MAQC
Reproducibility is science. Science demands reproducibility.
Nature MAQC-V Collection
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- Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nature Biotechnology, 42(7), 1133-1149 (2024). PMID: 37679543 (Ratio-based multi-omics profiling)
- Ren L, Duan X, Dong L, Zhang R, Yang J, Gao Y, Peng R, Hou W, Liu Y, Li J, Yu Y, Zhang N, Shang J, Liang F, Wang D, Chen H, Sun L, Hao L; Quartet Project Team; Scherer A, Nordlund J, Xiao W, Xu J, Tong W, Hu X, Jia P, Ye K, Li J, Jin L, Hong H, Wang J, Fan S, Fang X, Zheng Y, Shi L. Quartet DNA reference materials and datasets for comprehensively evaluating germline variants calling performance. Genome Biology, 24(1), 270 (2023). PMID: 38012772 (Quartet DNA reference materials)
- Yu Y, Hou W, Liu Y, Wang H, Dong L, Mai Y, Chen Q, Li Z, Sun S, Yang J, Cao Z, Zhang P, Zi Y, Liu R, Gao J, Zhang N, Li J, Ren L, Jiang H, Shang J, Zhu S, Wang X, Qing T, Bao D, Li B, Li B, Suo C, Pi Y, Wang X, Dai F, Scherer A, Mattila P, Han J, Zhang L, Jiang H, Thierry-Mieg D, Thierry-Mieg J, Xiao W, Hong H, Tong W, Wang J, Li J, Fang X, Jin L, Xu J, Qian F, Zhang R, Shi L, Zheng Y. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling. Nature Biotechnology, 42(7), 1118-1132 (2024). PMID: 37679545 (Quartet RNA reference materials)
- Tian S, Zhan D, Yu Y, Wang Y, Liu M, Tan S, Li Y, Song L, Qin Z, Li X, Liu Y, Li Y, Ji S, Wang S; Zheng Y, He F, Qin J, Ding C. Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics. Genome Biology, 24(1), 202 (2023). PMID: 37674236 (Quartet protein reference materials)
- Zhang N, Chen Q, Zhang P, Zhou K, Liu Y, Wang H, Duan S, Xie Y, Yu W, Kong Z, Ren L, Hou W, Yang J, Gong X, Dong L, Fang X, Shi L, Yu Y, Zheng Y. Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling. Genome Biology, 25(1), 34 (2024). PMID: 38268000 (Quartet metabolite reference materials)
- Yang J, Liu Y, Shang J, Chen QC, Chen QW, Ren L, Zhang N, Yu Y, Li Z, Song Y, Yang S, Scherer A, Tong W, Hong H, Xiao W, Shi L, Zheng Y. The Quartet Data Portal: integration of community-wide resources for multiomics quality control. Genome Biology, 24(1), 245 (2023). PMID: 37884999 (Quartet data portal)
- Yu Y, Zhang N, Mai Y, Ren L, Chen Q, Cao Z, Chen Q, Liu Y, Hou W, Yang J, Hong H, Xu J, Tong W, Dong L, Shi L, Fang X, Zheng Y. Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method. Genome Biology, 24(1), 201 (2023). PMID: 37674217 (Batch-effect correction)
- Jia P, Dong L, Yang X, Wang B, Bush SJ, Wang T, Lin J, Wang S, Zhao X, Xu T, Che Y, Dang N, Ren L, Zhang Y, Wang X, Liang F, Wang Y, Ruan J, Xia H, Zheng Y, Shi L, Lv Y, Wang J, Ye K. Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet. Genome Biology, 24(1), 277 (2023). PMID: 38049885 (Quartet genome assemblies)
- Wang S, Lin J, Jia P, Xu T, Li X, Liu Y, Xu D, Bush SJ, Meng D, Ye K. De novo and somatic structural variant discovery with SVision-pro. Nature Biotechnology, 2024 Mar 22. doi: 10.1038/s41587-024-02190-7. Online ahead of print. PMID: 38519720 (Structural variation detection)
- Wang D, Liu Y, Zhang Y, Chen Q, Han Y, Hou W, Liu C, Yu Y, Li Z, Li Z, Zhao J, Shi L, Zheng Y, Li J, Zhang R. A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials. Nature Communications, 15(1), 6167 (2024). PMID: 39039053 (RNA-seq proficiency testing)
- Chen Q, Guo X, Wang H, Sun S, Jiang H, Zhang P, Shang E, Zhang R, Cao Z, Niu Q, Zhang C, Liu Y, Shi L, Yu Y, Hou W, Zheng Y. Plasma-free samples as a potential alternative to whole blood for transcriptomic analysis. Phenomics, 4(2), 109-124 (2024). PMID: 38884056 (Plasma-free blood RNA-seq)
- Yu Y#, Hou W#, Chen Q#, Guo X, Sang L, Xue H, Wang D, Li J, Fang X, Zhang R, Dong L, Shi L, Zheng Y. Construction of RNA reference materials for improving the quantification of transcriptomic data. Nature Protocols, in the press (RNA-seq protocols)
- Yu Y, Mai Y, Zheng Y, Shi L. Assessing and mitigating batch effects in large-scale omics studies. Genome Biology, 25(1), 254 (2024). PMID: 39363244 (Review on batch-effect correction)
