Publications

2022 (Click to expand or collapse the publication details)

  1. Miaomiao Li, Tianyang Zhang, Wei Chen*. (2022) Development of necroptosis-related gene signature to predict the prognosis of colon adenocarcinoma. Front Genet, DOI:10.3389/fgene.2022.1051800. [pdf]
  2. Fulei Nie, Qiang Tang, Ying Liu, Huaizhi Qin, Shilong Liu, Meng Wu, Pengmian Feng*, Wei Chen*. (2022) RNAME: A comprehensive database of RNA modification enzymes. Computational and Structural Biotechnology Journal, 20(2022)6244–6249. [pdf]
  3. Tianyang Zhang, Qiang Tang, Fulei Nie, Qi Zhao, Wei Chen*. (2022) DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters. Briefings in Bioinformatics, DOI:10.1093/bib/bbac447. [pdf]
  4. Qiang Tang, Fulei Nie, Qi Zhao, Wei Chen*. (2022) A merged molecular representation deep learning method for blood-brain barrier permeability prediction. Briefings in Bioinformatics, 23(5):1-10. [pdf]
  5. Hua Tang, Qin Yang, Qiang Tang, Xianhai Li, Weijun Ding, Wei Chen*. (2022) Integrated transcriptomics unravels implications of glycosylation-regulating signature in diagnosis, prognosis and therapeutic benefits of hepatocellular carcinoma. COMPUTERS IN BIOLOGY AND MEDICINE, 148:105886. [pdf]
  6. Shaoqin Shen, Nan Li, Yujie Wang, Rong Zhou, Pengchuan Sun, Hao Lin, Wei Chen, Tong Yu, Zhuo Liu, Zhiyuan Wang, Xiao Tan, Changping Zhu, Shuyan Feng, Yu Zhang, Xiaoming Song. (2022) High‐quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways. PLANT BIOTECHNOLOGY JOURNAL, 20(11):2107-2122. [pdf]
  7. Liu Xiang, Yue Lin, Xianhai Li, Qiang Tang, Fanbo Meng, Wei Chen*. (2022) The underlying mechanisms of Wujiayizhi granule in treating Alzheimer's disease. Current Bioinformatics, DOI: 10.2174/1574893617666220509190343. [pdf]
  8. Yue Lin, Liu Xiang, Xianhai Li, Qiang Tang, Fanbo Meng, Wei Chen*. (2022) Exploring the Mechanism of Yi-Jing Decoction in Treating Polycystic Ovary Syndrome by Using Network Pharmacology. Current Medicinal Chemistry, DOI:10.2174/0929867329666220508180611. [pdf]
  9. Fanbo Meng, Qiang Tang, Tianzhe Chu, Xianhai Li, Yue Lin, Xiaoming Song*, Wei Chen*. (2022) TCMPG: an Integrative Database for Traditional Chinese Medicine Plant Genome. Horticulture Research, 9:uhac060. [pdf]
  10. Xianhai Li, Qiang Tang, Fanbo Meng, PufengDu*, Wei Chen*. (2022) INPUT: An intelligent network pharmacology platform unique for traditional Chinese medicine. Computational and Structural Biotechnology Journal, 20:1345-1351. [pdf]
  11. Xianhai Li, Liu Xiang, Yue Lin, Qiang Tang, Fanbo Meng, Wei Chen*. (2022) Computational Analysis Illustrates the Mechanism of Qingfei Paidu Decoction in Blocking the Transition of COVID-19 Patients from Mild to Severe Stage. Current Gene Therapy, 22(3):277-289. [pdf]

2021 (Click to expand or collapse the publication details)

  1. Meng Wu, Fulei Nie, Haibin Liu, Tianyang Zhang, Miaomiao Li, Xiaoming Song*, Wei Chen*. (2021) The evolution of N6-methyladenosine regulators in plants. Methods, S1046-2023(21)00270-X. [pdf]
  2. Zhaotian Zhang, Qiang Tang, Qiong Wang, Fulei Nie, Limei Sun, Delun Luo, Wei Chen*, Xiaoyan Ding*. (2021) HODD: a manually curated database of human ophthalmic diseases with symptom characteristics and genetic variants towards facilitating quick and definite diagnosis. Interdisciplinary Sciences: Computational Life Sciences, doi:10.1007/s12539-021-00494-9. [pdf]
  3. Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan, Jun Cheng, Hailong Zheng, Dong Wang*, Xi Su*, Wei Chen* and Yan Huang*. (2021) RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. Nucleic Acids Research, 50(D1):D326-D332. [pdf]
  4. Fanbo Meng, Tianzhe Chu, Qiang Tang, Wei Chen*. (2021) A tetraploidization event shaped the Aquilaria sinensis genome and contributed to the ability of sesquiterpenes synthesis. BMC Genomics , 22(1):647. [pdf]
  5. Hasan Zulfiqar, Fu-Ying Dao, Hui Yang, Hao Lv, Peng Zhou, Wei Chen*, Hao Lin*. (2021) Identification of Potent Inhibitors against SARS-Cov-2 through Computational Drug Repurposing Study. Current Bioinformatics, 16:1320-1327. [pdf]
  6. Pengmian Feng, Wei Chen*. (2021) iRNA-m5U: a sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisia. Methods, S1046-2023(21)00105-5. [pdf]
  7. Qiang Tang, Fulei Nie, Juanjuan Kang, Wei Chen*. (2021) mRNALocater: enhance the prediction accuracy of eukaryotic mRNA subcellular localization by using model fusion strategy. Molecular Therapy, 29(8):2617-2623. [pdf]
  8. Xianhai Li, Hua Tang, Qiang Tang, Wei Chen*. (2021) Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking. Frontiers Cell and Developmental Biology, 9:638366. [pdf]
  9. Wenya Zhang, Junhai Xu*, Jun Wang, Hangyu Liu, Wei Chen*, Pufeng Du*.(2021) KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides. Briefings in Bioinformatics, 22(4):bbaa284. [pdf]
  10. Chichi Dai, Pengmian Feng, Lizhen Cui, Ran Su*,Wei Chen*, Leyi Wei*. (2021) Iterative feature representation algorithm to improve the predictive performance of N7-methylguanosine sites. Briefings in Bioinformatics, 22(4):bbaa278. [pdf]
  11. Meng-Lu Liu, Wei Su, Zheng-Xing Guan, Dan Zhang, Wei Chen*, Li Liu*, Hui Ding*. (2021) An Overview on Predicting Protein Subchloroplast Localization by Using Machine Learning Methods. Current Protein & Peptide Science, 21(12):1229-1241. [pdf]
  12. Zhaoyue Zhang, Yuye Yang, Hui Ding, Dong Wang*, Wei Chen*, Hao Lin*. (2021) Design powerful predictor for mRNA subcellular location prediction in Homo sapiens. Briefings in Bioinformatics, 22(1):526-535. [pdf]
  13. PengmianFeng*, WeiweiLiu, CongHuang, ZhaohuiTang. (2021) Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions. International Journal of Biological Macromolecules, 167:1575-1578. [pdf]

2020 (Click to expand or collapse the publication details)

  1. Qiang Tang, Fulei Nie, Juanjuan Kang, Wei Chen*. (2020) ncPro-ML: an integrated computational tool for identifying non-coding RNA promoters in multiple species. Computational and Structural Biotechnology Journal, 18:2445-2452. [pdf]
  2. Fulei Nie, Pengmian Feng, Xiaoming Song, Meng Wu, Qiang Tang, Wei Chen*. (2020) RNAWRE: a resource of writers, readers and erasers of RNA modifications. Database, 2020:baaa049. [pdf]
  3. Kewei Liu, Lei Cao, Pufeng Du, Wei Chen*. (2020) im6A-TS-CNN: identifying N6-methyladenine site in multiple tissues by using convolutional neural network. Molecular Therapy-Nuleic Acids, 21:1044-1049. [pdf]
  4. Pengmian Feng*, Lijing Feng.(2020) Recent advances on antioxidant identification based on machine learning methods. Current Drug Metabolism, 21(10):804-809. [pdf]
  5. Wei Chen*, Pengmian Feng, Kewei Liu, Meng Wu, Hao Lin*. (2020) Computational Identification of Small Interfering RNA Targets in SARS-CoV-2. Virologica Sinica, 35(3):359-361. [pdf]
  6. Hao Lv, Fu-Ying Dao, Dan Zhang, Zheng-Xing Guan, Hui Yang, Wei Su, Meng-Lu Liu, Hui Ding, Wei Chen, Hao Lin*. (2020) iDNA-MS: an integrated computational tool for detecting DNA modification sites in multiple genomes. iScience, 23(4):100991. [pdf]
  7. Xiaoming Song, Jinpeng Wang, ..., Wei Chen, ..., Xiyin Wang*. (2020) Deciphering the High Quality Genome Sequence of Coriander that Causes Controversial Feeling. Plant Biotechnology Journal, 18(6): 1444-1456. [pdf]
  8. Wei Chen*, Pengmian Feng, Fulei Nie. (2020) iATP: a sequence based method for identifying anti-tubercular peptides. Medicinal Chemistry, 16(5):620-625. [pdf]
  9. Hui Yang, Wuritu Yang, Fu-Ying Dao, Hao Lv, Hui Ding*, Wei Chen*, Hao Lin*. (2020) A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae. Briefings in Bioinformatics, 21(5):1568-1580. [pdf]
  10. Hao Lv, Zimei Zhang, Shihao Li, Jiuxin Tan, Wei Chen*, Hao Lin*.(2020) Evaluation of different computational methods on 5-methylcytosine sites identification. Briefings in Bioinformatics, 21(3):982-995. [pdf]
  11. Xianhai Li, Qiang Tang, Hua Tang and Wei Chen*. (2020) Identifying Antioxidant Proteins by Combining Multiple Methods. Frontiers in Bioengineering and Biotechnology, 8:858. [pdf]
  12. Pengmian Feng*, Lijing Feng.(2020) Sequence based prediction of pattern recognition receptors by using feature selection technique. International Journal of Biological Macromolecules, 162(1):931-934. [pdf]
  13. Qiang Tang, Juanjuan Kang, Jiaqing Yuan, Hua Tang, Xinahai Li, Hao Lin*, Jian Huang*, Wei Chen*. (2020) DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species. Bioinformatics, 36(11):3327-3335. [pdf]
  14. Kewei Liu,Wei Chen*. (2020) iMRM: a platform for simultaneously identifying multiple kinds of RNA modifications. Bioinformatics, 36(11):3336-3342. [pdf]
  15. Jun Wang, Pufeng Du*, Xinyu Xue, Guangping Li, Yuanke Zhou, Wei Zhao, Hao Lin, Wei Chen*. (2020) VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences. Bioinformatics, 36(4):1277-1278. [pdf]
  16. Wei Chen*, Kewei Liu. (2020) Analysis and Comparison of RNA Pseudouridine Site Prediction Tools. Current Bioinformatics,15(4):279 - 286. [pdf]
  17. Wei Chen*, Fulei Nie, Hui Ding*.(2020) Recent advances of computational methods for identifying bacteriophage virion proteins. Protein & Peptide Letters, 27:259-264. [pdf]
  18. Yuan Liu, Dasheng Chen, Ran Su*, Wei Chen* and Leyi Wei*. (2020) iRNA5hmC: the first predictor to identify RNA 5-hydroxymethylcytosine modifications using machine learning. Frontiers in Bioengineering and Biotechnology,8:227. [pdf]
  19. Xiaoming Song#, Fulei Nie#, Wei Chen#, ..., Xiyin Wang*.(2020) Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander.Horticulture Research,7:55. [pdf]
  20. Wei Chen. (2020) Editorial: Computational RNA Epigenetics. Current Genomics, 21(1):1. [pdf]
  21. Kewei Liu, Wei Chen*, Hao Lin*. (2020) XG-PseU: an eXtreme Gradient Boosting based method for identifying pseudouridine sites. Molecular Genetics and Genomics, 295: 13–21. [pdf]
  22. Liangsheng Zhang*, Fei Chen, ..., Wei Chen, ..., Yves Van de Peer, Haibao Tang. (2020) The water lily genome and the early evolution of flowering plants. Nature, 577(7788):79-84. [pdf]

2019 (Click to expand or collapse the publication details)

  1. Wei Chen*, Hao Lv, Fulei Nie, Hao Lin*. (2019) i6mA-Pred:Identifying DNA N6-methyladenine sites in the rice genome. Bioinformatics, 35(16):2796-2800. [pdf]
  2. Wei Chen*, Xiaoming Song, Hao Lv, Hao Lin*. (2019) iRNA-m2G: identifying N2-methylguanosine sites based on sequence derived information. Molecular Tehrapy-Nucleic Acids, 18:253-258. [pdf]
  3. Wei Chen*, Pengmian Feng, Xiaoming Song, Hao Lv, Hao Lin*. (2019) iRNA-m7G: identifying N7-methylguanosine sites by fusing multiple features. Molecular Tehrapy-Nucleic Acids, 18:269-274. [pdf]
  4. Shihao Li#, Jun Zhang#, Yawei Zhao, Fu-Ying Dao, Hui Ding*, Wei Chen*, Hua Tang* (2019) iPhoPred: a predictor for identifying phosphorylation sites in human protein. IEEE Access, 7: 177517 - 177528.
  5. Hao Lv, Fuying Dao, Zhengxing Guan, Dan Zhang, Jiuxin Tan, Yong Zhang*, Wei Chen* and Hao Lin*. (2019) iDNA6mA-Rice: a computational tool for detecting N6-methyladenine sites in rice. Frontiers in Genetics, 10:793. [pdf]
  6. Zhaochun Xu, Pengmian Feng, Hui Yang, Wei Chen*, Hao Lin*. (2019) iRNAD: a computational tool for identifying D modification sites in RNA sequence. Bioinformatics, 35(23):4922-4929.
  7. Hao Lin*, Zhiyong Liang, Hua Tang, Wei Chen*. (2019) Identifying sigma70 promoters with novel pseudo nucleotide composition. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(4): 1316-1321. [pdf]
  8. Fuying Dao, Hao Lv, Fang Wang, Chaoqin Feng, Hui Ding*, Wei Chen*, Hao Lin*. (2019) Identify origin of replication in Sccharomyces cerevisiae using two-step feature selection technique. Bioinformatics, 35(12):2075-2083. [pdf]
  9. Xiaojuan Zhu, Chaoqin Feng, Hongyan Lai, Wei Chen*, Hao Lin*. (2019) Predicting protein structural classes for low-similarity sequences by evaluating different features. Knowledge-Based Systems, 163: 787-793. [pdf]
  10. Jiuxin Tan, Hao Lv, Fang Wang, Fuying Dao, Wei Chen*, Hui Ding*. (2019) A survey for predicting enzyme family classes using machine learning methods. Current Drug Targets, 20(5):540-550. [pdf]
  11. Hongyan Lai, Zhaoyue Zhang, Zhendong Su, Wei Su, Hui Ding, Wei Chen*, Hao Lin*. (2019) iProEP: a computational predictor for predicting promoter. Molecular Therapy - Nucleic Acids, 17: 337-346. [pdf]
  12. ChaoqQin Feng, Zhaoyue Zhang, Xiaojuan Zhu, Yan Lin, Wei Chen*, Hua Tang*, Hao Lin*. (2019) iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators. Bioinformatics, 35(9): 1469-1477. [pdf]
  13. Pengmian Feng*, Zhenyi Wang. (2019) Recent Advances in computational methods for idetifying anticancer peptides, Current Drug Target, 20:481-487. [pdf]
  14. Pengmian Feng*, Zhaochun Xu, Hui Yang, Hao Lv, Hui Ding, Li Liu. (2019) Identification of D-modification sites by integrating heterogeneous features in Saccharomyces cerevisiae, Molecules, 24(3):380. [pdf]
  15. Wei Chen*, Pengmian Feng, Tao Liu, Dianchuan Jin. (2019) Recent advances in machine learning methods for predicting heat shock proteins. Current Drug Metabolism, 20(5): 540-550. [pdf]
  16. JiuXin Tan, Shi-Hao Li, Zimei Zhang, Cuixia Chen,Wei Chen*, Hua Tang*, Hao Lin*. (2019) Identification of hormone binding proteins based on machine learning methods. Mathematical Biosciences and Engineering, 16(4): 2466-2480. [pdf]
  17. Wei Chen*, Xiaoming Song, Hao Lin*. (2019) Combinatorial pattern of histone modifications in exon skipping event. Frontiers in Genetics, 10: 122. [pdf]
  18. Pengmian Feng, Hui Yang, Hui Ding, Hao Lin*, Wei Chen*, Kuochen Chou*. (2019) iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites sites by incorporating nucleotide physicochemical properties into PseKNC. Genomics, 111(1): 96-102. [pdf]
  19. Xiao-Juan Zhu, Chao-Qin Feng, Hong-Yan Lai, Wei Chen*, Hao Lin*. (2019) Predicting protein structural classes for low-similarity sequences by evaluating different features. Knowledge-Based Systems, 163: 787-793. [pdf]

2018 (Click to expand or collapse the publication details)

  1. Zhendong Su, Yan Huang, Zhaoyue Zhang, Yawei Zhao, Dong Wang, Wei Chen*, Kuochen Chou*, Hao Lin*. (2018) iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinformatics, 34(24): 4196-4204. [pdf]
  2. Hui Yang, Hao Lv, Hui Ding, Wei Chen*, Hao Lin*. (2018) iRNA-2OM: A sequence-based predictor for identifying 2’-O-methylation sites in Homo sapiens. Journal of Computational Biology, 25(11): 1266-1277. [pdf]
  3. HongYan Lai, Chao-Qin Feng, Zhaoyue Zhang, Hua Tang, Wei Chen*, Hao Lin*. (2018) A brief survey of machine learning application in cancerlectins identification. Current Gene Therapy, 18(5): 257-267. [pdf]
  4. Jinghui Cheng, Hui Yang, Menglu Liu, Wei Su, Pengmian Feng, Hui Ding*, Wei Chen*, Hao Lin*. (2018) Prediction of bacteriophage proteins located in the host cell using hybrid features. Chemometrics and Intelligent Laboratory Systems, 180: 64-69. [pdf]
  5. Jiu-Xin Tan, Fu-Ying Dao, Hao Lv, Peng-Mian Feng *, Hui Ding * (2018) Identifying Phage Virion Proteins by Using Two-Step Feature Selection Methods. Molecules, 23(8): 2000. [pdf]
  6. Wei Chen*, Pengmian Feng, Hui Ding, Hao Lin*. (2018) Classifying included and excluded exons in exon skipping event using histone modifications. Frontiers in Genetics, 9:433. [pdf]
  7. Wei Chen*, Hui Ding, Xu Zhou, Hao Lin*, Kuochen Chou*. (2018) iRNA(m6A)-PseDNC: Identifing N6-methyladenosine sites using pseudo dinucleotide composition. Analytical Biochemistry,561-562:59-65. [pdf]
  8. Hui Yang, Wangren Qiu, Guoqing Liu, Fengbiao Guo, Wei Chen*, Kuochen Chou*, Hao Lin*. (2018) iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC. International Journal of Biological Sciences, 14(8): 883-891. [pdf]
  9. Jidong Zhang, Pengmian Feng, Hao Lin*, Wei Chen*. (2018) Identifying RNA N6-methyladenosine sites in Escherichia coli genome. Frontiers in Microbiology, 9: 955. [pdf]
  10. Wei Chen*, Pengmian Feng, Hui Yang, Hui Ding, Hao Lin*, Kuochen Chou*. (2018) iRNA-3typeA: identifying 3-types of modification at RNA’s adenosine sites. Molecular Therapy-Nucleic Acids, 11: 468-474. [pdf]

2017 (Click to expand or collapse the publication details)

  1. Pengmian Feng, Jidong Zhang, Hua Tang, Wei Chen*, Hao Lin* (2017) Predicting the Organelle Location of Noncoding RNAs Using Pseudo Nucleotide Compositions. Interdisciplinary Sciences: Computational Life Sciences, 9: 540–544. [pdf]
  2. Wei Chen*, Hui Yang, Pengmian Feng, Hui Ding, Hao Lin*, (2017) iDNA4mC: identifying DNA N4methylcytosine sites based on nucleotide chemical properties. Bioinformatics, 33(22): 3518-3523. [pdf]
  3. Yawei Zhao, Zhen-Dong Su, Wuritu Yang, Hao Lin*, Wei Chen*, Hua Tang* (2017) IonchanPred 2.0: a tool to predict ion channels and their types. International Journal of Molecular Sciences, 18: 1838. [pdf]
  4. Pengmian Feng, Hui Ding, Hao Lin*, Wei Chen*. (2017) AOD: the antioxidant protein database. Scientific Reports, 7: 7449. [pdf]
  5. Fuying Dao, Hui Yang, Zhendong Su, Wuritu Yang, Yun Wu, Ding Hui, Wei Chen*, Hua Tang*, Hao Lin*. (2017) Recent advances in conotoxin classification by using machine learning methods. Molecules, 22: 1057. [pdf]
  6. Hongyan Lai, Xinxin Chen, Wei Chen, Hua Tang*, Hao Lin*. (2017) Sequence-based predictive modeling to identify cancerlectins. Oncotarget, 8(17): 28169-28175. [pdf]
  7. Pengmian Feng, Hui Ding, Hui Yang, Wei Chen*, Hao Lin*, and Kuochen Chou*. (2017) iRNA-PseColl: Identifying the occurrence sites of different RNA modifications by incorporating collective effects of nucleotides into PseKNC. Molecular Therapy - Nucleic Acids, 7: 155–163. [pdf]
  8. Wei Chen*, Hua Tang, Hao Lin*. (2017) MethyRNA: a web server for identification of N6methyladenosine sites. Journal of Biomolecular Structure & Dynamics, 35(3): 683-687. [pdf]
  9. Zhiyong Liang, Hongyan Lai, Huan Yang, Changjian Zhang, Hui Yang, Huan-Huan Wei, Xin-Xin Chen, Ya-Wei Zhao, Zhen-Dong Su, Wen-Chao Li, En-Ze Deng, Hua Tang, Wei Chen*, Hao Lin* (2017) Pro54DB: a database for experimentally verified sigma-54 promoters. Bioinformatics, 33(3): 467-469. [pdf]
  10. Wei Chen*, Pengmian Feng, Hui Yang, Hui Ding, Hao Lin*, Kuochen Chou. (2017) iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences. Oncotarget, 8(3): 4208-4217. [pdf]
  11. Wei Chen*, Hao Lin*. (2017) Recent Advances in Identification of RNA Modifications. Noncoding RNA, 3(1):1. [pdf]
  12. Jing Ye, Wei Chen*, Dianchuan Jin. (2017) Predicting the Types of Plant Heat Shock Proteins. Letters in Organic Chemistry, 14(9):684-689. [pdf]
  13. Wei Chen*,Pengwei Xing, Quan Zou*. (2017) Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines. Scienctific Reports,7:40242. [pdf]
  14. Jinpeng Wang, Pengchuan Sun, Yuxian Li, Yinzhe Liu, Jigao Yu, Xuelian Ma, Sangrong Sun, Nanshan Yang, Ruiyan Xia, Tianyu Lei, Xiaojian Liu, Beibei Jiao, Yue Xing, Weina Ge, Li Wang, Zhenyi Wang, Xiaoming Song, Min Yuan, Di Guo, Lan Zhang, Jiaqi Zhang, Dianchuan Jin, Wei Chen, Yuxin Pan, Tao Liu, Ling Jin, Jinshuai Sun, Jiaxiang Yu, Rui Cheng, Xueqian Duan, Shaoqi Shen, Jun Qin, Mengchen Zhang, Andrew H. Paterson, Xiyin Wang*. (2017) Hierarchically aligning 10 legume genomes establishes a family-level genomics platform. Plant Physiology,174(1):284-300. [pdf]
  15. Jinpeng Wang, Pengchuan Sun, Yuxian Li, Yinzhe Liu, Nanshan Yang, Jigao Yu, Xuelian Ma, Sangrong Sun, Ruiyan Xia, Xiaojian Liu, Dongcen Ge, Sainan Luo, Yinmeng Liu, Youting Kong, Xiaobo Cui, Tianyu Lei, Li Wang, Zhenyi Wang, Weina Ge, Lan Zhang, Xiaoming Song, Min Yuan, Di Guo, Dianchuan Jin, Wei Chen, Yuxin Pan, Tao Liu, Guixian Yang, Yue Xiao, Jinshuai Sun, Cong Zhang, Zhibo Li, Haiqing Xu, Xueqian Duan, Shaoqi Shen, Zhonghua Zhang, Sanwen Huang, and Xiyin Wang*. (2017) An Overlooked Paleo tetraploidization in Cucurbitaceae. Molecular Biology and Evolution, 35(1):16-26. [pdf]

2016 (Click to expand or collapse the publication details)

  1. Changjian Zhang, Hua Tang, Wenchao Li, Hao Lin*, Wei Chen*, Kuochen Chou*. (2016) iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition. Oncotarget, 7(43): 69783-69793. [pdf]
  2. Wei Chen*, Pengmian Feng, Hui Ding, Hao Lin*. (2016) PAI: Predicting adenosine to inosine editing sites by using pseudo nucleotide compositions. Scientific Reports, 6: 3512. [pdf]
  3. Yawei Zhao, Hongyan Lai, Hua Tang, Wei Chen*, Hao Lin*. (2016) Prediction of phosphothreonine sites in human proteins by fusing different features. Scientific Reports, 6: 34817. [pdf]
  4. Wei Chen*, Pengmian Feng, Hui Ding, Hao Lin*. (2016) Identifying N(6)-methyladenosine sites in the Arabidopsis thaliana transcriptome. Molecular Genetics and Genomics, 291(6): 2225-2229. [pdf]
  5. Pengmian Feng, Hui Ding, Wei Chen*, Hao Lin*. (2016) Identifying RNA 5-methylcytosine sites via pseudo nucleotide compositions. Molecular BioSystems, 12(11): 3307-3311. [pdf]
  6. Hui Ding, Wuritu Yang, Hua Tang, Pengmian Feng, Jian Huang, Wei Chen*, Hao Lin*. (2016) PHYPred: a tool for identifying bacteriophage enzymes and hydrolases. Virologica Sinica, 31(2): 350-352. [pdf]
  7. Huan Yang, Hua Tang, Xinxin Chen, Changjian Zhang, Pan-Pan Zhu, Hui Ding, Wei Chen*, Hao Lin*. (2016) Identification of secretory proteins in mycobacterium tuberculosis using pseudo amino acid composition. BioMed Research International, 2016: 5413903. [pdf]
  8. Wei Chen*, Pengmian Feng, Hua Tang, Hui Ding, Hao Lin*. (2016) RAMPred: identifying the N-1-methyladenosine sites in eukaryotic transcriptomes. Scientific Reports, 6: 31080. [pdf]
  9. Hua Tang*, Ping Zou, Chunmei Zhang, Rong Chen, Wei Chen*, Hao Lin*. (2016) Identification of apolipoprotein using feature selection technique. Scientific Reports, 6: 30441. [pdf]
  10. Wei Chen*, Hua Tang, Jing Ye, Hao Lin*, Kuochen Chou*. (2016) iRNA-PseU: Identifying RNA pseudouridine sites. Molecular Therapy - Nucleic Acids, 5: e332. [pdf]
  11. Hua Tang*, Zhendong Su, Huanhuan Wei, Wei Chen, Hao Lin*. (2016) Prediction of cell-penetrating peptides with feature selection techniques. Biochemical and Biophysical Research Communications, 477: 150-154. [pdf]
  12. Xinxin Chen, Hua Tang, Wenchao Li, Hao Wu, Wei Chen*, Hui Ding*, Hao Lin*. (2016) Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition. BioMed Research International, 2016: 1654623. [pdf]
  13. Wei Chen*, Pengmian Feng, Hua Tang, Hui Ding, Hao Lin*. (2016) Identifying 2′-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions. Genomics, 107: 255-258. [pdf]
  14. Pengmian Feng, Wei Chen*, Hao Lin*. (2016) Identifying antioxidant proteins by using optimal dipeptide compositions. Interdisciplinary Sciences: Computational Life Sciences, 8: 186-191. [pdf]
  15. Yun Wu, Hua Tang, Wei Chen, Hao Lin*. (2016) Predicting human enzyme family classes by using pseudo amino acid composition. Current Proteomics, 13(2): 99-104. [pdf]
  16. Wei Chen*, Hui Ding, Pengmian Feng, Hao Lin*, Kuochen Chou*. (2016) iACP: a sequence-based tool for identifying anticancer peptides. Oncotarget, 7(13): 16895-16909. [pdf]
  17. Hua Tang*, Wei Chen, Hao Lin*. (2016) Identification of immunoglobulins using Chou’s pseudo amino acid composition with feature selection technique. Molecular BioSystems, 12: 1269-1275. [pdf]
  18. Hui Ding*, Zhiyong Liang, Fengbiao Guo, Jian Huang, Wei Chen*, Hao Lin*. (2016) Predicting bacteriophage proteins located in host cell with feature selection technique. Computers in Biology and Medicine, 71: 156–161. [pdf]
  19. Wei Chen*, Pengmian Feng, Hui Ding, Hao Lin*, Kuochen Chou*. (2016) Using deformation energy to analyze nucleosome positioning in genomes. Genomics, 107: 69–75. [pdf]
  20. Chuan Dong, Yazhou Yuan, Fazhan Zhang, Hongli Hua, Yuannong Ye, Abraham Alemayehu Labena, Hao Lin, Wei Chen, Fengbiao Guo*. (2016) Combining pseudo dinucleotide composition with the Z curve method to improve the accuracy of predicting DNA elements: a case study in recombination spots. Molecular BioSystems, 12(9): 2893-2900. [pdf]

2015 (Click to expand or collapse the publication details)

  1. Wei Chen, Liqing Zhang*. (2015) The pattern of DNA cleavage intensity around indels. Scientific Reports, 5:8333. [pdf]
  2. Hao Lin*, Weixin Liu, Jiao He, Xinhui Liu, Hui Ding, Wei Chen*. (2015) Predicting cancerlectins by the optimal g-gap dipeptides. Scientific Reports, 5:16964. [pdf]
  3. Wei Chen*, Pengmian Feng, Hui Ding, Hao Lin*, Kuochen Chou*.(2015) iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide compositions. Analytical Biochemistry, 490:26-33. [pdf]
  4. Wei Chen*, Hao Lin*, Kuochen Chou*. (2015) Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences. Molecular BioSystems, 11:2620-2634. [pdf]
  5. Panpan Zhu, Wen-Chao Li, Zhejin Zhong, Enze Deng, Hui Ding*, Wei Chen*, Hao Lin*. (2015) Predicting subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition. Molecular Biosystems,11:558-563. [pdf]
  6. Wenchao Li, Enze Deng, Hui Ding*, Wei Chen*, Hao Lin*. (2015) iORI-PseKNC: a predictor for identifying origin of replication with pseudo k-tuple nucleotide composition. Chemometrics and Intelligent Laboratory Systems,7(43):69783-69793. [pdf]
  7. Wei Chen*, Xitong Zhang, Jordan Brooker, Hao Lin, Liqing Zhang*, Kuo-Chen Chou*. (2015) PseKNC-General: A cross-platform package for generating various modes of pseudo nucleotide compositions. Bioinformatics,31(1):119-20. [pdf]
  8. Wei Chen*, Hong Tran, Zhiyong Liang, Hao Lin, and Liqing Zhang*. (2015) Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome. Scientific Reports,5:13859. [pdf]

2014 (Click to expand or collapse the publication details)

  1. Hao Lin*, Enze Deng, Hui Ding, Wei Chen*, Kuochen Chou*. (2014) iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. Nucleic Acids Research, 42(21): 12961-12972. [pdf]
  2. Wenchao Li, Zhejin Zhong, Panpan Zhu, Enze Deng, Hui Ding*, Wei Chen*, Hao Lin*. (2014) Sequence analysis of origins of replication in the Saccharomyces cerevisiae genomes. Frontiers in Microbiology, 5: 574. [pdf]
  3. Pengmian Feng*, Wei Chen, Hao Lin*. (2014) Prediction of CpG island methylation status by integrating DNA physicochemical properties. Genomics, 104(4): 229-233. [pdf]
  4. Wei Chen*, Hao Lin*, Pengmian Feng, Jinpeng Wang. (2014) Exon skipping event prediction based on histone modifications. Interdisciplinary Sciences: Computational Life Sciences, 6(3): 241-249. [pdf]
  5. Hui Ding, Hao Lin*, Wei Chen*, Ziqiang Li, Fenbiao Guo, Jian Huang, Nini Rao. (2014) Prediction of protein structural classes based on feature selection technique. Interdisciplinary Sciences: Computational Life Sciences, 6(3): 235-240. [pdf]
  6. Wei Chen*, Pengmian Feng, Enze Deng, Hao Lin*, Kuochen Chou*. (2014) iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Analytical Biochemistry, 462: 76-83. [pdf]
  7. Wexin Liu, Enze Deng, Wei Chen, Hao Lin*. (2014) Identifying the subfamilies of voltage-gated potassium channels using feature selection technique. International Journal of Molecular Sciences, 15: 12940-12951. [pdf]
  8. Hui Ding*, Pengmian Feng, Wei Chen*, Hao Lin*. (2014) Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis. Molecular Biosystems, 10: 2229-2235. [pdf]
  9. Hui Ding*, Enze Deng, Lufeng Yuan, Li Liu, Hao Lin*, Wei Chen*, Kuochen Chou. (2014) iCTX-Type: A sequence-based predictor for identifying the types of conotoxins in targeting ion channels. BioMed Research International, 2014:286419. [pdf]
  10. Shohui Guo, Enze Deng, Liqin Xu, Hui Ding, Hao Lin*, Wei Chen*, Kuochen Chou*. (2014) iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinformatics, 30(11): 1522-1529. [pdf]
  11. Wei Chen*, Pengmian Feng, Hao Lin*, Kuochen Chou. (2014) iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition. BioMed Research International, 2014:623149. [pdf]
  12. Wei Chen*, Tiayu Lei, DiancChuan Jin, Hao Lin*, Kuochen Chou*. (2014) PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition. Analytical Biochemistry, 456: 53-60. [pdf]
  13. Pengmian Feng*, Hao Lin*, Wei Chen, Yongchun Zuo. (2014) Predicting the types of J-proteins using clustered amino acids. BioMed Research International, 2014:935719. [pdf]
  14. Wei Chen*, Hao Lin*, Pengmian Feng. (2014) DNA physical parameters modulate nucleosome positioning in the Saccharomyces cerevisiae genome. Current Bioinformatics, 9(2): 188-193. [pdf]
  15. YongchunZuo*, YongPeng, LiLiu, Wei Chen, LeiYang*, Guoliang Fan*. (2014) Predicting peroxidase subcellular location by hybridizing different descriptors of Chou’pseudo amino acid patterns. Analytical Biochemistry, 458:14-19. [pdf]

2013 (Click to expand or collapse the publication details)

  1. Hao Lin*, Wei Chen*, Hui Ding. (2013) AcalPred: A sequence-based tool for discriminating between acidic and alkaline enzymes. PloS One, 8(10): e75726. [pdf]
  2. Pengmian Feng, Wei Chen*, Hao Lin*, Kuo-Chen Chou*. (2013) iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition. Analytical Biochemistry, 442(1): 118-125. [pdf]
  3. Pengmian Feng, Hao Lin*, Wei Chen*. (2013) Identification of antioxidants from sequence information using Naive Bayes. Computational and Mathematical Methods in Medicine, ID 567529. [pdf]
  4. Hao Lin*, Wei Chen*, Lu-Feng Yuan, Zi-Qiang Li, Hui Ding. (2013) Using over-represented tetrapeptides to predict protein submitochondria locations. Acta Biotheoretica, 61(2): 259-268. [pdf]
  5. Pengmian Feng, Hui Ding, Wei Chen*, Hao Lin*. (2013) Naive Bayes classifier with feature selection to identify phage virion proteins. Computational and Mathematical Methods in Medicine, ID 530696. [pdf]
  6. Hui Ding*, Shou-Hui Guo, En-Ze Deng, Lu-Feng Yuan, Feng-Biao Guo, Jian Huang, Nini Rao, Wei Chen*, Hao Lin*. (2013) Prediction of Golgi-resident protein types by using feature selection technique. Chemometrics and Intelligent Laboratory Systems, 124: 9-13. [pdf]
  7. Wei Chen*, Pengmian Feng, Hao Lin*, Kuo-Chen Chou*. (2013) iRSpot-PseDNC: Identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Research, 41(6): e68. [pdf]
  8. Hao Lin*, Chen Ding, Lu-Feng Yuan, Wei Chen*, Hui Ding, Ziqiang Li, Feng-Biao Guo, Jian Huang, Ni-Ni Rao. (2013) Predicting subchloroplast locations of proteins based on the general form of Chou's pseudo amino acid composition: approached from optimal tripeptide composition. International Journal of Biomathematics, 6(2): 1350003. [pdf]
  9. Lufeng Yuan, Chen Ding, Shohui Guo, Hui Ding*, Wei Chen*, Hao Lin*. (2013) Prediction of the types of ion channel-targeted conotoxins based on Radial Basis Function Network. Toxicology in Vitro, 27: 852-856. [pdf]
  10. Yongchun Zuo, Wei Chen, Guoliang Fan, Qianzhong Li*. (2013) A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins. Amino acids, 44(2):573-58. [pdf]

2012 (Click to expand or collapse the publication details)

  1. Chen Ding, Lu-Feng Yuan, Shou-Hui Guo, Hao Lin*, Wei Chen*. (2012) Identification of mycobacterial membrane proteins and their types using over-represented tripeptide compositions. Journal of Proteomics, 77: 321-328. [pdf]
  2. Wei Chen*, Hao Lin*, Peng-Mian Feng, Chen Ding, Yong-Chun Zuo, Kuo-Chen Chou*. (2012) iNuc-PhysChem: A sequence-based predictor for identifying nucleosomes via physicochemical properties. PLoS One, 7(10): e47843. [pdf]
  3. Hao Lin*, Chen Ding, Qiang Song, Ping Yang, Hui Ding, Ke-Jun Deng, Wei Chen*. (2012) The prediction of protein structural class using averaged chemical shifts. Journal of Biomolecular Structure & Dynamics, 29(6): 643-648. [pdf]
  4. Wei Chen*, Pengmian Feng, Hao Lin*. (2012) Prediction of replication origins by calculating DNA structural properties. FEBS Letters, 586(6): 934-938. [pdf]
  5. Wei Chen*, Hao Lin*. (2012) Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine. Computers in Biology and Medicine, 42(4): 504-507. [pdf]
  6. Wei Chen*, Pengmian Feng, Hao Lin*. (2012) Prediction of ketoacyl synthase family using reduced amino acid alphabet. Journal of Industrial Microbiology & Biotechnology, 39(4): 579-584. [pdf]
  7. Shouhui Guo, Liqin Xu, Wei Chen, Guoqing Liu, Hao Lin*. (2012) Recombination spots prediction using DNA physical properties in the saccharomyces cerevisiae genome. AIP Conference Proceedings 1479(1):1556-1559. [pdf]
  8. Andrew H. Paterson*, Jonathan F. Wendel, Heidrun Gundlach, Hui Guo, Jerry Jenkins, Dianchuan Jin, Danny Llewellyn, Kurtis C. Showmaker, Shengqiang Shu, Joshua Udall, Mi-jeong Yoo, Robert Byers, Wei Chen, ..., Xiyin Wang, Jeremy Schmutz. (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fiber. Nature, 2012(492):423-427. [pdf]

2011 (Click to expand or collapse the publication details)

  1. Hao Lin*, Wei Chen. (2011) Prediction of thermophilic proteins using feature selection technique. Journal of Microbiological Methods, 84(1): 67-70. [pdf]

2010 (Click to expand or collapse the publication details)

  1. Wei Chen*, Hao Lin*. (2010) Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information. Biochemical and Biophysical Research Communications, 401(3): 382-384. [pdf]
  2. Wei Chen, Liaofu Luo*, Lirong Zhang. (2010) The organization of nucleosomes around splice sites. Nucleic acids research, 38(9):2788-2798. [pdf]
  3. Jun Lu, Liaofu Luo, Lirong Zhang, Wei Chen, Ying Zhang. (2010) Increment of diversity with quadratic discriminant analysis-an efficient tool for sequence pattern recognition in bioinformatics. Open Access Bioinformatics, 2:89-96. [pdf]

2009 (Click to expand or collapse the publication details)

  1. Wei Chen, Liaofu Luo*. (2009) Classification of antimicrobial peptide using diversity measure with quadratic discriminant analysis. Journal of Microbiological Methods, 78(1),94-96. [pdf]
  2. Wei Chen, Liaofu Luo*, Lirong Zhang, Yongqiang Xing. (2009) Nucleosome Positioning and RNA splicing. Progress in Biochemistry and Biophysics, 36(8):1035-1040. [pdf]
  3. Wei Chen, Liaofu Luo*,Lirong Zhang, Hao Lin. (2009) Recognition of DNase I hypersensitive sites in multiple cell lines. International journal of bioinformatics research and applications, 5(4):378-384. [pdf]