1Identification of Robust and Key Differentially Expressed Genes during C2C12 Cell Myogenesis Based on Multiomics Data

作者： Zhang, Song; Zhang, Yuanyuan; Chen, Choulin; Hu, Qingqing; Fu, Yang; Xu, Lingna; Wang, Chao; Liu, Yuwen; Zhang, Song; Zhang, Yuanyuan; Chen, Choulin; Hu, Qingqing; Fu, Yang; Xu, Lingna; Wang, Chao; Liu, Yuwen; Zhang, Yuanyuan; Chen, Choulin; Hu, Qingqing; Wang, Chao; Chen, Choulin; Hu, Qingqing; Wang, Chao; Liu, Yuwen; SCI

机构： Chinese Acad Agr Sci, Key Lab Livestock & Poultry Multiom MARA, Guangdong Lab Lingnan Modern Agr, Agr Genom Inst Shenzhen,Shenzhen Branch, Shenzhen 518124, Peoples R China; Chinese Acad Agr Sci, Innovat Grp Pig Genome Design & Breeding, Res Ctr Anim Genome, Agr Genom Inst Shenzhen, Shenzhen, Peoples R China; Henan Univ, Sch Life Sci, Kaifeng 475004, Peoples R China; Huazhong Agr Univ, Breeding & Reprod Minist Educ, Key Lab Agr Anim Genet, Wuhan 430070, Peoples R China; Huazhong Agr Univ, Key Lab Swine Genet & Breeding, Minist Agr, Coll Anim Sci & Technol, Wuhan 430070, Peoples R China; Chinese Acad Agr Sci, Kunpeng Inst Modern Agr, Foshan 528226, Peoples R China;

来源：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

关键词： myogenesis; differentially expressed genes; robust rank aggregation; KLF5; enhancer

年份：2022

2A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity

作者： Li, Zhaohong; Zhang, Yuanyuan; Qin, Shenghua; Chen, Yun; Chen, Choulin; Bao, Yongzhou; Xu, Lingna; Xie, Long; Deng, Biao; Zuo, Erwei; Liu, Yuwen; Li, Zhaohong; Zhang, Yuanyuan; Qin, Shenghua; Chen, Yun; Chen, Choulin; Bao, Yongzhou; Xu, Lingna; Deng, Biao; Liu, Yuwen; Peng, Bo; Ni, Jian-Quan; Peng, Bo; Ni, Jian-Quan; Zhang, Qian; Liu, Gang; Zhu, Yuqi; Hong, Yi; Sun, Tongjun; Liu, Binghua; Liu, Qian; Wang, Hongyan; Shao, Changwei; Chen, Xi; Wang, Jing; Wang, Guirong; Ma, Xinhao; Mei, Chugang; Yao, Yilong; Tang, Zhonglin; Liu, Yuwen; Li, Jiaying; Wang, Ningli; De, Baojun; Chen, Yuting; Cao, Junwei; Li, Tian; Zhu, Fangjie; Liu, Ranran; Ni, Jian-Quan; SCI

机构： Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Key Lab Livestock & Poultry Multi MARA, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr, Buxin Rd 97, Shenzhen 518124, Peoples R China; Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Res Ctr Anim Genome, Innovat Grp Pig Genome Design & Breeding, Buxin Rd 97, Shenzhen 518124, Peoples R China; Tsinghua Univ, Sch Basic Med Sci, Gene Regulatory Lab, 30 Shuangqing Rd, Beijing 100084, Peoples R China; Tsinghua Univ, State Key Lab Mol Oncol, 30 Shuangqing Rd, Beijing 100084, Peoples R China; Chinese Acad Sci, State Key Lab Mycol, Inst Microbiol, 1 Beichen West Rd, Beijing 100101, Peoples R China; Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Genome Anal Lab, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,M, 7 Pengfei Rd, Shenzhen 518124, Peoples R China; Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Maricultural Biobreeding & Sustainab, 106 Nanjing Rd, Qingdao 266071, Shandong, Peoples R China; Chinese Acad Agr Sci, Minist Agr & Rural Affairs, Guangdong Lab Lingnan Modern Agr, Key Lab Synthet Biol,Agr Genom Inst Shenzhen, Buxin Rd 97, Shenzhen 518124, Peoples R China; Northwest A&F Univ, Coll Grassland Agr, Coll Anim Sci & Technol, Natl Beef Cattle Improvement Ctr, 3 Taicheng Rd, Yangling 712100, Shaanxi, Peoples R China; Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Green Hlth Aquaculture Res Ctr, Bldg 26 Lihe Technol Pk,Auxiliary Rd Xinxi Ave Sou, Foshan 528226, Peoples R China; Capital Med Univ, Beijing Tongren Hosp, Beijing Tongren Eye Ctr, Dept Ophthalmol,Beijing Inst Ophthalmol, Dongjiaomin lane 1, Beijing 100101, Peoples R China; Inner Mongolia Agr Univ, Coll Life Sci, Inner Mongolia Autonomous Reg Key Lab Biomfg, 306 Zhaowuda Rd, Hohhot 010018, Peoples R China; Fujian Agr & Forestry Univ FAFU, Haixia Inst Sci & Technol, Coll JUNCAO Sci & Ecol, Natl Engn Res Ctr JUNCAO, 15 Shangxiadian Rd, Fuzhou 0350002, Peoples R China; Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China; Shanxi Med Univ, Tsinghua Collaborat Innovat Ctr Frontier Med, SXMU, 56 Xinjian South Rd, Taiyuan 030001, Peoples R China;

来源：NUCLEIC ACIDS RESEARCH

年份：2024

3Identification, Design, and Application of Noncoding Cis-Regulatory Elements

作者： Xu, Lingna; Liu, Yuwen; Xu, Lingna; Liu, Yuwen; Liu, Yuwen; SCI

机构： Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Key Lab Livestock, Shenzhen 518124, Peoples R China; Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Res Ctr Anim Genome, Innovat Grp Pig Genome Design & Breeding, Shenzhen 518124, Peoples R China; Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Foshan 528226, Peoples R China;

来源：BIOMOLECULES

关键词： CREs; MPRA; predicting CRE activity; de novo designing CREs

年份：2024

4Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development

作者： Zhang, Song; Wang, Chao; Qin, Shenghua; Chen, Choulin; Bao, Yongzhou; Zhang, Yuanyuan; Xu, Lingna; Li, Kui; Tang, Zhonglin; Liu, Yuwen; Zhang, Song; Wang, Chao; Qin, Shenghua; Chen, Choulin; Bao, Yongzhou; Zhang, Yuanyuan; Xu, Lingna; Li, Kui; Tang, Zhonglin; Liu, Yuwen; Wang, Chao; Chen, Choulin; Wang, Chao; Chen, Choulin; Liu, Qingyou; Zhao, Yunxiang; Li, Kui; Tang, Zhonglin; Liu, Yuwen; SCI

机构： Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Shenzhen Branch,Key Lab Livestock & Poultry Multi, Shenzhen 518124, Peoples R China; Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Res Ctr Anim Genome, Innovat Grp Pig Genome Design & Breeding, Shenzhen 518124, Peoples R China; Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China; Huazhong Agr Univ, Coll Anim Sci & Technol, Key Lab Swine Genet & Breeding, Minist Agr, Wuhan 430070, Peoples R China; Foshan Univ, Sch Life Sci & Engn, Guangdong Prov Key Lab Anim Mol Design & Precise B, Foshan 528225, Peoples R China; Guangxi Univ, Coll Anim Sci & Technol, Guangxi Key Lab Anim Breeding Dis Control & Preven, Nanning 530004, Peoples R China; Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Agr Genom Inst Shenzhen, Foshan 528226, Peoples R China;

来源：GENOME RESEARCH

年份：2024