ArticleNature biotechnology2024
Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.
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Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers, 1 of them a synthesis that pooled it.
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77citing papers in PubMed, 1 pooled it
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Who cites it
77 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dietary Omega-3 PUFAs in Metabolic Disease Research: A Decade of Omics-Enabled Insights (2014-2024).Nutrients · 2025Pooled it
- Toward Precision Cardiac Rehabilitation: Current Limitations and Future Opportunities of Omics and Artificial Intelligence.Sports medicine (Auckland, N.Z.) · 2026Review
- Multi-omics characterization of chronic social defeat stress recall-activated nuclei in Arc-GFP mice.Molecular psychiatry · 2026Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Ensuring multiomics data reproducibility for artificial intelligence with reference materials as a common calibrator.Nature biotechnology · 2026Article
- Distinct multi-omics signatures of clinical subgroups of type 2 diabetes define heterogeneous responses to an insulin sensitizer.Nature communications · 2026Article
- Amazonian Bioactives in Biopolymer-Based Systems for Biomedical Applications: Current Advances and Future Perspectives.Materials (Basel, Switzerland) · 2026Review
- Orthogonal nanopores cross-validation for multiplex single-molecule profiling.Chemical science · 2026Article
- Artificial intelligence needs a common ruler.Innovation (Cambridge (Mass.)) · 2026Article
- An interpretable breast cancer risk stratification model via multi-omics integration: multi-method development and cross-cohort validation.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs.Molecular biology and evolution · 2026Article
- Mapping the path to clinical implementation of multi-omics.Nature genetics · 2026Review
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Proteomics in bone malignancies: from bulk profiling to single-cell and ultra-low-input technologies.Journal of translational medicine · 2026Review
- Leveraging AI and integrated genomic-enviromic prediction for intelligent sugarcane breeding.Plant communications · 2026Review
- Artificial intelligence and multi-omics integration in liquid biopsy for genitourinary cancers: a systematic scoping review.International urology and nephrology · 2026Article
- A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.Nature communications · 2026Article
- Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression.Briefings in bioinformatics · 2026Review
- AI-driven nanomedicine for cancer theranostics.Molecular cancer · 2026Review
- Multimodal phenotyping of ARDS: design and preliminary insights from the prospective BIOWARE cohort for precision critical management.Respiratory research · 2026Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
61 authors.
Yuanting Zheng *State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China. zhengyuanting@fudan.edu.cn.ORCID http://orcid.org/0000-0003-4480-8303
Yaqing Liu *State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-9356-9164
Jingcheng Yang *State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Lianhua Dong *National Institute of Metrology, Beijing, China.
Rui Zhang *National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.ORCID http://orcid.org/0000-0003-4660-2042
Sha Tian *State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Ying YuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-4084-908X
Luyao RenState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Wanwan HouState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Feng ZhuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Yuanbang MaiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Jinxiong HanVazyme Biotech Co. Ltd., Nanjing, China.
Lijun ZhangVazyme Biotech Co. Ltd., Nanjing, China.
Hui JiangMGI, BGI-Shenzhen, Shenzhen, China.
Ling LinZhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China.
Jingwei LouZhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China.
Ruiqiang LiNovogene Bioinformatics Institute, Beijing, China.
Jingchao LinMetabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China.
Huafen LiuCalibra Diagnostics, Hangzhou, China.
Ziqing KongCalibra Diagnostics, Hangzhou, China.
Depeng WangNextomics Biosciences Institute, Wuhan, China.
Fangping DaiGenome Decoding Institute, Nantong, China.
Ding BaoState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Zehui CaoState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Qiaochu ChenState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-7384-7574
Qingwang ChenState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-7191-5801
Xingdong ChenState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Yuechen GaoState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
He JiangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-0673-0605
Bin LiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Bingying LiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Jingjing LiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-0142-5495
Ruimei LiuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Tao QingState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Erfei ShangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Jun ShangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-5767-1492
Shanyue SunState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Haiyan WangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Xiaolin WangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Naixin ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Peipei ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Ruolan ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Sibo ZhuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Andreas SchererInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.ORCID http://orcid.org/0000-0002-4254-7122
Jiucun WangState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-2765-0620
Jing WangNational Institute of Metrology, Beijing, China.
Yinbo HuoKey Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China.
Gang LiuKey Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China.
Chengming CaoKey Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China.
Li ShaoKey Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China.
Joshua XuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.ORCID http://orcid.org/0000-0001-5313-5847
Huixiao HongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.ORCID http://orcid.org/0000-0001-8087-3968
Wenming XiaoOffice of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.ORCID http://orcid.org/0000-0003-4096-9724
Xiaozhen LiangShanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
Daru LuState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
Li JinState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-9201-2321
Weida TongKey Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China.ORCID http://orcid.org/0000-0003-3488-6148
Chen DingState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China. chend@fudan.edu.cn.ORCID http://orcid.org/0000-0001-8673-3464
Jinming LiNational Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China. jmli@nccl.org.cn.
Xiang FangNational Institute of Metrology, Beijing, China. fangxiang@nim.ac.cn.
Leming ShiState Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China. lemingshi@fudan.edu.cn.ORCID http://orcid.org/0000-0002-2981-4150
Funding
National Natural Science Foundation of China (National Science Foundation of China) 31720103909National Natural Science Foundation of China (National Science Foundation of China) 32170657Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission) 2017SHZDZX01State Key Laboratory of Genetic Engineering (SKLGE) SKLGE-2117
Abstract
Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
Indexed as
MetabolomicsGene Expression ProfilingGenomicsHumansMultiomicsProteomicsReference StandardsTranscriptome
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