Ningxin Dang
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View article: Deciphering Complex Interactions Between LTR Retrotransposons and Three <i>Papaver</i> Species Using LTR_Stream
Deciphering Complex Interactions Between LTR Retrotransposons and Three <i>Papaver</i> Species Using LTR_Stream Open
Long terminal repeat retrotransposons (LTR-RTs), a major type of class I transposable elements, are the most abundant repeat element in plants. The study of the interactions between LTR-RTs and the host genome relies on high-resolution cha…
View article: Deciphering complex interactions between LTR retrotransposons and three <i>Papaver</i> species using LTR_Stream
Deciphering complex interactions between LTR retrotransposons and three <i>Papaver</i> species using LTR_Stream Open
Long terminal repeat retrotransposons (LTR-RTs), a major type of class I transposable elements (TEs), are the most abundant repeat element in plants. The study of the interactions between LTR-RTs and the host genome relies on high-resoluti…
View article: Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae
Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae Open
Background Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown. Results We constructed near …
View article: Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae
Near telomere-to-telomere genome assemblies of two Chlorella species unveil the composition and evolution of centromeres in green algae Open
Background: Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown. Results: We constructed nea…
View article: Additional file 1 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Additional file 1 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet Open
Additional file 1: Table S1. Sequencing summary of the Chinese Quartet. Table S2. Summary of phased reads from two haplotypes. Table S3. Summary statistics of the Chinese Quartet assemblies. Table S4. Assembly summary of the Chinese Quarte…
View article: Integrating cell interaction with transcription factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma
Integrating cell interaction with transcription factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma Open
Objective: The efficacy of immunotherapy for cholangiocarcinoma (CCA) is blocked by a high degree of tumor heterogeneity. Cell communication contributes to heterogeneity in the tumor microenvironment. This study aimed to explore critical c…
View article: Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet Open
As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two m…
View article: Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet Open
As the state-of-the-art sequencing technologies and computational methods enable investigation of challenging regions in the human genome, an update variant benchmark is demanded. Herein, we sequenced a Chinese Quartet, consisting of two m…
View article: Integrating cell interaction with transcript factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma
Integrating cell interaction with transcript factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma Open
Background The efficacy of immunotherapy in cholangiocarcinoma (CCA) is blocked by its high degree of tumor heterogeneity. Methods We constructed empirical Bayes and Markov random field models to calculate transcription factors, interactio…
View article: Cellular heterogeneity and transcriptomic profiles during intrahepatic cholangiocarcinoma initiation and progression
Cellular heterogeneity and transcriptomic profiles during intrahepatic cholangiocarcinoma initiation and progression Open
Background and Aims Intrahepatic cholangiocarcinoma (ICC) is not fully investigated, and how stromal cells contribute to ICC formation is poorly understood. We aimed to uncover ICC origin, cellular heterogeneity, and critical modulators du…
View article: Integrating bulk and single‐cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma
Integrating bulk and single‐cell RNA sequencing reveals cellular heterogeneity and immune infiltration in hepatocellular carcinoma Open
Efficacy of immunotherapy in hepatocellular carcinoma (HCC) is blocked by its high degree of inter‐ and intra‐tumor heterogeneity and immunosuppressive tumor microenvironment. However, the correlation between tumor heterogeneity and immuno…
View article: High-Quality <i>Arabidopsis Thaliana</i> Genome Assembly with Nanopore and HiFi Long Reads
High-Quality <i>Arabidopsis Thaliana</i> Genome Assembly with Nanopore and HiFi Long Reads Open
Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains a significant number of missing segmen…
View article: High-quality <i>Arabidopsis thaliana</i> Genome Assembly with Nanopore and HiFi Long Reads
High-quality <i>Arabidopsis thaliana</i> Genome Assembly with Nanopore and HiFi Long Reads Open
Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains significant number of missing segments…
View article: A novel CD4+ CTL subtype characterized by chemotaxis and inflammation is involved in the pathogenesis of Graves’ orbitopathy
A novel CD4+ CTL subtype characterized by chemotaxis and inflammation is involved in the pathogenesis of Graves’ orbitopathy Open
Graves’ orbitopathy (GO), the most severe manifestation of Graves’ hyperthyroidism (GH), is an autoimmune-mediated inflammatory disorder, and treatments often exhibit a low efficacy. CD4+ T cells have been reported to play vital roles in G…
View article: gCAnno: a graph-based single cell type annotation method
gCAnno: a graph-based single cell type annotation method Open
Background Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering…
View article: gCAnno: a graph-based single cell type annotation method
gCAnno: a graph-based single cell type annotation method Open
Background Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering…
View article: gCAnno: A Graph-based Single Cell Type Annotation Method
gCAnno: A Graph-based Single Cell Type Annotation Method Open
Background Current single cell analysis methods annotate cell types at cluster-level rather than ideally at single cell level. Multiple exchangeable clustering methods and many tunable parameters have a substantial impact on the clustering…
View article: Additional file 8 of gCAnno: a graph-based single cell type annotation method
Additional file 8 of gCAnno: a graph-based single cell type annotation method Open
Additional file 8: Table S3. The tSNE result, cell barcodes and cell type labels of (a) mCel-seq2 liver, (b) 10x liver, (c) Drop-seq pancreas and (d) Smart-seq2 pancreas.
View article: Additional file 16 of gCAnno: a graph-based single cell type annotation method
Additional file 16 of gCAnno: a graph-based single cell type annotation method Open
Additional file 16: Table S6. The statistic of kappa coefficient in dropout test.
View article: Additional file 13 of gCAnno: a graph-based single cell type annotation method
Additional file 13 of gCAnno: a graph-based single cell type annotation method Open
Additional file 13: Table S5. The statistic of kappa coefficient in overall performance test (Fig. 2a-d).
View article: Additional file 18 of gCAnno: a graph-based single cell type annotation method
Additional file 18 of gCAnno: a graph-based single cell type annotation method Open
Additional file 18: Table S7. The statistic of kappa coefficient in imbalance test.
View article: Additional file 19 of gCAnno: a graph-based single cell type annotation method
Additional file 19 of gCAnno: a graph-based single cell type annotation method Open
Additional file 19: Table S8. The statistic of kappa coefficient in cross platform test.
View article: Additional file 6 of gCAnno: a graph-based single cell type annotation method
Additional file 6 of gCAnno: a graph-based single cell type annotation method Open
Additional file 6: Table S2. The large dataset kappa coefficient result (Fig. 2e) and tSNE result.
View article: Additional file 12 of gCAnno: a graph-based single cell type annotation method
Additional file 12 of gCAnno: a graph-based single cell type annotation method Open
Additional file 12: Table S4. The statistic of select state of reported marker genes from the corresponding publications in four datasets with selected genes.
View article: Additional file 20 of gCAnno: a graph-based single cell type annotation method
Additional file 20 of gCAnno: a graph-based single cell type annotation method Open
Additional file 20: Table S9. Runtime statistic of gCAnno.
View article: Additional file 4 of gCAnno: a graph-based single cell type annotation method
Additional file 4 of gCAnno: a graph-based single cell type annotation method Open
Additional file 4: Table S1. The tSNE result, cell barcodes and cell type labels of (a) liver, (b) pancreas, (c) HCC & ICCA and (d) AT root datasets.