EasyMetagenome: A user‐friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research

Authors: Defeng Bai, Tong Chen, Jiani Xun, Chuang Ma, Hao Luo, Haifei Yang, Chen Cao, Xiaofeng Cao, Jianzhou Cui, Yuan‐Ping Deng, Zhaochao Deng, Wenxin Dong, Wenxue Dong, Juan Du, Qunkai Fang, Wei Fang, Yue Fang, Fangtian Fu, Min Fu, Yi‐Tian Fu, He Gao, Jingping Ge, Qinglong Gong, Lunda Gu, Peng Guo, Yuhao Guo, Tang Hai, Hao Liu, Jieqiang He, Zi‐Yang He, Huiyu Hou, Can Huang, Shuai Ji, ChangHai Jiang, Gui‐Lai Jiang, Lingjuan Jiang, Ling N. Jin, Yuhe Kan, Da Kang, Jin Kou, Ka‐Lung Lam, Changchao Li, Chong Li, Fuyi Li, Liwei Li, Miao Li, Xin Li, Ye Li, Zheng‐Tao Li, Jing Liang, Yongxin Lin, Changzhen Liu, Danni Liu, Fengqin Liu, Jia Liu, Tianrui Liu, Tingting Liu, Xinyuan Liu, Yaqun Liu, Bangyan Liu, Minghao Liu, Wenbo Lou, Yaning Luan, Yuanyuan Luo, Hujie Lv, Tengfei Ma, Zongjiong Mai, Jiayuan Mo, Dongze Niu, Zhuo Pan, Heyuan Qi, Zhanyao Shi, Chunjiao Song, Fuxiang Sun, Yan Sun, Sihui Tian, Xiulin Wan, Guoliang Wang, Hongyang Wang, Hongyu Wang, Huanhuan Wang, Jing Wang, Jun Wang, Kang Wang, Leli Wang, Shao‐kun Wang, Xinlong Wang, Yao Wang, Zufei Xiao, Huichun Xing, Yifan Xu, Shu‐yan Yan, Li Yang, Song Yang, Yuanming Yang, Xiaofang Yao, Salsabeel Yousuf, Hao Yu, Yu Lei, Zhengrong Yuan, Meiyin Zeng, Chunfang Zhang, Chunge Zhang, Huimin Zhang, Jing Zhang, Na Zhang, Tianyuan Zhang, Yi‐Bo Zhang, Yupeng Zhang, Zheng Zhang, Mingda Zhou, Yuanping Zhou, Chengshuai Zhu, Lin Zhu, Yue Zhu, Zhihao Zhu, Hongqin Zou, Anna Zuo, Wenxuan Dong, Tao Wen, Shifu Chen, Guoliang Li, Yunyun Gao, Yong‐Xin Liu

Source: iMeta, Vol 4, Iss 1, Pp n/a-n/a (2025)

Subject Terms: metagenome, microbiome, microbiota, pipeline, visualization, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/2770-596X

Access URL: https://doaj.org/article/9e02ebd1b25b4e5fb372b6e50eee325f

iMeta Conference 2024: Building an innovative scientific research ecosystem for microbiome and One Health

Authors: Yao Wang, Huiyu Hou, Hao Luo, Jiani Xun, Chuang Ma, Haifei Yang, Defeng Bai, Salsabeel Yousuf, Hujie Lyu, Tianyuan Zhang, Xiulin Wan, Xiaofang Yao, Tengfei Ma, Yuanping Zhou, Zhihao Zhu, Meiyin Zeng, Sanqi An, Qing Bai, Yao Bai, Guodong Cao, Tingting Cao, Yongkai Cao, Chihmin Chang, Lijia Chang, Bo Chen, Dai Chen, Dijun Chen, Hanqing Chen, Jiali Chen, Jinfeng Chen, Wei‐Hua Chen, Xinhai Chen, Yue Chen, Zhangran Chen, Cheng Cheng, Quan Cheng, Xi‐Jian Dai, Chaowen Deng, Feilong Deng, Jingwen Deng, Chang‐Sheng Dong, Lei Dong, Lianhui Duan, Yi Duan, Qingjie Fan, Chao Fang, Tingyu Fang, Wensheng Fang, Zhencheng Fang, Min Fu, Minjie Fu, Cong Gao, Hao Gao, Weiwei Gao, Xinrui Gao, Yi‐Zhou Gao, Yan Geng, Wenping Gong, Shaohua Gu, Xia Gu, Zhengquan Gu, Jian‐Wei Guo, Junjie Guo, Qiuyan Guo, Xiang Guo, Xiaoqian Guo, Dongfei Han, Ziyi Han, Yanan Hao, Jiale He, Jianquan He, Jianyu He, Ruolin He, Guosen Hou, Bin Hu, Haibo Hu, Yi Hu, Yongfei Hu, Yucan Hu, Guanyin Huang, Haiyun Huang, Jiaomei Huang, Shenghui Huang, Baolei Jia, Xingxing Jian, Chao Jiang, Kun Jiang, Lanyan Jiang, Shuaiming Jiang, Jian‐Yu Jiao, Hao Jin, Jiajia Jin, Siyuan Kong, Xinxing Lai, Yuxin Leng, Bang Li, Bing Li, Fang Li, Hao Li, Huanjie Li, Jing Li, Kai Li, Lanqi Li, Leyuan Li, Minghan Li, Pengsong Li, Wei Li, Xianyu Li, Li Xuemeng, Yafei Li, Yuantao Li, Zhi Li, Liqin Liang, Rong Liang, Zhuobin Liang, Qingya Liu, Dejian Liu, Huiheng Liu, Jinchao Liu, Li Liu, Lihui Liu, Moyang Liu, Ran Liu, Shuai Liu, Tianyang Liu, Wei Liu, Wenjuan Liu, Xiaomin Liu, Yang Liu, Yichen Liu, Yina Liu, Yuan Liu, Zhe Liu, Zhipeng Liu, Zhiquan Liu, Chunhao Long, Yun Long, Changying Lu, Chao Lu, Cheng Lu, Qi Lu, Yaning Luan, Peng Luo, Sheng Luo, Ning Ma, Xiao‐Ya Ma, Yan Ma, Wenjun Mao, Yuanfa Meng, Yan Ni, Yawen Ni, Kang Ning, Dongze Niu, Kai Peng, Zhengwu Peng, Xubo Qian, Zhiguang Qiu, Hui Qu, Zepeng Qu, Yan Ren, Zhigang Ren, Youming Shen, Lin Shi, Linlin Shi, Wenxuan Shi, Yongpeng Shi, Tianyuan Song, Xiaohui Song, Xiaoming Song, Xiaowei Song, Qi Su, Yufan Su, Lifang Sun, Qiang Sun, Tiefeng Sun, Yunke Sun, Hua Tang, Wenjing Tang, Tao Yu, Simon Tian, Shuo Wang, Bowen Wang, Cheng Wang, Wang Jin, Leli Wang, Liangliang Wang, Lixiao Wang, Mingbang Wang, Ming‐Ke Wang, Pingyi Wang, Shaolin Wang, Shaopu Wang, Xinxia Wang, Xueqiang Wang, Mi Wei, Yan Wei, Yanxia Wei, Yongjun Wei, Chaoliang Wen, Xin Wen, Linkun Wu, Shengru Wu, Yuting Wu, Shuting Xia, Xiaodong Xia, Yu Xia, Xionggen Xiang, Chuanxing Xiao, Weihua Xiao, Yingping Xiao, Ruohan Xie, Rui Xing, Hui Xu, Wei Xu, Zhimin Xu, Hongliang Xue, Chao Yan, Qiu‐Long Yan, Shaofei Yan, Xiuchuan Yan, Mengli Yang, Yufan Yang, Zhipeng Yang, Ziyuan Yang, Guixiang Yao, Yanlai Yao, Xianfu Yi, Chong Yin, Mingliang Yin, Shicheng Yu, Ying Yu, Yongyao Yu, Fusong Yuan, Shao‐Lun Zhai, Bo Zhang, Chen Zhang, Fang Zhang, Feng‐Li Zhang, Hengguo Zhang, Jinping Zhang, Junya Zhang, Kun Zhang, Li Zhang, Lin Zhang, Lingxuan Zhang, Meng Zhang, Qian Zhang, Runan Zhang, Tongtong Zhang, Tongxue Zhang, Weipeng Zhang, Yong Zhang, Yuchao Zhang, Yujun Zhang, Zeng Zhang, Zhengxiao Zhang, Zhi‐Feng Zhang, Boxi Zhao, Yanyan Zhao, Yibing Zhao, Ziwei Zhao, Diwei Zheng, Ying Zheng, Wenqiang Zhi, Jixin Zhong, Xiangjian Zhong, Wei Zhou, Xin Zhou, Zhemin Zhou, Zhichao Zhou, Congmin Zhu, Feiying Zhu, Xiaodie Zhu, Yutian Zou, Hongling Zhou, Lei Lei, Yanliang Bi, Hubing Shi, Hui‐Zeng Sun, Shuangxia Jin, Wenkai Ren, Lei Dai, Xin Wang, Canhui Lan, Hongwei Liu, Shuang‐Jiang Liu, Yulong Yin, Chun‐Lin Shi, Ren‐You Gan, Fangqing Zhao, Jun Yu, Tong Chen, Xin Hong, Hua Yang, Bangzhou Zhang, Shifu Chen, Xiaodong Li, Yunyun Gao, Yong‐Xin Liu

Source: iMeta, Vol 3, Iss 6, Pp n/a-n/a (2024)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/2770-596X

Access URL: https://doaj.org/article/b1cad213f15a4279977c19c6427e8bcc

Integrative radiomics analyses identify universal signature for predicting prognosis and therapeutic vulnerabilities across primary and secondary liver cancers: A multi-cohort study

Authors: Hongjie Xin, Qianwei Lai, Yanping Liu, Naying Liao, Ying Wang, Bihong Liao, Keyang Zhou, Yuchen Zhou, Yang Bai, Zhihua Chen, Yuanping Zhou

Source: Pharmacological Research, Vol 210, Iss , Pp 107535- (2024)

Subject Terms: Liver cancer, Machine learning, Radiomics profiling, Biomarker, Prognosis, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1043661824004808; https://doaj.org/toc/1096-1186

Access URL: https://doaj.org/article/45f1c1e431874bafa5d7a68e9c611811

USEARCH 12: Open‐source software for sequencing analysis in bioinformatics and microbiome

Authors: Yuanping Zhou, Yong‐Xin Liu, Xuemeng Li

Source: iMeta, Vol 3, Iss 5, Pp n/a-n/a (2024)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/2770-596X

Access URL: https://doaj.org/article/f9d42a10d86d498d817ab4049391266b

Automatic origin prediction of liver metastases via hierarchical artificial-intelligence system trained on multiphasic CT data: a retrospective, multicentre studyResearch in context

Authors: Hongjie Xin, Yiwen Zhang, Qianwei Lai, Naying Liao, Jing Zhang, Yanping Liu, Zhihua Chen, Pengyuan He, Jian He, Junwei Liu, Yuchen Zhou, Wei Yang, Yuanping Zhou

Source: EClinicalMedicine, Vol 69, Iss , Pp 102464- (2024)

Subject Terms: Liver metastases, Primary liver cancer, Artificial intelligence, Computed tomography, Primary origin, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589537024000439; https://doaj.org/toc/2589-5370

Access URL: https://doaj.org/article/185bdcbe03c844559397ea5147561d4b

Developmental potential of non- and mono-pronuclear zygotes and associated clinical outcomes in IVF cycles

Authors: Mengyi Zhu, Qiyin Dong, Yurong Zhu, Yun Le, Tengfei Wang, Yuanping Zhou, Sheng Yang

Source: Frontiers in Endocrinology, Vol 15 (2024)

Subject Terms: 0PN and 1PN zygotes, blastocyst culture, developmental potential, pregnancy rates, neonatal outcomes, Diseases of the endocrine glands. Clinical endocrinology, RC648-665

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fendo.2024.1361734/full; https://doaj.org/toc/1664-2392

Access URL: https://doaj.org/article/25d2b40a64df483d82d8fbd3a34ed522

Comparison of early and fully expanded blastocysts on pregnancy and birth outcomes in patients with fresh IVF/ICSI cycles: A retrospective cohort study.

Authors: Xiaoqin Pan, Yuanping Zhou, Liwen Shen

Source: PLoS ONE, Vol 19, Iss 8, p e0308130 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/3824a5c5d3704a32bdb53ad4ff7b9cda

Distinguishing infectivity in patients with pulmonary tuberculosis using deep learning

Authors: Yi Gao, Yiwen Zhang, Chengguang Hu, Pengyuan He, Jian Fu, Feng Lin, Kehui Liu, Xianxian Fu, Rui Liu, Jiarun Sun, Feng Chen, Wei Yang, Yuanping Zhou

Source: Frontiers in Public Health, Vol 11 (2023)

Subject Terms: pulmonary tuberculosis, deep learning, disease control and prevention, infectivity identification, CT, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpubh.2023.1247141/full; https://doaj.org/toc/2296-2565

Access URL: https://doaj.org/article/3aef9ef16c6f43e6958d8d0a464add2e

Reduced‐dimension MVDR beamformer based on sub‐array optimization

Authors: Tuanning Liu, Wenqiang Liu, Yuanping Zhou, Kesong Fan

Source: IET Communications, Vol 16, Iss 18, Pp 2183-2192 (2022)

Subject Terms: Telecommunication, TK5101-6720

File Description: electronic resource

Relation: https://doaj.org/toc/1751-8628; https://doaj.org/toc/1751-8636

Access URL: https://doaj.org/article/bfce538727d049369e38ea830a644379

Noninvasive evaluation of neutrophil extracellular traps signature predicts clinical outcomes and immunotherapy response in hepatocellular carcinoma

Authors: Hongjie Xin, Qianwei Lai, Yuchen Zhou, Jian He, Yangda Song, Minjun Liao, Jiarun Sun, Meng Li, Mingxia Zhang, Weifang Liang, Yang Bai, Yongyuan Zhang, Yuanping Zhou

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: hepatocellular carcinoma, neutrophil extracellular traps, computed tomography, radiomics, prognosis, programmed death receptor-1, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1134521/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/c1ebcb0da5bf4c45a954a0c24434fa6a

PPP2R5D promotes hepatitis C virus infection by binding to viral NS5B and enhancing viral RNA replication

Authors: Muhammad Ikram Anwar, Ni Li, Qing Zhou, Mingxiao Chen, Chengguang Hu, Tao Wu, Haihang Chen, Yi-Ping Li, Yuanping Zhou

Source: Virology Journal, Vol 19, Iss 1, Pp 1-12 (2022)

Subject Terms: Hepatitis C virus, PPP2R5D, Protein–protein interaction, RNA dependent RNA polymerase, Phosphatase activity, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://doaj.org/toc/1743-422X

Access URL: https://doaj.org/article/5a6a00b2f7cb47bd97dfa197892131fa

Hepatitis C virus hypervariable region 1 antibodies interrupt E2-SR-B1 interaction to suppress viral infection

Authors: Kai Deng, Qing Zhou, Zhanxue Xu, Yuhao Yang, Xi Liu, Chunna Li, Mingxiao Chen, Zhenzhen Zhang, Haihang Chen, Ling Ma, Muhammad Ikram Anwar, Changlong Zheng, Liang Rong, Mingxing Huang, Jinyu Xia, Yuanping Zhou, Yi-Ping Li

Source: iScience, Vol 26, Iss 4, Pp 106421- (2023)

Subject Terms: Immunology, Virology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004223004984; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/8bfcc8f21cda40ea9d9e0294d0c755b8

Dynamic changes in fractional amplitude of low-frequency fluctuations in patients with chronic insomnia

Authors: Wei Chen, Hui Wang, Tianze Sun, Qi Wu, Wenxuan Han, Qian Li, Yong Liu, Yuanping Zhou, Xiuyong He

Source: Frontiers in Neuroscience, Vol 16 (2022)

Subject Terms: dynamic fractional amplitude of low-frequency fluctuations, chronic insomnia, sleep disorder, multivariate pattern analysis, instable brain activity, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnins.2022.1050240/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/53c811af961242c88c02965ad9c011a1

Application of a Chitosan–Cinnamon Essential Oil Composite Coating in Inhibiting Postharvest Apple Diseases

Authors: Wanli Zhang, Gulden Goksen, Yuanping Zhou, Jun Yang, Mohammad Rizwan Khan, Naushad Ahmad, Tao Fei

Source: Foods, Vol 12, Iss 18, p 3518 (2023)

Subject Terms: apple fruit, chitosan coating, cinnamon essential oil, postharvest, Chemical technology, TP1-1185

File Description: electronic resource

Relation: https://www.mdpi.com/2304-8158/12/18/3518; https://doaj.org/toc/2304-8158

Access URL: https://doaj.org/article/516910f6ba454406aced55fe1084421f

Summer Rice–Winter Potato Rotation Suppresses Various Soil-Borne Plant Fungal Pathogens

Authors: Yuanping Zhou, Wenjiao Luo, Maoxing Li, Qiong Wang, Yongxin Liu, Huachun Guo

Source: Agronomy, Vol 13, Iss 8, p 2143 (2023)

Subject Terms: crop rotation, soil fungal community, diversity analysis, fungal pathogens, bipartite co-occurrence networks, soil physiochemical properties, Agriculture

File Description: electronic resource

Relation: https://www.mdpi.com/2073-4395/13/8/2143; https://doaj.org/toc/2073-4395

Access URL: https://doaj.org/article/b1a7e5dcc9204953a563d75366ac247a

Real-world effectiveness and safety of OBT/PTV/r and dasabuvir for patients with chronic HCV genotype 1b infection in China: A multicenter prospective observational study

Authors: Yusheng Jie, Chaoshuang Lin, Jing Yuan, Zhixin Zhao, Yujuan Guan, Yuanping Zhou, Xiaohui Zhou, Bihui Zhong, Yinong Ye, Lihua Zhang, Ling Tao, Jianping Li, Xiaohong Zhang, Yutian Chong

Source: Liver Research, Vol 4, Iss 3, Pp 153-158 (2020)

Subject Terms: Hepatitis C virus (HCV), Direct-acting antiviral agent (DAA), Real-world research, Ombitasvir (OBT), Paritaprevir (PTV), Ritonavir, Diseases of the digestive system. Gastroenterology, RC799-869

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2542568420300258; https://doaj.org/toc/2542-5684

Access URL: https://doaj.org/article/4fed04a836be40309643c55654932ccb

Novel Role of Long Non-Coding RNA ASAP1-IT1 in Progression of Hepatocellular Carcinoma

Authors: Yanping Liu, Chengguang Hu, Xiaoyong Qu, Honghui Chen, Logen Liu, Linlin Zhou, Side Liu, Guoqing Li, Yuanping Zhou

Source: Frontiers in Oncology, Vol 12 (2022)

Subject Terms: hepatocellular carcinoma, long non-coding RNA, cell proliferation, metastasis, prognosis, miR-221-3p, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2022.746896/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/80bfac7f7bf94a6eb1373e7bb2c46d05

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Authors: Maoxing Li, Yuanping Zhou, Kaifeng Li, Huachun Guo

Source: Plants, Vol 12, Iss 8, p 1731 (2023)

Subject Terms: Ipomoea species, sweet potato, R2R3-MYB gene family, expression analysis, anthocyanin biosynthesis, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/12/8/1731; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/871b4cd9257a413bb8723f0ad3f1fa70

Evidence that the second human pegivirus (HPgV-2) is primarily a lymphotropic virus and can replicate independent of HCV replication

Authors: Zhengwei Wan, Junwei Liu, Fengyu Hu, Jingwei Shui, Linghua Li, Haiying Wang, Xiaoping Tang, Chengguang Hu, Yuanhao Liang, Yuanping Zhou, Weiping Cai, Shixing Tang

Source: Emerging Microbes and Infections, Vol 9, Iss 1, Pp 485-495 (2020)

Subject Terms: HPgV-2, persistent infection, resolved infection, lymphotropic, HCV, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2222-1751

Access URL: https://doaj.org/article/ac8a13771648486baab3b4596cb35260

Difference of Intrahost Dynamics of the Second Human Pegivirus and Hepatitis C Virus in HPgV-2/HCV-Coinfected Patients

Authors: Yuanhao Liang, Fengyu Hu, Hang Fan, Linghua Li, Zhengwei Wan, Haiying Wang, Jingwei Shui, Yuanping Zhou, Yigang Tong, Weiping Cai, Shixing Tang

Source: Frontiers in Cellular and Infection Microbiology, Vol 11 (2021)

Subject Terms: HPgV-2, HCV, HCV/HPgV-2 coinfection, intrahost variants, cytokine, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcimb.2021.728415/full; https://doaj.org/toc/2235-2988

Access URL: https://doaj.org/article/149e13b793364e8f8aa3d1efbe94fa2c