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Publications

Papers

2024

Poor prognosis of stage I lung adenocarcinoma patients determined by elevated expression over pre/minimally invasive status of COL11A1 and THBS2 in the focal adhesion pathway Jun Shang#, Yue Zhao#, He Jiang#, Jingcheng Yang, ..., Leming Shi*, Haiquan Chen*, Yuanting Zheng*. Under Review

BEdeepon: an in silico tool for prediction of base editor efficiencies and outcomes Chengdong Zhang#, Daqi Wang#, ..., Jingcheng Yang, ..., Yongming Wang*. Under Review

Chronic PM2.5 Exposure Disrupts Intestinal Barrier Integrity via Microbial Dysbiosis-Triggered TLR2/5-MyD88-NLRP3 Inflammasome Activation Zihan Ran#, Jingcheng Yang#, Liang Liu#, Shaobo Wu, YanPeng An, Wanwan Hou, Tianyuan Cheng, Youyi Zhang, Yiqing Zhang, Yechao Huang, Qianyue Zhang, Jiaping Wan, Xuemei Li, Baoling Xing, Yuchen Ye, Penghao Xu, Zhenghu Chen*, Jinzhuo Zhao*, Rui Li* Environmental Research DOI: 10.1016/j.envres.2024.119415 PMID: 38906446

rNMPID: a database for riboNucleoside MonoPhosphates in DNA Jingcheng Yang#, Mo Sun#, Zihan Ran, Taehwan Yang, Deepali L Kundnani, Francesca Storici*, Penghao Xu*. Bioinformatics Advances DOI: 10.1093/bioadv/vbae063 PMID: 38736683

2023

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials Yuanting Zheng#, Yaqing Liu#, Jingcheng Yang#, ..., Leming Shi*. Nature Biotechnology DOI: 10.1038/s41587-023-01934-1 PMID: 37679543

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling Ying Yu, Wanwan Hou, Yaqing Liu, Haiyan Wang, Lianhua Dong, Yuanbang Mai, Qingwang Chen, Zhihui Li, Shanyue Sun, Jingcheng Yang, Zehui Cao, Peipei Zhang, Yi Zi, Ruimei Liu, Jian Gao, Naixin Zhang, Jingjing Li, Luyao Ren, He Jiang, Jun Shang, Sibo Zhu, Xiaolin Wang, Tao Qing, Ding Bao, …Yuanting Zheng Nature Biotechnology DOI: 10.1038/s41587-023-01867-9 PMID: 37679545

Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance Luyao Ren#, Xiaoke Duan#, Lianhua Dong#, Rui Zhang#, Jingcheng Yang#, ..., Leming Shi, Huixiao Hong, Jing Wang*, Shaohua Fan*, Xiang Fang*, Yuanting Zheng*. Genome Biology DOI: 10.1186/s13059-023-03109-2 PMID: 38012772

The Quartet Data Portal: integration of community-wide resources for multiomics quality control Jingcheng Yang#, Yaqing Liu#, Jun Shang#, ..., Yuanting Zheng*, Leming Shi*. Genome Biology DOI: 10.1186/s13059-023-03091-9 PMID: 37884999

Singe-cell morphological and topological atlas reveals ecosystem diversity of human breast cancer Shao Zhao#, Depin Chen#, Tong Fu#, Jingcheng Yang#, ..., Wentao Yang*, Yizhou Jiang*, Jun Xu*, Zhiming Shao*. Nature Communications DOI: 10.1038/s41467-023-42504-y PMID: 37880211

Differences of molecular events driving pathological and radiological progression of lung adenocarcinoma Jun Shang#, He Jiang#, Yue Zhao#, ..., Jingcheng Yang*, Haiquan Chen*, Yuanting Zheng*. EBioMedicine DOI: 10.1016/j.ebiom.2023.104728 PMID: 37506543

Prediction of base editor off-targets by deep learning Chengdong Zhang#, Yuan Yang#, Tao Qi#, ..., Jingcheng Yang, ..., Hui Wang*, Bo Yu*, Yongming Wang*. Nature Communications DOI: 10.1038/s41467-023-41004-3 PMID: 37660097

2022

GlioMarker: An integrated database for knowledge exploration of diagnostic biomarkers in gliomas Zihan Ran#, Jingcheng Yang#, Yaqing Liu#, ..., Tao Yang*. Frontiers in Oncology DOI: 10.3389/fonc.2022.792055 PMID: 36081550

BioVisReport: a lightweight website-builder for reproducible and interactive visualization of biomedical data of peer-reviewed publications Jingcheng Yang, Yaqing Liu, Jun Shang, Yechao Huang, Ying Yu, ..., Leming Shi, Zihan Ran*. Computational and Structural Biotechnology Journal DOI: 10.1016/j.csbj.2022.06.009 PMID: 35782729

Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats Xintong Yao, Shanyue Sun, Yi Zi, Yaqing Liu, Jingcheng Yang, Luyao Ren, ..., Yuanting Zheng. Scientific Data DOI: 10.1038/s41597-022-01285-7 PMID: 35551205

A deep learning framework to predict multi-omics molecular features, subtypes and prognosis of triple-negative breast cancer from pathological images Shen Zhao#, Chaoyang Yan#, Hong Lv#, Jingcheng Yang#, ..., Wentao Yang*, Yizhou Jiang*, Jun Xu*, Zhiming Shao*. Fundamental Research DOI: 10.1016/j.fmre.2022.06.008

A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers Qingwang Chen#, Yaqing Liu#, Yuechen Gao#, ..., Ding Ma*, Jingcheng Yang*, Zhiming Shao*, Ying Yu*. Scientific Data DOI: 10.1038/s41597-022-01681-z PMID: 36153392

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing Bohu Pan#, Luyao Ren#, Vitor Onuchic#, ..., Jingcheng Yang, ..., Jun Shang, ..., Yuanting Zheng*, Huixiao Hong*. Genome Biology DOI: 10.1186/s13059-021-02569-8 PMID: 34980216

Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats Xintong Yao#, Shanyue Sun#, Yi Zi, Yaqing Liu, Jingcheng Yang, ..., Quanzhen Li*, Ying Yu*, Yuanting Zheng*. Scientific Data DOI: 10.1038/s41597-022-01285-7 PMID: 35551205

Advances in Exosome Biomarkers for Cervical Cancer Zihan Ran, Shaobo Wu, Zijing Ma, Xiuwen Chen, Jing Liu, Jingcheng Yang*. Cancer Medicine DOI: 10.1002/cam4.4828 PMID: 35578572

2021

A global metagenomic map of urban microbiomes and antimicrobial resistance Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, ..., Bittner L. Cell

Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient Yuanting Zheng, Binying Li, ..., Jingcheng Yang, ..., Ying Yu*, Jiaxue Wu*, Xichun Hu*, Leming Shi*. Breast Cancer Research

Subchronic exposure to concentrated ambient PM2. 5 perturbs gut and lung microbiota as well as metabolic profiles in mice Zihan Ran#, Yanpeng An#, Ji Zhou, Jingmin Yang, Youyi Zhang, Jingcheng Yang, ..., Rui Li*. Environmental Pollution

2020

ECCDIA: an interactive web tool for the comprehensive analysis of clinical and survival data of esophageal cancer patients Jingcheng Yang, Jun Shang, Qian Song, ..., Leming Shi*. BMC Cancer

Comprehensive analysis of CTLA-4 in the tumor immune microenvironment of 33 cancer types Zhang C, Chen J, Song Q, Sun X, Xue M, Yang Z, Shang J*. International Immunopharmacology

Transcription factor RUNX3 promotes CD8 T cell recruitment by CCL3 and CCL20 in lung adenocarcinoma immune microenvironment Song Q, Shang J, Zhang C, Chen J, Zhang L, Wu X. Journal of Cellular Biochemistry

Blood molecular markers associated with COVID-19 immunopathology and multi-organ damage Chen Y, Zheng Y, Yu Y, Wang Y, Huang Q, Qian F, Sun L, Song Z, Chen Z, Feng J, An Y, Yang J, Su Z, Sun S, Dai F, Chen Q, Lu Q, Li P, Ling Y, Yang Z, Tang H, Shi L, Jin L, Holmes EC, Ding C, Zhu T, Zhang Y. The EMBO Journal

Development and validation of a 10-gene prognostic signature for acute myeloid leukaemia Yang Z, Shang J, Li N, Zhang L, Tang T, Tian G, Chen X. Journal of Cellular and Molecular Medicine

2019

Construction of immune‐related risk signature for renal papillary cell carcinoma Wang Z, Song Q, Yang Z, Chen J, Shang J*, Ju W*. Cancer Medicine

Genomic and immune profiling of pre-invasive lung adenocarcinoma Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, ..., Shang J, ..., Shi L, Meyerson M. Nature Communications

Identification of Prognostic Signatures for Predicting the Overall Survival of Uveal Melanoma Patients Xue M, Shang J, Chen B, Yang Z, Song Q, Sun X, Chen J, Yang J. Journal of Cancer

Impact of the homogeneous and heterogeneous risk factors on the incidence and survival outcome of bone metastasis in NSCLC patients Song Q, Shang J, Zhang C, Zhang L, Wu X. Journal of Cancer Research and Clinical Oncology

Pseudogene CHIAP2 inhibits proliferation and invasion of lung adenocarcinoma cells by means of the WNT pathway Shang J, Wang Z, Chen W, Yang Z, Zheng L, Wang S, Li S. Journal of Cellular Physiology

Identification of an immune signature predicting prognosis risk of patients in lung adenocarcinoma Song Q, Shang J, Yang Z, Zhang L, Zhang C, Chen J, Wu X. Journal of Translational Medicine

Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies Jiang Y, Ma D, Suo C, Shi J, Xue M, Hu X, Xiao Y, Yu K, Liu Y, Yu Y, Zheng Y, Li X, Zhang C, Hu P, Zhang J, Hua Q, Zhang J, Hou W, Ren L, Bao D, Li B, Yang J, Yao L, Zuo W, Zhao S, Gong Y, Ren Y, Zhao Y, Yang Y, Niu Z, Cao Z, Stover DG, Verschraegen C, Kaklamani V, Daemen A, Benson JR, Takabe K, Bai F, Li DQ, Wang P, Shi L, Huang W, Shao Z. Cancer Cell

PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs Yu Y, Wang Y, Xia Z, Zhang X, Jin K, Yang J, Ren L, Zhou Z, Yu D, Qing T, Zhang C, Jin L, Zheng Y, Guo L, Shi L. Nucleic Acids Research

MicroRNA-302d promotes the proliferation of human pluripotent stem cell-derived cardiomyocytes by inhibiting LATS2 in the Hippo pathway Xu F, Yang J, Shang J, Lan F, Li M, Shi L, Shen L, Wang Y, Ge J. Clinical Science

Commensal microbes affect host humoral immunity to Bordetella pertussis infection Zhang Y, Ran Z, Tian M, Zhou Y, Yang J, Yin J, Lu D, Li R, Zhong J. Infection and Immunity

2018

Analysis of PD-1 related immune transcriptional profile in different cancer types Shang J, Song Q, Yang Z, Sun X, Xue M, Chen W, Yang J, Wang S. Cancer Cell International

2017

Local application of paeonol prevents early restenosis: a study with a rabbit vein graft model Zhang JY, Shang J, Huo TM, Zhang B, Chen G, Zeng ZY, Li SK. Journal of Surgical Research

Identification of lung adenocarcinoma specific dysregulated genes with diagnostic and prognostic value across 27 TCGA cancer types Shang J, Song Q, Yang Z, Li D, Chen W, Luo L, Wang Y, Yang J, Li S. Oncotarget

2014

Analysis of lncRNA expression profiles in non-small cell lung cancers (NSCLC) and their clinical subtypes Yang J, Lin J, Liu T, Chen T, Pan S, Huang W, Li S*. Lung Cancer

A meta-analysis of microRNA expression in liver cancer Yang J, Han S, Huang W, Chen T, Liu Y, Pan S, Li S*. PLoS One

Online Systems and Databases

Quartet Data Portal

An Online Platform for Quality Control and Data Integration of Multi-omics Profiling

QuartetDataPortal

Category: Database; Omics Data Analysis; Quality Control

Description: The Quartet Project provides publicly accessible multi-omics reference materials and practical tools to enhance the reproducibility and reliability of multi-omics results. Well-characterized multiomics reference materials and quality control metrics pertinent to precision medicine study purposes can be used to measure and mitigate technical variation, enabling more accurate cross-batch and cross-omics data integration in increasingly large-scale and longitudinal studies such as the International Human Phenome Project.

Website: https://chinese-quartet.org/#/dashboard

Group Members: Jingcheng Yang, Yaqing Liu, Jun Shang (View the publication for the full list of authors)

Publication: https://doi.org/10.1186/s13059-023-03091-9

GlioMarker

An Integrated Database for Knowledge Exploration of Diagnostic Biomarkers in Gliomas

GlioMarker

Category: Database; Knowledge Curation

Description: GlioMarker is the first diagnostic biomarker database in the field of gliomas to provide biomarker knowledge exploration, including comprehensive literature mining, ontology annotations, precision medical knowledge exploration, and online omics data analysis and visualization. It may serve as a specialist ploatform for clinicians and researchers by providing rapid and comprehensive knowledge, which in turn will facilitate high-quality research and biomarker applications.

Website: http://gliomarker.prophetdb.org/#/home

Group Members: Zihan Ran, Jingcheng Yang, XiuWen Chen, Zijing Ma

Publication: https://doi.org/10.3389/fonc.2022.792055

Last update: 2025-04-23
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