Zobrazeno 1 - 10
of 425
pro vyhledávání: '"Leming Shi"'
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-27 (2024)
Abstract Batch effects in omics data are notoriously common technical variations unrelated to study objectives, and may result in misleading outcomes if uncorrected, or hinder biomedical discovery if over-corrected. Assessing and mitigating batch eff
Externí odkaz:
https://doaj.org/article/e4d1fd198605488094a3a3deb05ff281
Autor:
Boshu Ouyang, Caihua Shan, Shun Shen, Xinnan Dai, Qingwang Chen, Xiaomin Su, Yongbin Cao, Xifeng Qin, Ying He, Siyu Wang, Ruizhe Xu, Ruining Hu, Leming Shi, Tun Lu, Wuli Yang, Shaojun Peng, Jun Zhang, Jianxin Wang, Dongsheng Li, Zhiqing Pang
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-20 (2024)
Abstract Due to low success rates and long cycles of traditional drug development, the clinical tendency is to apply omics techniques to reveal patient-level disease characteristics and individualized responses to treatment. However, the heterogeneou
Externí odkaz:
https://doaj.org/article/8aac615be03543ea9d2dc6da5e77d9d9
Autor:
Duo Wang, Yaqing Liu, Yuanfeng Zhang, Qingwang Chen, Yanxi Han, Wanwan Hou, Cong Liu, Ying Yu, Ziyang Li, Ziqiang Li, Jiaxin Zhao, Leming Shi, Yuanting Zheng, Jinming Li, Rui Zhang
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-21 (2024)
Abstract Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As
Externí odkaz:
https://doaj.org/article/ae2e7e53a9394d0a822c998df5bb0f2f
Autor:
Daniall Masood, Luyao Ren, Cu Nguyen, Francesco G. Brundu, Lily Zheng, Yongmei Zhao, Erich Jaeger, Yong Li, Seong Won Cha, Aaron Halpern, Sean Truong, Michael Virata, Chunhua Yan, Qingrong Chen, Andy Pang, Reyes Alberto, Chunlin Xiao, Zhaowei Yang, Wanqiu Chen, Charles Wang, Frank Cross, Severine Catreux, Leming Shi, Julia A. Beaver, Wenming Xiao, Daoud M. Meerzaman
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)
Abstract Background Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the per
Externí odkaz:
https://doaj.org/article/cc6fa948e2fb4ac38130b50d9697979b
Autor:
Binsheng Gong, Dan Li, Yifan Zhang, Rebecca Kusko, Samir Lababidi, Zehui Cao, Mingyang Chen, Ning Chen, Qiaochu Chen, Qingwang Chen, Jiacheng Dai, Qiang Gan, Yuechen Gao, Mingkun Guo, Gunjan Hariani, Yujie He, Wanwan Hou, He Jiang, Garima Kushwaha, Jian-Liang Li, Jianying Li, Yulan Li, Liang-Chun Liu, Ruimei Liu, Shiming Liu, Edwin Meriaux, Mengqing Mo, Mathew Moore, Tyler J. Moss, Quanne Niu, Ananddeep Patel, Luyao Ren, Nedda F. Saremi, Erfei Shang, Jun Shang, Ping Song, Siqi Sun, Brent J. Urban, Danke Wang, Shangzi Wang, Zhining Wen, Xiangyi Xiong, Jingcheng Yang, Lihui Yin, Chao Zhang, Ruolan Zhang, Ambica Bhandari, Wanshi Cai, Agda Karina Eterovic, Dalila B. Megherbi, Tieliu Shi, Chen Suo, Ying Yu, Yuanting Zheng, Natalia Novoradovskaya, Renee L. Sears, Leming Shi, Wendell Jones, Weida Tong, Joshua Xu
Publikováno v:
Scientific Reports, Vol 14, Iss 1, Pp 1-9 (2024)
Abstract Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive
Externí odkaz:
https://doaj.org/article/f6ac02a15b704d26872b588b34da0a59
Autor:
Naixin Zhang, Qiaochu Chen, Peipei Zhang, Kejun Zhou, Yaqing Liu, Haiyan Wang, Shumeng Duan, Yongming Xie, Wenxiang Yu, Ziqing Kong, Luyao Ren, Wanwan Hou, Jingcheng Yang, Xiaoyun Gong, Lianhua Dong, Xiang Fang, Leming Shi, Ying Yu, Yuanting Zheng
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)
Abstract Background Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. Results As part of the Quartet Project, we establish a publicly available sui
Externí odkaz:
https://doaj.org/article/ccfb67b87ce8402caf29ab9693397306
Autor:
Peng Jia, Lianhua Dong, Xiaofei Yang, Bo Wang, Stephen J. Bush, Tingjie Wang, Jiadong Lin, Songbo Wang, Xixi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yujing Zhang, Xia Wang, Fan Liang, Yang Wang, Jue Ruan, Han Xia, Yuanting Zheng, Leming Shi, Yi Lv, Jing Wang, Kai Ye
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-25 (2023)
Abstract Background Recent state-of-the-art sequencing technologies enable the investigation of challenging regions in the human genome and expand the scope of variant benchmarking datasets. Herein, we sequence a Chinese Quartet, comprising two monoz
Externí odkaz:
https://doaj.org/article/693c72c4aed949f9a781485d8e548871
Autor:
Xiangrong Yu, Xuejing Li, Qingwang Chen, Siyu Wang, Ruizhe Xu, Ying He, Xifeng Qin, Jun Zhang, Wuli Yang, Leming Shi, Ligong Lu, Yuanting Zheng, Zhiqing Pang, Shaojun Peng
Publikováno v:
Advanced Science, Vol 11, Iss 15, Pp n/a-n/a (2024)
Abstract The heterogeneity of triple‐negative breast cancers (TNBC) remains challenging for various treatments. Ferroptosis, a recently identified form of cell death resulting from the unrestrained peroxidation of phospholipids, represents a potent
Externí odkaz:
https://doaj.org/article/5ae21326d72a4e579a0c9786e3816a6f
Autor:
Luyao Ren, Xiaoke Duan, Lianhua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, Rongxue Peng, Wanwan Hou, Yaqing Liu, Jingjing Li, Ying Yu, Naixin Zhang, Jun Shang, Fan Liang, Depeng Wang, Hui Chen, Lele Sun, Lingtong Hao, The Quartet Project Team, Andreas Scherer, Jessica Nordlund, Wenming Xiao, Joshua Xu, Weida Tong, Xin Hu, Peng Jia, Kai Ye, Jinming Li, Li Jin, Huixiao Hong, Jing Wang, Shaohua Fan, Xiang Fang, Yuanting Zheng, Leming Shi
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-31 (2023)
Abstract Background Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as th
Externí odkaz:
https://doaj.org/article/d7d0e8a3126440d98263385aaeddd458
Autor:
Wenbin Li, Lin Gao, Xin Yi, Shuangfeng Shi, Jie Huang, Leming Shi, Xiaoyan Zhou, Lingying Wu, Jianming Ying
Publikováno v:
Genomics, Proteomics & Bioinformatics, Vol 21, Iss 5, Pp 962-975 (2023)
Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Ac
Externí odkaz:
https://doaj.org/article/b7c25fd985ea486b8e413214da343df5