56 Works

Latent Space Model for Higher-order Networks and Generalized Tensor Decomposition

Zhongyuan Lyu, Dong Xia & Yuan Zhang
We introduce a unified framework, formulated as general latent space models, to study complex higher-order network interactions among multiple entities. Our framework covers several popular models in recent network analysis literature, including mixture multi-layer latent space model and hypergraph latent space model. We formulate the relationship between the latent positions and the observed data via a generalized multilinear kernel as the link function. While our model enjoys decent generality, its maximum likelihood parameter estimation is...

Population genetics and forensic efficiency of 30 InDel markers in four Chinese ethnic groups residing in Sichuan

Fei Wang, Guanglin He, Zheng Wang, Mengge Wang, Jing Liu, Xing Zou, Shouyu Wang, Mengyuan Song, Ziwei Ye, Mingkun Xie & Yiping Hou
Sichuan Province is located at the transitional junction regions of the Qinghai-Tibet Plateau and the low-altitude plains. It also serves as the corridor of Sino-Tibetan-speaking population migration and expansion since neolithic expansion of Proto-Tibeto-Burman populations from Middle/Upper Yellow River during Majiayao period (3300–2000 BC). However, the population structure and the corresponding genetic diversity of forensic-related markers in this region remain unclear. Thus, we genotyped 30 insertion-deletion (InDel) markers in 444 samples from four ethnic groups...

Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

Dongxia Wang, Dong Cao, Yuan Zong, Yun Li, Jinmin Wang, Zongren Li & Baolong Liu
The awnless trait is the favorite trait for wheat breeding in Qinghai, China, but the major gene underlying the trait is unknown. This study aimed to analyze a recombinant inbred line (RIL) population containing 112 lines by crossing common wheat varieties GY448 (awnless) and GY115 (awned) using genotyping-by-sequencing analysis. A total of 56.62 Gb of clean sequence data were generated. A major gene was identified for the awnless trait based on 101,275 single-nucleotide polymorphisms by...

Long non-coding RNA BCAR4 aggravated proliferation and migration in esophageal squamous cell carcinoma by negatively regulating p53/p21 signaling pathway

Shuo Yan, Jichong Xu, Bingyan Liu, Lin Ma, Hao Feng, Huaqiao Tan & Chun Fang
Long non-coding RNA breast cancer antiestrogen resistance 4 (lncRNA BCAR4) is an independent factor on the survival prognosis of patients with multiple cancers. However, the role of lncRNA BCAR4 in esophageal squamous cell cancer (ESCC) remains unknown. Here, we unraveled that lncRNA BCAR4 was upregulated in ESCC and predicted poor prognosis. Functionally, lncRNA BCAR4 knockdown induced cell apoptosis and G1/S arrest, while inhibited cell proliferation and migration in vitro; conversely, overexpressing lncRNA BCAR4 promoted proliferation...

Transcriptome analysis identifies key genes involved in anthocyanin biosynthesis in black and purple fruits (Lycium ruthenicum Murr. L)

Xuemei Bao, Xiaolong Gan, Guanghui Fan, Guangrui Liu, Xiaolin Ma, Baolong Liu & Yuan Zong
Lycium ruthenicum is a characteristic plant resource in Northwest China. The fruit with high anthocyanin content is the main reason for its high nutritional value and economic value, while the regulation of key genes regulating anthocyanin biosynthesis in black fruit is not clear. In this study, high-throughput sequencing technology was used to compare the expression differences of all genes in black and purple fruits. The purple samples obtained 45.13 and 51.49 M Raw reads, while...

Additional file 10 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 10: Table S7: Two-way ANOVA test F-value of genes expression levels related to cytokinin biosynthesis and signaling transduction for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

Additional file 14 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 14: Table S11: Two-way ANOVA test F-value of genes expression levels related to jasmonic biosynthesis and signaling transduction for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

Supporting Information

Jing-Jing Fan, Qiang Wang, Gang-Jian Wei, Jie Li, Lin Ma & Xiu-Zheng Zhang
Table 1: Whole-rock B and Mo contents and isotopic compositions for the Yardoi Cenozoic granites. S1. P-T pseudosection analyses and calculations and B system modeling S2. Supplementary Figures S3. Supplementary Tables

Identification of downstream targets and signaling pathways of long non-coding RNA NR_002794 in human trophoblast cells

Yinyao Ma, Hua Wu, Xuxia Liang, Chun Zhang, Yanhua Ma, Yanfen Wei, Jing Li & Hui Chen
Preeclampsia (PE) is a huge threat to pregnant women. Our previous study demonstrated that long non-coding RNA (lncRNA) NR_002794 was highly expressed in placentas of PE patients and could regulate the phenotypes of trophoblast cells. However, the downstream regulatory mechanisms of NR_002794 remain unknown. In this text, some potential downstream targets or signaling pathways of NR_002794 were identified through RNA sequencing (RNA-seq) and bioinformatics analysis in SWAN71 trophoblast cells. Western blot assay demonstrated that NR_002794...

sj-xlsx-2-hpq-10.1177_13591053221129705 – for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C)

Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu & Junfen Fu
sj-xlsx-2-hpq-10.1177_13591053221129705 for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C) by Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu and Junfen Fu in Journal of Health Psychology

sj-xlsx-2-hpq-10.1177_13591053221129705 – for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C)

Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu & Junfen Fu
sj-xlsx-2-hpq-10.1177_13591053221129705 for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C) by Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu and Junfen Fu in Journal of Health Psychology

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

Additional file 13 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 13: Table S10: Two-way ANOVA test F-value of genes expression levels related to salicylic acid biosynthesis and signaling transduction for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

Additional file 8 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 8: Table S5: Two-way ANOVA test F-value of expression levels of the genes related to flowering time and flower development for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

Additional file 9 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 9: Table S6: Two-way ANOVA test F-value of genes expression levels related to auxin biosynthesis and signaling transduction for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

miR-146b-5p regulates bone marrow mesenchymal stem cell differentiation by SIAH2/PPARγ in aplastic anemia children and benzene-induced aplastic anemia mouse model

Huanhuan Li, Xueju Xu, Dao Wang, Li Zeng, Bai Li, Yuan Zhang, Shufang Su, Linlin Wei, Hongliang You, Yingqi Fang, Yingchao Wang & Yufeng Liu
This study aimed to reveal the mechanism of miR-146b-5p in the differentiation of bone marrow mesenchymal stem cells (BMSCs) derived from children with aplastic anemia (AA). Here, we found that miR-146b-5p was highly expressed in BMSCs from children with AA, and the BMSCs surface markers expressions in BMSCs derived from children with AA and the healthy controls exerted no significant differences. Besides, the overexpression of miR-146b-5p in normal human-derived BMSCs promoted the adipogenic differentiation of...

Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

Dongxia Wang, Dong Cao, Yuan Zong, Yun Li, Jinmin Wang, Zongren Li & Baolong Liu
The awnless trait is the favorite trait for wheat breeding in Qinghai, China, but the major gene underlying the trait is unknown. This study aimed to analyze a recombinant inbred line (RIL) population containing 112 lines by crossing common wheat varieties GY448 (awnless) and GY115 (awned) using genotyping-by-sequencing analysis. A total of 56.62 Gb of clean sequence data were generated. A major gene was identified for the awnless trait based on 101,275 single-nucleotide polymorphisms by...

Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering

Yifeng Zhang, Lin Ma, Ping Su, Luqi Huang & Wei Gao
As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the...

Additional file 14 of Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

Xiaohan Xu, Jing Tao, Anqi Xing, Zichen Wu, Yuqin Xu, Yi Sun, Jiangyuan Zhu, Xiang Dai & Yuhua Wang
Additional file 14: Table S11: Two-way ANOVA test F-value of genes expression levels related to jasmonic biosynthesis and signaling transduction for three C. sinensis cultivars (BY1, HJY and SCZ) affected by development stage (S) and cultivar (C).

DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility

Zexi Liao, Minhan Yi, Jiaxin Li & Yuan Zhang
The results of associations between single nucleotide polymorphisms (SNPs) of genes in DNA repairing pathway and lung cancer (LC) risk are inconsistent. We applied allele, dominant and recessive models to explore the risk of researched variants to LC in total LC and subgroups by ethnicity or LC subtypes with a cutoff point of p < 0.05. A total of 76,935 cases and 88,649 controls from 192 articles were included. Among the analyzed 40 variants from...

Long non-coding RNAs PGM5-AS1 upregulates Decorin (DCN) to inhibit cervical cancer progression by sponging miR-4284

Huimin Wang, Dan Wang, Qiong Wei, Chun Li, Chunyan Li & Jing Yang
Long non-coding RNAs (lncRNAs) have been widely studied and play crucial roles in cervical cancer (CC) progression. Here, we investigated the function and mechanism of lncRNA PGM5-AS1 action in CC cells. Using real-time quantitative polymerase chain reaction or western blotting, PGM5-AS1 and decorin (DCN) were downregulated in CC tissues and cells, whereas miR-4284 was upregulated. Luciferase assay, RNA pull-down assay, and western blotting showed that PGM5-AS1 could sponge miR-4284 to upregulate DCN expression in CC...

Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens

Dan Wang, Jun Teng, Chao Ning, Wenwen Wang, Shuai Liu, Qin Zhang & Hui Tang
Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA...

Additional file 2 of Quantifying substantial carcinogenesis of genetic and environmental factors from measurement error in the number of stem cell divisions

Xinhui Liu, Jifeng Yang, Hongkai Li, Qing Wang, Yuanyuan Yu, Xiaoru Sun, Shucheng Si, Lei Hou, Lu Liu, Fan Yang, Ran Yan, Yifan Yu, Zhentao Fu, Zilong Lu, Dejin Li, Hao Xue, Xiaolei Guo, Fuzhong Xue & Xiaokang Ji
Additional file 2: Table S1. Ranked matrix of LCR in global scope and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S2. Ranked matrix of LCR in national-wide of China and the contribution of the genetic and environmental factors on the variation in cancer risk. Table S3. Ranked matrix of LCR in counties of Shandong province, China and the contribution of the genetic and environmental factors on the...

sj-sav-6-hpq-10.1177_13591053221129705 – for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C)

Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu & Junfen Fu
sj-sav-6-hpq-10.1177_13591053221129705 for Psychometric and cross-cultural generalizability outcomes of the Chinese version of the Kids-Palatable Eating Motives Scale (K-PEMS-C) by Dan Wang, Mary M Boggiano, Ke Huang, Yuzheng Hu and Junfen Fu in Journal of Health Psychology

Additional file 2 of Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

Dan Wang, Kerui Xie, Yanyan Wang, Jiaqing Hu, Wenqiang Li, Aiguo Yang, Qin Zhang, Chao Ning & Xinzhong Fan
Additional file 2: Table S1. Genotype accuracy and concordance of imputation obtained with the three pipelines on 15 individuals. Table S2. Genotype accuracy and concordance of imputation by the three pipelines with the MAF ranges. Table S3. Genotype accuracy and concordance of imputation with different sample size and depth by BaseVar + STITCH. Table S4. Variant analysis by regions and functions. Table S5. LD decay in the Angora rabbit population. Table S6. Genes located in...

Registration Year

  • 2023
    4
  • 2022
    35
  • 2021
    12
  • 2020
    5

Resource Types

  • Dataset
    56

Affiliations

  • Shaanxi Provincial People's Hospital
    56
  • Zhejiang University
    41
  • Shanghai Jiao Tong University
    37
  • Shandong Agricultural University
    27
  • Shandong University
    26
  • Huazhong University of Science and Technology
    25
  • Southern Medical University
    24
  • First Affiliated Hospital of Zhengzhou University
    22
  • Affiliated Hospital of Qingdao University
    21
  • Sichuan University
    20