郑媛婷｜复旦大学｜学者主页

2026

RNA sequencing facilitates disease-associated alternative splicing detection: Advances and challenges

Jiaxin Zhao, Duo Wang, Yuanting Zheng, Jinming Li, Rui Zhang

Genes & Diseases

2026

Ensuring multiomics data reproducibility for artificial intelligence with reference materials as a common calibrator

Leming M. Shi, Wenjun Bao, Aedín C. Culhane, Xiang Fang, Cesare Furlanello, Ruixin Hao, Wendell D. Jones, Rebecca L. Kusko, Samir Lababidi, Christopher E. Mason, Andreas Scherer, Shraddha Thakkar, Weida Tong, Russell D. Wolfinger, Joshua Xu, Ying Yu, Rui Zhang, Yuanting Zheng

Nature Biotechnology

精选作品

期刊论文

RNA sequencing facilitates disease-associated alternative splicing detection: Advances and challenges

Ensuring multiomics data reproducibility for artificial intelligence with reference materials as a common calibrator

Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis

Distinct multi-omics signatures of clinical subgroups of type 2 diabetes define heterogeneous responses to an insulin sensitizer

Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants

Cancer stem cells orchestrate immune evasion through extracellular vesicle-mediated non-canonical signaling pathways

A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators

Integrative clinico-molecular analysis reveals actionable subtypes and biomarkers in lung adenocarcinoma

Mechanisms of Aristolochic Acid Resistance in Specialist Butterflies and Evolutionary Insights for Potential Protective Pathways

Genomic and transcriptomic dynamics in the stepwise progression of lung adenocarcinoma

A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Glycine–GLRA1–calmodulin signaling regulates endoplasmic reticulum calcium to sustain insulin secretion and β-cell function

Protein-level batch-effect correction enhances robustness in MS-based proteomics

Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing

Baseline Plasma GPX3 Level Predicts Efficacy of Insulin-Sensitization Drug Chiglitazar in Type 2 Diabetes

Molecular subtyping of stage I lung adenocarcinoma via molecular alterations in pre-invasive lesion progression

Construction of RNA reference materials for improving the quantification of transcriptomic data

Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study

PPARA variant rs1800234 had a dose dependent pharmacogenetics impact on the therapeutic response to chiglitazar

A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials

Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project

Assessing and mitigating batch effects in large-scale omics studies

Reference Materials for Improving Reliability of Multiomics Profiling

Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities

High Intensity Focused Ultrasound‐Driven Nanomotor for Effective Ferroptosis‐Immunotherapy of TNBC

Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials

Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

The Quartet Data Portal: integration of community-wide resources for multiomics quality control

Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis

Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method

Overexpression of CD99 is associated with tumor adaptiveness and indicates the tumor recurrence and therapeutic responses in gliomas

De novo assembly of a chromosome-level reference genome of the ornamental butterfly Sericinus montelus based on nanopore sequencing and Hi-C analysis

一种高通量自动化血浆miRNA文库构建方法及其跨批次性能评估

A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers

Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats

Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Hidden biases in germline structural variant detection

Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

Correction: Both IDO1 and TDO contribute to the malignancy of gliomas via the Kyn–AhR–AQP4 signaling pathway

Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Forty‐three key gene expressions involved in the effect of indoleamine 2,3‐dioxygenase 1 expression on cancer prognosis may be a potential indoleamine 2,3‐dioxygenase 1 inhibitor biomarker

三阴性乳腺癌基因组与转录组全景图：亚型及治疗策略

Blood molecular markers associated with COVID‐19 immunopathology and multi‐organ damage

Both IDO1 and TDO contribute to the malignancy of gliomas via the Kyn–AhR–AQP4 signaling pathway

Genomic and immune profiling of pre-invasive lung adenocarcinoma

Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies

精准医学时代的新药研发和个性化用药——标准、监管与伦理学挑战

生命质量标准——基因组标准

PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs

A Comprehensive Analysis of Gene Expression of Xenobiotic and Endogenous Metabolizing Enzymes and Transporters in Rat Multiple Organs

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

Advances in single-cell RNA sequencing and its applications in cancer research

Exploring functions of long noncoding RNAs across multiple cancers through co-expression network

Somatic mutations in ZFHX4 gene are associated with poor overall survival of Chinese esophageal squamous cell carcinoma patients

Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development

Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

Protective effect of 23‐hydroxybetulinic acid on doxorubicin‐induced cardiotoxicity: a correlation with the inhibition of carbonyl reductase‐mediated metabolism

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Differences in metabolite profile between blood plasma and serum.

23-Hydroxybetulinic acid from Pulsatilla chinensis (Bunge) Regel synergizes the antitumor activities of doxorubicin in vitro and in vivo.

20(S)-Ginsenoside Rh2 Noncompetitively Inhibits P-Glycoprotein In Vitro and In Vivo: A Case for Herb-Drug Interactions

Simultaneous Quantification of Benazepril, Gliclazide and Valsartan in Human Plasma by LC–MS–MS and Application for Rapidly Measuring Protein Binding Interaction between Rhein and These Three Drugs

Pharmacokinetic characterization of ginsenoside Rh2, an anticancer nutrient from ginseng, in rats and dogs.

Metabonomic phenotype and identification of “heart blood stasis obstruction pattern” and “qi and yin deficiency pattern” of myocardial ischemia rat models

Integrated Pharmacokinetic Study of Multiple Effective: Integrated Pharmacokinetic Study of Multiple Effective

Identification of the major metabolites of 5-n-butyl-4-{4-[2-(1H-tetrazole-5-yl)-1H-pyrrol-1-yl]phenylmethyl}-2,4-dihydro-2-(2,6-dichloridephenyl)-3H-1,2,4-triazol-3-one, a new angiotensin type 1 receptor antagonist, in rat bile by HPLC-diode array detection-MS and HPLC-MS/MS.

Determination of 5-n-Butyl-4-{4-[2-(1H-tetrazole-5-yl)-1H-pyrrol-1-yl]phenylmethyl}-2,4-dihydro-2-(2,6-dichloridephenyl)-3H-1,2,4-triazol-3-one, a New Angiotensin Type 1 Receptor Antagonist in Rat Plasma by LC-ESI-MS: Application to Pharmacokinetic Studies

Simultaneous determination of panax notoginsenoside R1, ginsenoside Rg1, Rd, Re and Rb1 in rat plasma by HPLC/ESI/MS: platform for the pharmacokinetic evaluation of total panax notoginsenoside, a typical kind of multiple constituent traditional Chinese medicine.

Quantitative determination of trans-polydatin, a natural strong anti-oxidative compound, in rat plasma and cellular environment of a human colon adenocarcinoma cell line for pharmacokinetic studies.

Quantitative analysis of 23-hydroxybetulinic acid, a novel anticancer substance, in the cellular environment of a human colon adenocarcinoma cell line for cellular pharmacokinetic studies.