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2020 – today
- 2024
[j104]Rongbo Shen, Meiling Cheng, Wencang Wang, Qi Fan, Huan Yan, Jiayue Wen, Zhiyuan Yuan, Jianhua Yao, Yixue Li, Jiao Yuan
:
Graph domain adaptation-based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics. Briefings Bioinform. 25(6) (2024)- [j103]Xiaoping Cen, Wei Dong, Wei Lv, Yi Zhao, Fred Dubee, Alexios-Fotios A. Mentis, Dragomirka Jovic, Huanming Yang, Yixue Li:
Towards interpretable imaging genomics analysis: Methodological developments and applications. Inf. Fusion 102: 102032 (2024) - [j102]Yikai Zheng, Bi Zeng, Yi-Chun Feng, Lu Zhou, Yi-Xue Li:
PLRTE: Progressive learning for biomedical relation triplet extraction using large language models. J. Biomed. Informatics 159: 104738 (2024) - [c12]Shaodan Zhai, Yuwei Chen, Yixue Li:
Embedding Based Deduplication in E-commerce AutoComplete. SIGIR 2024: 2955-2959 - [i1]Xiaosong Wang, Xiaofan Zhang, Guotai Wang, Junjun He, Zhongyu Li, Wentao Zhu, Yi Guo, Qi Dou, Xiaoxiao Li, Dequan Wang, Liang Hong, Qicheng Lao, Tong Ruan, Yukun Zhou, Yixue Li, Jie Zhao, Kang Li, Xin Sun, Lifeng Zhu, Shaoting Zhang:
OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine. CoRR abs/2402.18028 (2024) - 2023
- [j101]Yuexing Liu, Yixue Li, Tao Zeng:
Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study. Frontiers Bioinform. 3 (2023) - [j100]Ruifang Cao, Yunchao Ling, Jiayue Meng, Ao Jiang, Ruijin Luo, Qinwen He, Anan Li, Yujie Chen, Zoutao Zhang, Feng Liu, Yixue Li, Guoqing Zhang:
SMDB: a Spatial Multimodal Data Browser. Nucleic Acids Res. 51(W1): 553-559 (2023) - [j99]Bin Peng, Jiuchun Yang, Yixue Li, Shuwen Zhang:
Land-Use Optimization Based on Ecological Security Pattern - A Case Study of Baicheng, Northeast China. Remote. Sens. 15(24): 5671 (2023) - 2022
- [j98]Yixue Li:
A Beloved Bioinformatician Buddy - In Memory of Professor Weimin Zhu. Genom. Proteom. Bioinform. 20(6): 1037-1039 (2022) - [j97]Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yanqing Wang, Wan Liu, Xing Yan, Yunchao Ling, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yingke Ma, Yaokai Jia, Xinchang Zheng, Meili Chen, Ming Chen, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Mochen Zhang, Guoliang Wang, Lizhi Yi, Wei Zhao, Song Wu, Zhuang Xiong, Rujiao Li, Zheng Gong, Lin Liu, Zhao Li, Qianpeng Li, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhaohua Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Zhen Yang, Lun Li, Na Li, Ying Cui, Guangya Duan, Gangao Wu, Tianhao Huang, Enhui Jin, Hailong Kang, Zhonghuang Wang, Hua Chen, Mingkun Li, Wanshan Ning, Yu Xue, Yanhu Liu, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Leisheng Shi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Guoji Guo, Shanshan Fu, Xiaodan Tan, Weizhi Zhang, Mei Luo, Yubin Xie, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Ge Gao, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiangshang Li, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res. 50(D1): 27-38 (2022) - [j96]Weiran Chen, Md Wahiduzzaman, Quan Li, Yixue Li, Guangyong Zheng, Tao Huang:
Comparative analysis of NovaSeq 6000 and MGISEQ 2000 single-cell RNA sequencing data. Quant. Biol. 10(4): 333 (2022) - 2021
- [j95]Quanxue Li, Wentao Dai, Jixiang Liu, Qingqing Sang, Yi-Xue Li, Yuan-Yuan Li:
DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures in cancer. Bioinform. 37(3): 429-430 (2021) - [j94]Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Tao Zhang, Wang Kang, Fei Yang, Jing Qu, Weiqi Zhang, Guanghui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Hai-Chun Jing, Lianhe Zhao, Jiajia Wang, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir Ali Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res. 49(Database-Issue): D18-D28 (2021) - 2020
- [j93]Shiyan Li, Hongxin Liu, Shiyu Bian, Xianzheng Sha, Yixue Li, Yin Wang:
The accelerated aging model reveals critical mechanisms of late-onset Parkinson's disease. BioData Min. 13(1): 4 (2020) - [j92]Leilei Wu, Qinfang Deng, Ze Xu, Songwen Zhou, Chao Li, Yi-Xue Li:
A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA. BMC Bioinform. 21(1): 127 (2020) - [j91]Yidi Sun, Chen Li, Shichao Pang, Qianlan Yao, Luonan Chen, Yixue Li, Rong Zeng:
Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer. Genom. Proteom. Bioinform. 18(5): 525-538 (2020) - [j90]Hong Sun, Yangfan Guo, Xiaoping Lan, Jia Jia, Xiaoshu Cai, Guoqing Zhang, Jingjing Xie, Qian Liang, Yixue Li, Guangjun Yu:
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. Nucleic Acids Res. 48(Database-Issue): D977-D982 (2020)
2010 – 2019
- 2019
- [j89]Shichao Pang, Junchen Yang, Yilei Zhao, Yixue Li, Jingfang Wang:
Computational prediction and functional analysis of arsenic-binding proteins in human cells. Quant. Biol. 7(3): 182-189 (2019) - 2018
- [j88]Lu Zhou, Qingyu Xiao, Jie Bi, Zhen Wang, Yixue Li:
RabGTD: a comprehensive database of rabbit genome and transcriptome. Database J. Biol. Databases Curation 2018: bay075 (2018) - [j87]Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li, Yuan-Yuan Li:
Differential networking meta-analysis of gastric cancer across Asian and American racial groups. BMC Syst. Biol. 12(4): 17-28 (2018) - 2017
- [j86]Zhen Li, Qianlan Yao, Songjian Zhao, Zhen Wang, Yixue Li:
Protein coding gene CRNKL1 as a potential prognostic biomarker in esophageal adenocarcinoma. Artif. Intell. Medicine 76: 1-6 (2017) - [j85]Quanxue Li, Junyi Li, Wentao Dai, Yi-Xue Li, Yuan-Yuan Li:
Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. Artif. Intell. Medicine 77: 12-22 (2017) - [j84]Ru-Dong Li, Guohui Ding, Yixue Li:
Virtualisation of gene knockout experiments based on kinetic modelling: Escherichia coli as an algorithmic case. Int. J. Comput. Biol. Drug Des. 10(2): 157-188 (2017) - [j83]Zhen Wang, Zefeng Wang, Yixue Li:
Strategic planning for national biomedical big data infrastructure in China. Quant. Biol. 5(3): 272-275 (2017) - 2016
- [j82]Zhi Liu, Tuantuan Gui, Zhen Wang, Hong Li, Yunhe Fu, Xiao Dong, Yixue Li:
cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data. Bioinform. 32(21): 3291-3297 (2016) - [j81]Jing Yang, Su-Juan Wu, Shao-You Yang, Jia-Wei Peng, Shi-Nuo Wang, Fu-Yan Wang, Yu-Xing Song, Ting Qi, Yi-Xue Li, Yuan-Yuan Li:
DNetDB: The human disease network database based on dysfunctional regulation mechanism. BMC Syst. Biol. 10: 36 (2016) - [j80]Wentao Dai, Aiping Wu, Liang-Xiao Ma, Yi-Xue Li, Taijiao Jiang, Yuan-Yuan Li:
A novel index of protein-protein interface propensity improves interface residue recognition. BMC Syst. Biol. 10(4): 381-392 (2016) - [j79]Su-Juan Wu, Junyi Li, Mushui Cao, Jing Yang, Yi-Xue Li, Yuan-Yuan Li:
A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. BMC Syst. Biol. 10(S-3): 71 (2016) - [c11]Yi-Xue Li:
Whole genome sequencing of disease animal models. BIBM 2016: 2 - 2015
- [j78]Yingli Lv, Shuyuan Wang, Fanlin Meng, Lei Yang, Zhifeng Wang, Jing Wang, Xiaowen Chen, Wei Jiang, Yixue Li, Xia Li:
Identifying novel associations between small molecules and miRNAs based on integrated molecular networks. Bioinform. 31(22): 3638-3644 (2015) - [j77]Jing Yang, Su-Juan Wu, Yi-Xue Li, Yuan-Yuan Li:
DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism. Bioinform. 31(23): 3870-3872 (2015) - [j76]Hong Sun, Shuang Yang, Liangliang Tun, Yixue Li:
IAOseq: inferring abundance of overlapping genes using RNA-seq data. BMC Bioinform. 16(S-1): S3 (2015) - [j75]Bo Sun, Menghuan Zhang, Peng Cui, Hong Li, Jia Jia Dong, Yixue Li, Lu Xie:
Nonsynonymous Single-Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases. Comput. Math. Methods Medicine 2015: 124630:1-124630:12 (2015) - [j74]Tiancheng Liu, Lin Yu, Lei Liu, Hong Li, Yixue Li:
Comparative Transcriptomes and EVO-DEVO Studies Depending on Next Generation Sequencing. Comput. Math. Methods Medicine 2015: 896176:1-896176:10 (2015) - [j73]Tuantuan Gui, Xiao Dong, Ru-Dong Li, Yixue Li, Zhen Wang:
Identification of Hepatocellular Carcinoma-Related Genes with a Machine Learning and Network Analysis. J. Comput. Biol. 22(1): 63-71 (2015) - 2014
- [j72]Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yang, Michael O. Glocker, Liang-Xiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li, Lu Xie:
SysPTM 2.0: an updated systematic resource for post-translational modification. Database J. Biol. Databases Curation 2014 (2014) - [j71]Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, Yixue Li:
The 3DGD: a database of genome 3D structure. Bioinform. 30(11): 1640-1642 (2014) - [j70]Yixue Li, Luonan Chen:
Big Biological Data: Challenges and Opportunities. Genom. Proteom. Bioinform. 12(5): 187-189 (2014) - 2013
- [j69]Huayong Xu, Hui Yu, Kang Tu, Qianqian Shi, Chaochun Wei, Yuan-Yuan Li, Yi-Xue Li:
cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. BMC Syst. Biol. 7(S-2): S7 (2013) - [j68]Shan Cong, Xiao-Tu Ma, Yi-Xue Li, Jing-Fang Wang:
Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study. J. Chem. Inf. Model. 53(6): 1350-1357 (2013) - [j67]Adhemar Zerlotini, Eric R. G. R. Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil D. Young, Robin B. Gasser, Anna V. Protasio, Matthew Berriman, David S. Roos, Jessica C. Kissinger, Guilherme C. Oliveira:
SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Res. 41(Database-Issue): 728-731 (2013) - [c10]Piyush Diwan, Patricia Carey, Eric Franz, Yixue Li, Thomas Bitterman, David E. Hudak, Rajiv Ramnath:
Applying software product line engineering in building web portals for supercomputing services. SAC 2013: 1765-1771 - 2012
- [j66]Hui Yu, Kang Tu, Yi-Jie Wang, Jun-Zhe Mao, Lu Xie, Yuan-Yuan Li, Yi-Xue Li:
Combinatorial network of transcriptional regulation and microRNA regulation in human cancer. BMC Syst. Biol. 6: 61 (2012) - [j65]Chuanli Wang, Longyun Guo, Yixue Li, Zhuo Wang:
Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis. BMC Syst. Biol. 6(S-2): S9 (2012) - [j64]Yin Wang, Yuhua Zhou, Yixue Li, Zongxin Ling, Yan Zhu, Xiaokui Guo, Hong Sun:
An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification. BMC Syst. Biol. 6(S-3): S12 (2012) - [j63]Shu-Hao Yu, Lulu Zheng, Yun Li, Chunyan Li, Chenchen Ma, Yixue Li, Xuan Li, Pei Hao:
A cross-species analysis method to analyze animal models' similarity to human's disease state. BMC Syst. Biol. 6(S-3): S18 (2012) - [j62]Yajun Wang, Yao Yu, Bohu Pan, Pei Hao, Yixue Li, Zhifeng Shao, Xiaogang Xu, Xuan Li:
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. BMC Syst. Biol. 6(S-3): S21 (2012) - [j61]Ying Wang, Xiaolin Wu, Dong-Qing Wei, Yi-Xue Li, Jing-Fang Wang:
Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling. J. Chem. Inf. Model. 52(9): 2422-2429 (2012) - [j60]Ying He, Menghuan Zhang, Yuanhu Ju, Zhong-Hao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler, Yixue Li, Guoqing Zhang, Lu Xie:
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Res. 40(Database-Issue): 964-971 (2012) - [j59]Xin Zhao, Qi Liu, Qingqing Cai, Yanyun Li, Congjian Xu, Yixue Li, Zuofeng Li, Xiaoyan Zhang:
Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acids Res. 40(Database-Issue): 1041-1046 (2012) - [c9]Huayong Xu, Hui Yu, Kang Tu, Qianqian Shi, Chaochun Wei, Yuanyuan Li, Yixue Li:
cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets. ISB 2012: 113-117 - [c8]Bin Kang, Yuan-Yuan Li, Yixue Li:
Anti-clustering of circadian gene expression in mouse liver genome. ISB 2012: 273-279 - 2011
- [j58]Qianghu Wang, Jie Sun, Meng Zhou, Haixiu Yang, Yan Li, Xiang Li, Sali Lv, Xia Li, Yixue Li:
A novel network-based method for measuring the functional relationship between gene sets. Bioinform. 27(11): 1521-1528 (2011) - [j57]Kailin Tang, Ruixin Zhu, Yixue Li, Zhi-Wei Cao:
Discrimination of Approved Drugs from Experimental Drugs by Learning Methods. BMC Bioinform. 12: 157 (2011) - [j56]Hui Yu, Bao-Hong Liu, Zhi-Qiang Ye, Chun Li, Yi-Xue Li, Yuan-Yuan Li:
Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. BMC Bioinform. 12: 315 (2011) - [j55]Yan Ji, Yixiang Shi, Guohui Ding, Yixue Li:
A new strategy for better genome assembly from very short reads. BMC Bioinform. 12: 493 (2011) - [j54]Guangyong Zheng, Haibo Wang, Chaochun Wei, Yixue Li:
iGepros: an integrated gene and protein annotation server for biological nature exploration. BMC Bioinform. 12(S-14): S6 (2011) - [j53]Ru-Dong Li, Yuan-Yuan Li, Lingyi Lu, Cong Ren, Yi-Xue Li, Lei Liu:
An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis. BMC Syst. Biol. 5(S-1): S12 (2011) - [j52]Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Yejun Tan, Zhidong Tu, Yixue Li, Hongyue Dai, Lu Xie:
The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. Int. J. Comput. Biol. Drug Des. 4(1): 5-18 (2011) - [j51]Yun Li, Kang Tu, Siyuan Zheng, Jingfang Wang, Yixue Li, Pei Hao, Xuan Li:
Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds. J. Bioinform. Comput. Biol. 9(4): 503-519 (2011) - [j50]Jue Li, Dong-Qing Wei, Jing-Fang Wang, Yi-Xue Li:
A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations. J. Chem. Inf. Model. 51(12): 3217-3225 (2011) - [j49]Zhimin Huang, Liang Zhu, Yan Cao, Geng Wu, Xinyi Liu, Yingyi Chen, Qi Wang, Ting Shi, Yaxue Zhao, Yuefei Wang, Weihua Li, Yixue Li, Haifeng Chen, Guoqiang Chen, Jian Zhang:
ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 39(Database-Issue): 663-669 (2011) - [j48]Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Yuzong Chen, Yixue Li, Zhi-Wei Cao:
HIT: linking herbal active ingredients to targets. Nucleic Acids Res. 39(Database-Issue): 1055-1059 (2011) - [c7]Kaiyan Feng, Junhui Gao, Kairui Feng, Lei Liu, Yixue Li:
Active and Passive Nearest Neighbor Algorithm: A Newly-Developed Supervised Classifier. ICIC (2) 2011: 189-196 - [e1]Limin Angela Liu, Dong-Qing Wei, Yixue Li, Huimin Lei:
Handbook of Research on Computational and Systems Biology - Interdisciplinary Applications. IGI Global 2011, ISBN 978-1-60960-491-2 [contents] - 2010
- [j47]Bao-Hong Liu, Hui Yu, Kang Tu, Chun Li, Yi-Xue Li, Yuan-Yuan Li:
DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinform. 26(20): 2637-2638 (2010) - [j46]Yun-Qin Chen, Hui Yu, Yi-Xue Li, Yuan-Yuan Li:
Sorting out inherent features of head-to-head gene pairs by evolutionary conservation. BMC Bioinform. 11(S-11): S16 (2010) - [j45]Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie:
TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinform. 11(S-11): S5 (2010) - [j44]Yixiang Shi, Yi-Xue Li, Yuan-Yuan Li:
Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution. BMC Bioinform. 11(S-11): S9 (2010) - [j43]Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, Yixue Li:
dbDEPC: a database of Differentially Expressed Proteins in human Cancers. Nucleic Acids Res. 38(Database-Issue): 658-664 (2010) - [c6]Tao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie:
Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. BCB 2010: 502-507
2000 – 2009
- 2009
- [j42]Zhen Wang, Guohui Ding, Zhong-Hao Yu, Lei Liu, Yixue Li:
CHSMiner: a GUI tool to identify chromosomal homologous segments. Algorithms Mol. Biol. 4 (2009) - [j41]Hui Yu, Fudong Yu, Guoqing Zhang, Xiang Shen, Yun-Qin Chen, Yuan-Yuan Li, Yi-Xue Li:
DBH2H: vertebrate head-to-head gene pairs annotated at genomic and post-genomic levels. Database J. Biol. Databases Curation 2009 (2009) - [j40]Hong Li, Guohui Ding, Lu Xie, Yixue Li:
PAnnBuilder: an R package for assembling proteomic annotation data. Bioinform. 25(8): 1094-1095 (2009) - [j39]Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li:
Human gene expression sensitivity according to large scale meta-analysis. BMC Bioinform. 10(S-1) (2009) - [j38]Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li:
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinform. 10: 264 (2009) - [j37]Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang:
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. J. Comput. Biol. 16(8): 1183-1193 (2009) - [j36]Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, Hans-Jürgen Thiesen:
SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res. 37(Database-Issue): 267-273 (2009) - [j35]Su-Jun Li, Mao Peng, Hong Li, Boshu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li, Rong Zeng:
Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res. 37(Database-Issue): 907-912 (2009) - [j34]Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee, Yixue Li:
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. Nucleic Acids Res. 37(Database-Issue): 913-920 (2009) - 2008
- [j33]Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac:
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinform. 24(1): 102-109 (2008) - [j32]Siyuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, Yixue Li:
MPSQ: a web tool for protein-state searching. Bioinform. 24(20): 2412-2413 (2008) - [j31]Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li:
ITFP: an integrated platform of mammalian transcription factors. Bioinform. 24(20): 2416-2417 (2008) - [j30]Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, Yixue Li:
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinform. 9(S-1) (2008) - [j29]Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Yixue Li, Zhi-Wei Cao:
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies. BMC Bioinform. 9(S-12) (2008) - [j28]Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li:
The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. BMC Bioinform. 9 (2008) - [j27]Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, Yixue Li:
EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. Nucleic Acids Res. 36(Database-Issue): 255-262 (2008) - [j26]Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yi-Xue Li, Tieliu Shi:
AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. Nucleic Acids Res. 36(Database-Issue): 999-1008 (2008) - [j25]Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li:
Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation. PLoS Comput. Biol. 4(3) (2008) - [c5]Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang:
A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. RECOMB 2008: 167-180 - 2007
- [j24]Ziliang Qian, Lingyi Lu, Xiao-Jun Liu, Yu-Dong Cai, Yixue Li:
An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization. Bioinform. 23(18): 2449-2454 (2007) - [j23]Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao:
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinform. 8 (2007) - [j22]Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li:
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinform. 8 (2007) - [j21]Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li:
Modular co-evolution of metabolic networks. BMC Bioinform. 8 (2007) - [j20]Lingyi Lu, Ziliang Qian, Yu-Dong Cai, Yixue Li:
ECS: An automatic enzyme classifier based on functional domain composition. Comput. Biol. Chem. 31(3): 226-232 (2007) - [c4]Xiaojing Wang, Wu Wei, Siyuan Zheng, Zhi-Wei Cao, Yixue Li:
Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin. International Conference on Computational Science (2) 2007: 363-369 - [c3]Yixue Li:
Biological data integration and high-performance computing. China HPC 2007: 51-61 - 2006
- [j19]Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He, Yi-Xue Li:
In silico discovery of human natural antisense transcripts. BMC Bioinform. 7: 18 (2006) - [j18]Xiaojing Yu, Chuan Wang, Yixue Li:
Classification of protein quaternary structure by functional domain composition. BMC Bioinform. 7: 187 (2006) - [j17]Peilin Jia, Tieliu Shi, Yudong Cai, Yixue Li:
Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinform. 7: 271 (2006) - [j16]Jing Zhao, Hong Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li:
Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinform. 7: 386 (2006) - [j15]Sujun Li, Boshu Liu, Rong Zeng, Yudong Cai, Yixue Li:
Predicting O-glycosylation sites in mammalian proteins by using SVMs. Comput. Biol. Chem. 30(3): 203-208 (2006) - [j14]Guoqing Zhang, Zhi-Wei Cao, Qingming Luo, Yu-Dong Cai, Yixue Li:
Operon prediction based on SVM. Comput. Biol. Chem. 30(3): 233-240 (2006) - [j13]Xing-Ming Zhao, Ji-Xiang Du, Hong-Qiang Wang, Yunping Zhu, Yixue Li:
A new technique for selecting features from protein sequences. Int. J. Pattern Recognit. Artif. Intell. 20(2): 271-283 (2006) - [j12]Chun-Hou Zheng, Yan Chen, Xiu-Xia Li, Yi-Xue Li, Yunping Zhu:
Tumor classification based on independent component analysis. Int. J. Pattern Recognit. Artif. Intell. 20(2): 297-310 (2006) - [j11]Zhuo Fang, Jiong Yang, Yixue Li, Qing-ming Luo, Lei Liu:
Knowledge guided analysis of microarray data. J. Biomed. Informatics 39(4): 401-411 (2006) - [j10]Qiang Lu, Pei Hao, Vasa Curcin, Wei-Zhong He, Yuan-Yuan Li, Qing-ming Luo, Yike Guo, Yi-Xue Li:
KDE Bioscience: Platform for bioinformatics analysis workflows. J. Biomed. Informatics 39(4): 440-450 (2006) - [j9]Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li:
Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance. PLoS Comput. Biol. 2(7) (2006) - [j8]Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, Yixue Li:
Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families. PLoS Comput. Biol. 2(8) (2006) - [j7]Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li:
Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance. PLoS Comput. Biol. 2(8) (2006) - [c2]Yixue Li, Yu Xu, Gengzhong Feng, Wenqiang Dai:
On Loan-to-Value Ratios of Inventory Financing with Doubly Stochastic Poisson Default Processes. APSCC 2006: 663-666 - [c1]Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yi-Xue Li, Lei Liu:
Comparison of Modularization Methods in Application to Different Biological Networks. VDMB 2006: 185-195 - 2005
- [j6]Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Boshu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong:
MPSS: an integrated database system for surveying a set of proteins. Bioinform. 21(9): 2142-2143 (2005) - [j5]Jingchun Sun, Jinlin Xu, Zhen Liu, Qi Liu, Aimin Zhao, Tieliu Shi, Yi-Xue Li:
Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinform. 21(16): 3409-3415 (2005) - [j4]Guang-Zheng Zhang, De-Shuang Huang, Yunping Zhu, Yi-Xue Li:
Improving protein secondary structure prediction by using the residue conformational classes. Pattern Recognit. Lett. 26(15): 2346-2352 (2005) - 2004
- [j3]Yong Deng, Qi Liu, Yi-Xue Li:
Scoring hidden Markov models to discriminate -barrel membrane proteins. Comput. Biol. Chem. 28(3): 189-194 (2004) - 2003
- [j2]Qi Liu, Yisheng Zhu, Baohua Wang, Yi-Xue Li:
A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins. Comput. Biol. Chem. 27(1): 69-76 (2003) - [j1]Qi Liu, Yisheng Zhu, Baohua Wang, Yi-Xue Li:
Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure. Comput. Biol. Chem. 27(3): 355-361 (2003)
Coauthor Index
Yuanyuan Li
aka: Yuan-Yuan Li
aka: Yuan-Yuan Li
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