15 Result(s)

Article

Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset

Animal studies have demonstrated the ability of pancreatic acinar cells to transform into pancreatic ductal adenocarcinoma (PDAC). However, the tumorigenic potential of human pancreatic acinar cells remains un...

Yi Xu, Michael H. Nipper, Angel A. Dominguez, Zhenqing Ye… in Nature Communications (2024)

Article

Physiological and psychological responses to tended plant communities with varying color characteristics

Exposure to plants has been reported to promote health and reduce stress, and plant color has direct impacts on physical and mental health. We used images of common types of tended plant communities in Shenyan...

Siyuan Zheng, Yanzhen Zhou, Haiyan Qu in Journal of Forestry Research (2024)

Article

Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer

Subcutaneous patient-derived xenografts (PDXs) are an important tool for childhood cancer research. Here, we describe a resource of 68 early passage PDXs established from 65 pediatric solid tumor patients. Thr...

Funan He, Abhik M. Bandyopadhyay, Laura J. Klesse, Anna Rogo**a… in Nature Communications (2023)

Article

Depression severity mediates stigma and quality of life in clinically stable people with schizophrenia in rural China

Depressive symptoms associated with schizophrenia are closely related to stigma and quality of life(QOL). There is, however, no thorough research on the connection between the three. This study sought to inves...

Siyuan Zheng, Ruoqi Wang, Shaofei Zhang, Yangxu Ou, Xuanlian Sheng… in BMC Psychiatry (2023)

Article

PHF5A regulates the expression of the DOCK5 variant to promote HNSCC progression through p38 MAPK activation

Previously, we identified an oncogenic splicing variant of DOCK5 in head and neck squamous cell carcinoma (HNSCC); however, the mechanism for the generation of this specific DOCK5 variant remains unknown. This...

Chao Liu, Guo Li, Siyuan Zheng, Li She, Shanhong Lu, Yunyun Wang… in Biology Direct (2023)

Article

Genomic disparities between cancers in adolescent and young adults and in older adults

Cancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities betwe...

**ao**g Wang, Anne-Marie Langevin, Peter J. Houghton… in Nature Communications (2022)

Article

Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation

Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the ...

Nighat Noureen, Shaofang Wu, Yingli Lv, Juechen Yang… in Nature Communications (2021)

Article

Murine models of IDH-wild-type glioblastoma exhibit spatial segregation of tumor initiation and manifestation during evolution

Recent characterization of spatiotemporal genomic architecture of IDH-wild-type multifocal glioblastomas (M-GBMs) suggests a clinically unobserved common-ancestor (CA) with a less aggressive phenotype, generating...

Yinghua Li, Bo Li, Wei Li, Yuan Wang, Seçkin Akgül… in Nature Communications (2020)

Article

Benchmarking: contexts and details matter

Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Bio...

Siyuan Zheng in Genome Biology (2017)

Article

Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma

Incidence of hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) has been increasing in the United States and Europe during recent years. Although HCV-associated HCC shares many pathological charact...

Siyuan Zheng, William P Tansey, Scott W Hiebert, Zhongming Zhao in BMC Medical Genomics (2011)

Article

Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach

Siyuan Zheng, Zhongming Zhao in BMC Bioinformatics (2011)

Article

Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes

Hung-Chung Huang, Siyuan Zheng, Zhongming Zhao in BMC Bioinformatics (2010)

Article

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and a...

Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie **, Pei Hao… in BMC Bioinformatics (2009)

Article

Human gene expression sensitivity according to large scale meta-analysis

Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc....

Pei Hao, Siyuan Zheng, Jie **, Kang Tu, Christian Gieger… in BMC Bioinformatics (2009)

Article

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies

In the adaptive immune system, variable regions of immunoglobulin (IG) are encoded by random recombination of variable (V), diversity (D), and joining (J) gene segments in the germline. Partitioning the functi...

**ao**g Wang, Di Wu, Siyuan Zheng, **g Sun, Lin Tao, Yixue Li… in BMC Bioinformatics (2008)