasis through activation of NOTCH pathway in liver cancer Open
Metastatic hepatocellular carcinoma (HCC) seriously threatens patients' prognosis. It was previously suggested that the insulin growth factor binding protein (IGFBP) family could serve as cancer suppressors in the development and metastasi…
View article: Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis
Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis Open
View article: JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom
JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom Open
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provid…
View article: Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in <i>Panicum hallii</i>
Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in <i>Panicum hallii</i> Open
The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to s…
View article: JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom
JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom Open
Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait var…
View article: A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass
A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass Open
Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value …
View article: The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)
The genetic basis for panicle trait variation in switchgrass (Panicum virgatum) Open
View article: A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range
A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range Open
Significance Polyploidy, which occurs in roughly half of all flowering plants and an even higher percentage of grasses, is thought to be a major driver of adaptation. Higher numbers of copies of each gene in polyploid genomes can increase …
View article: Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass Open
View article: The heading-date gene Ghd7 inhibits seed germination by modulating the balance between abscisic acid and gibberellins
The heading-date gene Ghd7 inhibits seed germination by modulating the balance between abscisic acid and gibberellins Open
View article: QTL x environment interactions for panicle traits in switchgrass (Panicum virgatum)
QTL x environment interactions for panicle traits in switchgrass (Panicum virgatum) Open
Panicle traits exhibit quantitative variation controlled by genes, the environment, and their interaction. In switchgrass, a perennial biofuel crop, identification of quantitative trait loci (QTL) and QTL x E interactions controlling panic…
View article: <i>OsHOX1</i> and <i>OsHOX28</i> Redundantly Shape Rice Tiller Angle by Reducing <i>HSFA2D</i> Expression and Auxin Content
<i>OsHOX1</i> and <i>OsHOX28</i> Redundantly Shape Rice Tiller Angle by Reducing <i>HSFA2D</i> Expression and Auxin Content Open
Tiller angle largely determines plant architecture, which in turn substantially influences crop production by affecting planting density. A recent study revealed that HEAT STRESS TRANSCRIPTION FACTOR2D (HSFA2D) acts upstream …
View article: QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient
QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient Open
Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adapta…
View article: Gene Expression analysis associated with salt stress in a reciprocally crossed rice population
Gene Expression analysis associated with salt stress in a reciprocally crossed rice population Open
The rice landrace Horkuch, endemic to the southern saline coast of Bangladesh, is known to have salt tolerance traits and can therefore contribute to a high yielding recipient for breeding purposes. In this study, we reciprocally crossed H…
View article: Targeting Mybbp1a suppresses HCC progression via inhibiting IGF1/AKT pathway by CpG islands hypo-methylation dependent promotion of IGFBP5
Targeting Mybbp1a suppresses HCC progression via inhibiting IGF1/AKT pathway by CpG islands hypo-methylation dependent promotion of IGFBP5 Open
View article: The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass
The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass Open
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common gen…
View article: Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C<sub>4</sub> grass
Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C<sub>4</sub> grass Open
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the di…
View article: Screening and preliminary validation of T lymphocyte immunoregulation‑associated long non‑coding RNAs in diabetic foot ulcers
Screening and preliminary validation of T lymphocyte immunoregulation‑associated long non‑coding RNAs in diabetic foot ulcers Open
The present study aimed to investigate the existence of immunoregulation‑associated long non‑coding (lnc)RNAs mediated by T lymphocytes in the wound surfaces of diabetic foot ulcers (DFUs). The wound skin tissues of patients receiving debr…
View article: The genomic landscape of molecular responses to natural drought stress in Panicum hallii
The genomic landscape of molecular responses to natural drought stress in Panicum hallii Open
View article: Over Expression of Long Non-Coding RNA PANDA Promotes Hepatocellular Carcinoma by Inhibiting Senescence Associated Inflammatory Factor IL8
Over Expression of Long Non-Coding RNA PANDA Promotes Hepatocellular Carcinoma by Inhibiting Senescence Associated Inflammatory Factor IL8 Open
View article: KCTD11 inhibits growth and metastasis of hepatocellular carcinoma through activating Hippo signaling
KCTD11 inhibits growth and metastasis of hepatocellular carcinoma through activating Hippo signaling Open
A lack of effective prognostic biomarkers and molecular targets is a serious problem in hepatocellular carcinoma. KCTD11, reported as a tumor suppressor, are still not well understood. In this study, KCTD11 was found low-expressed in HCC t…
View article: Expression and Critical Role of Interleukin Enhancer Binding Factor 2 in Hepatocellular Carcinoma
Expression and Critical Role of Interleukin Enhancer Binding Factor 2 in Hepatocellular Carcinoma Open
Interleukin enhancer binding factor 2 (ILF2), a transcription factor, regulates cell growth by inhibiting the stabilization of mRNA. Currently, its role has gained recognition as a factor in the tumorigenic process. However, until now, lit…
View article: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C<sub>4</sub>grass
Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C<sub>4</sub>grass Open
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examin…
View article: Supplementary Material for: Hsp27 Acts as a Master Molecular Chaperone and Plays an Essential Role in Hepatocellular Carcinoma Progression
Supplementary Material for: Hsp27 Acts as a Master Molecular Chaperone and Plays an Essential Role in Hepatocellular Carcinoma Progression Open
Aims: Hsp27, a master molecular chaperone, plays an important role in cancer. However, the specific co-chaperones that partner with Hsp27 and the role of Hsp27 in hepatocellular carcinoma (HCC) are not fully enume…
View article: Supplementary Material for: Hsp27 Acts as a Master Molecular Chaperone and Plays an Essential Role in Hepatocellular Carcinoma Progression
Supplementary Material for: Hsp27 Acts as a Master Molecular Chaperone and Plays an Essential Role in Hepatocellular Carcinoma Progression Open
Aims: Hsp27, a master molecular chaperone, plays an important role in cancer. However, the specific co-chaperones that partner with Hsp27 and the role of Hsp27 in hepatocellular carcinoma (HCC) are not fully enume…
View article: Coordinated regulation of vegetative and reproductive branching in rice
Coordinated regulation of vegetative and reproductive branching in rice Open
Significance The patterns of lateral branching, including tillers and inflorescence branches, determine grain yields of many cereals. In this study, we characterized a regulatory network composed of microRNAs and transcription factor that …
View article: Hypoxia-inducible MiR-182 promotes angiogenesis by targeting RASA1 in hepatocellular carcinoma
Hypoxia-inducible MiR-182 promotes angiogenesis by targeting RASA1 in hepatocellular carcinoma Open
Our data showed that hypoxia regulated the expression of miR-182 and RASA1 to promote HCC angiogenesis.
View article: Downregulation of HDAC6 promotes angiogenesis in hepatocellular carcinoma cells and predicts poor prognosis in liver transplantation patients
Downregulation of HDAC6 promotes angiogenesis in hepatocellular carcinoma cells and predicts poor prognosis in liver transplantation patients Open
HDAC6, a member of histone deacetylation family, is reported to play critical roles in transcription regulation, cell cycle progression, and cancer development. However, the expression status and significance of HDAC6 in hepatocellular car…