Xueyi Dong
YOU?
Author Swipe
View article: Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2
Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 Open
Long-read single-cell RNA-sequencing enables the profiling of RNA isoform expression and alternative splicing at the single cell level. However, diverse single-cell technologies and sparse isoform data demand flexible, accurate, processing…
View article: Hypoxia upregulates the expression of PD-L1 via NPM1 in breast cancer
Hypoxia upregulates the expression of PD-L1 via NPM1 in breast cancer Open
Background A hypoxic microenvironment is the most frequent characteristic in tumor microenvironment. Programmed death-ligand 1 (PD-L1) is an important molecule and therapeutic target that mediates the immune response of tumor cells. Previo…
View article: Correction: Nrf2/ASPM axis regulated vasculogenic mimicry formation in hepatocellular carcinoma under hypoxia
Correction: Nrf2/ASPM axis regulated vasculogenic mimicry formation in hepatocellular carcinoma under hypoxia Open
View article: HMGA2 regulates CD44 expression to promote gastric cancer cell motility and sphere formation: Am J Cancer Res. 2017; 7(2): 260-274
HMGA2 regulates CD44 expression to promote gastric cancer cell motility and sphere formation: Am J Cancer Res. 2017; 7(2): 260-274 Open
[This corrects the article on p. 260 in vol. 7, PMID: 28337375.].
View article: Transcriptomic profiling of backfat and muscle in Lijiang pigs with divergent body size across growth stages
Transcriptomic profiling of backfat and muscle in Lijiang pigs with divergent body size across growth stages Open
View article: Desmoglein 2 and desmocollin 2 depletions promote malignancy through distinct mechanisms in triple-negative and luminal breast cancer
Desmoglein 2 and desmocollin 2 depletions promote malignancy through distinct mechanisms in triple-negative and luminal breast cancer Open
View article: Referee report. For: eXNVerify: coverage analysis for long and short-read sequencing data in clinical context [version 1; peer review: 2 approved]
Referee report. For: eXNVerify: coverage analysis for long and short-read sequencing data in clinical context [version 1; peer review: 2 approved] Open
View article: RSRC2 Expression Inhibits Malignant Progression of Triple-Negative Breast Cancer by Transcriptionally Regulating SCIN Expression
RSRC2 Expression Inhibits Malignant Progression of Triple-Negative Breast Cancer by Transcriptionally Regulating SCIN Expression Open
Triple-negative breast cancer (TNBC) has a shorter survival time and higher mortality rate than other molecular subtypes. RSRC2 is a newly discovered tumor suppressor gene. However, the potential functional mechanism of RSRC2 in TNBC remai…
View article: Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR Open
Differential expression analysis of RNA-seq is one of the most commonly performed bioinformatics analyses. Transcript-level quantifications are inherently more uncertain than gene-level read counts because of ambiguous assignment of sequen…
View article: Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data Open
View article: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data Open
Group heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the detection of differentially expressed genes. Since most bulk RNA-seq methods assume equal group variances, we introdu…
View article: Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR Open
Differential expression analysis of RNA-seq is one of the most commonly performed bioinformatics analyses. Transcript-level quantifications are inherently more uncertain than gene-level read counts because of ambiguous assignment of sequen…
View article: Supplementary Figure legends Tables and RSRC2 minigene sequence from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Supplementary Figure legends Tables and RSRC2 minigene sequence from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
Supplementary Figure legends; Table S1, S4, S7, S8, and RSRC2 minigene sequence. Table S1: The increased splicing factors expression induced by PTX treatment in MDA-MB-231 cells; Table S4. All AS events selected for validation were confirm…
View article: Supplementary Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma
Supplementary Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma Open
Supplementary Data. Table S1 shows the information of antibodies used in this study. Table S2 shows the results of immunohistochemistry.
View article: Data from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Data from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Vasculogenic mimicry (VM), a newly defined pattern of tumor blood supply, describes the functional plasticity of aggressive cancer cells that form vascular networks. In our previous study, breast cancer stem cells (CSC) were shown to poten…
View article: Data from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Data from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
Treatment of triple-negative breast cancer (TNBC) has been challenging, and paclitaxel resistance is one of the major obstacles to the better prognosis. Deregulation of alternative splicing (AS) may contribute to tumor progression and chem…
View article: Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma
Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma Open
This study was conducted to examine the effects of doxycycline on the survival time and proliferation of hepatocellular carcinoma (HCC) in vivo and on the biologic functions of HCC in vitro. This study was also designed to ev…
View article: Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma
Data from Doxycycline as an Inhibitor of the Epithelial-to-Mesenchymal Transition and Vasculogenic Mimicry in Hepatocellular Carcinoma Open
This study was conducted to examine the effects of doxycycline on the survival time and proliferation of hepatocellular carcinoma (HCC) in vivo and on the biologic functions of HCC in vitro. This study was also designed to ev…
View article: Supplementary Figure 2 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Figure 2 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Figure 2. AURKA overexpression induced extra centrosomes, ALDH1 positivity and USP44 upregulation.
View article: Supplementary Figure S1 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Supplementary Figure S1 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
The gene structure view of CALU (exon2 inclusion), RSRC2 (exon4 inclusion), CEACAM1 (exon7 inclusion), LMCD1 (exon3 exclusion), PALM (exon8 exclusion) and RFWD2 (exon7 exclusion).
View article: Supplementary Table 1 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Table 1 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Table 1. Multivariate analysis of independent prognostic factors in breast cancer patients.
View article: Supplementary Figure legends Tables and RSRC2 minigene sequence from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Supplementary Figure legends Tables and RSRC2 minigene sequence from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
Supplementary Figure legends; Table S1, S4, S7, S8, and RSRC2 minigene sequence. Table S1: The increased splicing factors expression induced by PTX treatment in MDA-MB-231 cells; Table S4. All AS events selected for validation were confirm…
View article: Supplementary Table 1 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Table 1 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Table 1. Multivariate analysis of independent prognostic factors in breast cancer patients.
View article: Table S5 S6: TRA2A expression was significantly associated with poorer survival from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Table S5 S6: TRA2A expression was significantly associated with poorer survival from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
Supplementary Table 5 and 6: TRA2A expression was significantly associated with poorer survival
View article: Supplementary Figure S1 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Supplementary Figure S1 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
The gene structure view of CALU (exon2 inclusion), RSRC2 (exon4 inclusion), CEACAM1 (exon7 inclusion), LMCD1 (exon3 exclusion), PALM (exon8 exclusion) and RFWD2 (exon7 exclusion).
View article: Supplementary Figure legends from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Figure legends from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Figure legends. Figure legends for Supplementary Figure 1-3.
View article: Table S2: TRA2A-regulated AS events from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Table S2: TRA2A-regulated AS events from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
Table S2: TRA2A-regulated AS events
View article: Supplementary Figure 3 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Figure 3 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Figure 3. USP44 KD inhibited IL-6 and IL-8 expression in breast CSCs.
View article: Supplementary Figure 3 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry
Supplementary Figure 3 from USP44<sup>+</sup> Cancer Stem Cell Subclones Contribute to Breast Cancer Aggressiveness by Promoting Vasculogenic Mimicry Open
Supplementary Figure 3. USP44 KD inhibited IL-6 and IL-8 expression in breast CSCs.
View article: Supplementary Figure S2 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing
Supplementary Figure S2 from TRA2A Promoted Paclitaxel Resistance and Tumor Progression in Triple-Negative Breast Cancers via Regulating Alternative Splicing Open
qRT-PCR showed that MELK, CEACAM1, LMCD1 and RFWD2 AS events weren't shown during PTX treatment.