Publication

2024
2024
2023
2022
2021
2020
2019
Before

2025

· Dongqing Su, Honghao Li, Tao Wang,et al.Yongchun Zuo* and Lei Yang*. Integrated Somatic Mutation Network Diffusion Model for Stratification of Breast Cancer into Different Metabolic Mutation Subtypes.Current Bioinformatics, Volume 20, Issue 3, Mar 2025, p. 246 - 256.(2025 IF:2.4)

2024

· Yuanyuan He, Haodong Wei, Siqing Liao, Ruiming Ou, Yuqiang Xiong, Yongchun Zuo* , Lei Yang*. Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer.Current Bioinformatics, Volume 19, Issue 10, Dec 2024, p. 963 - 976.(2024 IF:2.4)

· Yanan Zhao, Chunshen Long, Wenjing Shang, Zhihao Si, Zhigang Liu, Zhenxing Feng*, Yongchun Zuo*. A composite scaling network of EfficientNet for improving spatial domain identification performance.Commun Biol. 2024 Nov 25;7(1):1567. doi: 10.1038/s42003-024-07286-z.PMID: 39587274.(2024 IF:5.2)

· Shuchun Guo, Yanfang Zhang, Ying Shao, Lingmin Zhao, Yongchun Zuo,Suping Li, Hui Nie, Yingnan Mou, Congzi Zhang,Yingxue Che, Haiyang Zhang, Hongmei Miao,Haifeng Yu. Transcriptome analysis reveals the potential molecular mechanism involved in fatty acids biosynthesis of Sunflower.

· Wen Jin, Jianchao Jia, Yangming Si, Jianli Liu, Hanshuang Li, Hao Zhu, Zhouying Wu,Yongchun Zuo*, Lan Yu. Identification of key lncRNAs associated with immune infiltration and prognosis in gastric cancer. Biochem Genet. 2024 Apr 24. doi: 10.1007/s10528-024-10801-w.PMID: 38658494 .(2024 IF:2.1)

· Siqi Yang, Dongyang Liu, Yancheng Song, Yuchao Liang, Haoyu Yu, Yongchun Zuo*. Designing a structure-function alphabet of helix based on reduced amino acid clusters. Arch Biochem Biophys. 2024 Apr:754:109942. doi: 10.1016/j.abb.2024.109942. Epub 2024 Feb 20. PMID:38387828. (2024 IF:3.165)

· Chuanqing Zhou, Yue Zhang, Teng Ma, Dabala Wu, Yanyan Yang, Daqing Wang, et al. Yongchun Zuo*, Guifang Cao. Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number. Animals (Basel). 2024 Feb 21;14(5):677. doi: 10.3390/ani14050677. PMID:38473062. PMCID:PMC10931107. (2024 IF:3.231)

· Yan Hong, Hanshuang Li, Chunshen Long, Pengfei Liang, Jian Zhou, Yongchun Zuo*. An increment of diversity method for cell state trajectory inference of time-series scRNA-seq data. Fundamental Research. 2024. (2024 IF:6.2)

· Pengfei Liang, Hanshuang Li, Chunshen Long, Mingzhu Liu, Jian Zhou, Yongchun Zuo*. Chromatin region binning of gene expression for improving embryo cell subtype identification. Comput Biol Med. 2024 Mar:170:108049. doi: 10.1016/j.compbiomed.2024.108049. Epub 2024 Jan 28. PMID:38290319. (2024 IF:1.836)

· Zhihao Si, Hanshuang Li, Wenjing Shang, Yanan Zhao, Lingjiao Kong, Chunshen Long, Yongchun Zuo*, Zhenxing Feng. SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network. Brief Bioinform. 2024 May 23;25(4):bbae259. doi: 10.1093/bib/bbae259. PMID:38811360. PMCID:PMC11136618. (2024 IF:13.994)

· Honghao Li, Dongqing Su, Xinpeng Zhang, Yuanyuan He, Xu Luo, Yuqiang Xiong, et al. Yongchun Zuo*,Lei Yang.Machine learning-based prediction of diabetic patients using blood routine data. Methods.2024 Sep:229:156-162.doi: 10.1016/j.ymeth.2024.07.001.Epub 2024 Jul 15.PMID:39019099.(2024 IF:4.647)

· Tao Wang, Xiaojun Su, Yuchao Liang, Xu Luo, Xiao Hu, Ting Xia, Xuebin Ma,Yongchun Zuo*,Huilin Xia, Lei Yang.Integrated deep learning model for automatic detection and classification of stenosis in coronary angiography.Computational Biology and Chemistry.2024:108184.(2024 IF:2.6)

· Siqi Yang, Jixiang Xing, Dongyang Liu, Yancheng Song, Haoyu Yu, Shuhua Xu,Yongchun Zuo*. Review and new insights into the catalytic structural domains of the Fe (ll) and 2-Oxoglutarate families.Int J Biol Macromol.2024 Aug 15:134798.doi: 10.1016/j.ijbiomac.2024.134798.PMID:39153678.(2024 IF:8.2)

· Yuchao Liang, Yuting Guo, Yifei Zhai, Jian Zhou, Wuritu Yang, Yongchun Zuo*. Disease trend analysis platform accurately predicts the occurrence of cervical cancer under mixed diseases. Methods.2024 Aug 5:230:108-115.doi: 10.1016/j.ymeth.2024.07.011.Online ahead of print.PMID:39111721.(2024 IF:4.647)

2023

· Shanghua Liu, Yuchao Liang, Jinzhao Li, Siqi Yang, Ming Liu, Chengfang Liu, Dezhi Yang, Yongchun Zuo*. Integrating reduced amino acid composition into PSSM for improving copper ion-binding protein prediction. Int J Biol Macromol. 2023 Jul 31;244:124993. doi: 10.1016/j.ijbiomac.2023.124993. Epub 2023 Jun 10. PMID: 37307968. (2023 IF: 8.2)

· Zhao X, Yi L, Zuo Y, Gao F, Cheng Y, Zhang H, Yongchun Zuo, Jia X, Su S, Zhang D, Zhang X, Ren Y, Mu Y, Jin X, Li Q, Bateer S, Lu Z. High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement. Plants (Basel). 2023 Jul 26;12(15):2773. doi: 10.3390/plants12152773. PMID: 37570928; PMCID: PMC10421198.(2023 IF: 4.5)

· Dongqing Su, Haoxin Zhang, Yuqiang Xiong, Haodong Wei, Yao Yu, Honghao Li, Tao Wang,Yongchun Zuo*, Lei Yang*. Stratification of ovarian cancer patients from the prospect of drug target-related transcription factor protein activity: the prognostic and genomic landscape analyses. Brief Funct Genomics. 2023 Jul 17;22(4):351-365. doi: 10.1093/bfgp/elad008. PMID: 37103222. (2023 IF: 4.0)

· Hao Lin , Yongchun Zuo , Ettayapuram Ramaprasad Azhagiya Singam. Editorial: Computational analysis of promoters in prokaryotic genomes. Front Microbiol. 2023 Jul 10;14:1242139. doi: 10.3389/fmicb.2023.1242139. PMID: 37492255; PMCID: PMC10364605. (2023 IF: 5.2)

· Dongqing Su, Yuqiang Xiong, Haodong Wei,et.al. Yongchun Zuo*, Lei Yang*. Integrated analysis of ovarian cancer patients from prospective transcription factor activity reveals subtypes of prognostic significance. Heliyon. 2023 May 11;9(5):e16147. doi: 10.1016/j.heliyon.2023.e16147. PMID: 37215759; PMCID: PMC10199194. (2023 IF: 4.0)

· Jinzhao Li, Xiang He, Shuang Gao, Yuchao Liang, Zhi Qi, Qilemuge Xi,Yongchun Zuo*, Yongqiang Xing*. The Metal-binding Protein Atlas (MbPA): An Integrated Database for Curating Metalloproteins in All Aspects. J Mol Biol. 2023 Apr 21:168117. doi: 10.1016/j.jmb.2023.168117. Epub ahead of print. PMID: 37086947. (2023 IF: 6.151)

· Mingzhu Liu, Jian Zhou, Qilemuge Xi,et al. Yongchun Zuo*. A computational framework of routine test data for the cost-effective chronic disease prediction. Brief Bioinform. 2023 Mar 19;24(2):bbad054. doi: 10.1093/bib/bbad054. PMID: 36772998. (2023 IF: 13.994)

· Hanshuang Li, Chunshen Long, Yan Hong, Liaofu Luo*, Yongchun Zuo*. Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator. Research (Wash D C). 2023 Apr 11;6:0118. doi: 10.34133/research.0118. PMID: 37223479; PMCID: PMC10202187. (2023 IF: 11.036)

· Hao Wang, Zhaoyue Zhang, Haicheng Li, et al. Yongchun Zuo*. A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery. Cell Bioscience. 2023 Feb 28;13(1):41. doi: 10.1186/s13578-023-00991-y. PMID: 36849879; PMCID: PMC9972636. (2023 IF: 9.584)

· Lei Zheng, Pengfei Liang, Chunshen Long, et al. Yongchun Zuo*. EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis. Nucleic Acids Res. 2023 Jan 6;51(D1):D924-D932. doi: 10.1093/nar/gkac848. PMID: 36189903; PMCID: PMC9825456. (2023 IF: 19.160)

2022

· Lemuge Chao, Siqi Yang, Hanshuang Li, Chunshen Long, Qilemuge Xi, Yongchun Zuo*. Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells. Biochim Biophys Acta Gene Regul Mech. 2022 Oct;1865(7):194861. doi: 10.1016/j.bbagrm.2022.194861. Epub 2022 Aug 20. PMID: 35998875. (2022 IF:6.304)

· Pengfei Liang, Hao Wang, Yuchao Liang, Jian Zhou, Haicheng Li, Yongchun Zuo*. Feature-scML: an open-source Python package for the feature importance visualization of single-cell omics with machine learning. Current Bioinformatics. (2021 IF: 4.850)

· Lei Zheng, Dongyang Liu, Yuan Alex Li, Siqi Yang, Yuchao Liang, Yongqiang Xing*, Yongchun Zuo*. RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets. Nucleic Acids Res. 2022 Jul 5;50(W1):W633-W638. doi: 10.1093/nar/gkac415. PMID: 35639512; PMCID: PMC9252778. (2022 IF: 19.160)

· Yuchao Liang, Siqi Yang, Lei Zheng, et al. Yongchun Zuo*. Research progress of reduced amino acid alphabets in protein analysis and prediction. Comput Struct Biotechnol J. 2022 Jul 4;20:3503-3510. doi: 10.1016/j.csbj.2022.07.001. PMID: 35860409; PMCID: PMC9284397. (2022 IF: 6.155)

· Hanshuang Li, Chunshen Long, Yan Hong, Lemuge Chao, Yong Peng, Yongchun Zuo*. The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming. Int J Mol Sci. 2022 Jan 29;23(3):1567. doi: 10.3390/ijms23031567. PMID: 35163490; PMCID: PMC8835745. (2022 IF: 6.208)

· Yu Sun, Haicheng Li, Lei Zheng.et al. Yongchun Zuo*, Wenyi Zhang*, Heping Zhang*. iProbiotics: a machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences. Brief Bioinform. 2022 Jan 17;23(1):bbab477. doi: 10.1093/bib/bbab477. PMID: 34849572. (2022 IF: 13.994)

2021

· Pengfei Liang, Lei Zheng, Chunshen Long, Wuritu Yang, Lei Yang, Yongchun Zuo*. HelPredictor models single-cell transcriptome to predict human embryo lineage allocation. Brief Bioinform. 2021 Nov 5;22(6):bbab196. doi: 10.1093/bib/bbab196. PMID: 34037706. (2021 IF: 13.994)

· Hao Wang, Pengfei Liang, Lei Zheng, ChunShen Long, HanShuang Li, Yongchun Zuo*. eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition. Bioinformatics. 2021 Aug 9;37(15):2157-2164. doi: 10.1093/bioinformatics/btab071. PMID: 33532815. (2020 IF: 6.937)

· Chunshen Long, Hanshuang Li, Xinru Li, Wuritu Yang, Yongchun Zuo*. Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways. Int J Mol Sci. 2021 Jul 30;22(15):8187. doi: 10.3390/ijms22158187. PMID: 34360962; PMCID: PMC8347363. (2020 IF: 6.208)

· Jian Zhou, Suling Bo, Hao Wang, Lei Zheng, Pengfei Liang, Yongchun Zuo*. Identification of Disease-Related 2-Oxoglutarate/Fe (II)-Dependent Oxygenase Based on Reduced Amino Acid Cluster Strategy. Front Cell Dev Biol. 2021 Jul 16;9:707938. doi: 10.3389/fcell.2021.707938. PMID: 34336861; PMCID: PMC8323781. (2020 IF: 6.081)

· Hanshuang Li, Chunshen Long, Jinzhu Xiang, Pengfei Liang, Xueling Li, Yongchun Zuo*. Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region. Brief Bioinform. 2021 Jul 20;22(4):bbaa342. doi: 10.1093/bib/bbaa342. PMID: 33316032. (2021 IF: 13.994)

· Lei Zheng, Dongyang Liu, Wuritu Yang, Lei Yang, Yongchun Zuo*. RaacLogo: a new sequence logo generator by using reduced amino acid clusters. Brief Bioinform. 2021 May 20;22(3):bbaa096. doi: 10.1093/bib/bbaa096. PMID: 32524143. (2020 IF: 11.622) ESI 1%高被引论文

· Gai-Fang Dong, Lei Zheng, Sheng-Hui Huang, Jing Gao, Yongchun Zuo*. Amino Acid Reduction Can Help to Improve the Identification of Antimicrobial Peptides and Their Functional Activities. Front Genet. 2021 Apr 20;12:669328. doi: 10.3389/fgene.2021.669328. PMID: 33959153; PMCID: PMC8093877. (2021 IF: 4.772)

· Zerong Wang, Dongyang Liu, Baofang Xu, Ruixia Tian, Yongchun Zuo*. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform. 2021 May 20;22(3):bbaa215. doi: 10.1093/bib/bbaa215. PMID: 32987405. (2020 IF: 11.622)

· Qilemuge Xi, Hao Wang, Liuxi Yi, Jian Zhou, Yuchao Liang, Xiaoqing Zhao, Yongchun Zuo*. ANPrAod: Identify Antioxidant Proteins by Fusing Amino Acid Clustering Strategy and N-Peptide Combination. Comput Math Methods Med. 2021 Apr 8;2021:5518209. doi: 10.1155/2021/5518209. PMID: 33927782; PMCID: PMC8049822.

· Hao Wang, Qilemuge Xi, Pengfei Liang, Lei Zheng, Yan Hong, Yongchun Zuo*. IHEC_RAAC: a online platform for identifying human enzyme classes via reduced amino acid cluster strategy. Amino Acids. 2021 Feb;53(2):239-251. doi: 10.1007/s00726-021-02941-9. Epub 2021 Jan 23. PMID: 33486591. (2020 IF: 3.789)

· Baofang Xu, Dongyang Liu, Zerong Wang, Ruixia Tian, Yongchun Zuo*. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci. 2021 Jan;78(1):129-141. doi: 10.1007/s00018-020-03594-9. Epub 2020 Jul 8. PMID: 32642789. (2020 IF: 9.261)

2020

· Zijie Sun, Shenghui Huang, Lei Zheng, Pengfei Liang, Wuritu Yang, Yongchun Zuo*. ICTC-RAAC: An improved web predictor for identifying the types of ion channel-targeted conotoxins by using reduced amino acid cluster descriptors. Comput Biol Chem. 2020 Dec;89:107371. doi: 10.1016/j.compbiolchem.2020.107371. Epub 2020 Sep 7. PMID: 32950852. (2020 IF: 3.737)

· Pengbo Cao, Hanshuang Li, Yongchun Zuo*, Buhe Nashun*. Characterization of DNA Methylation Patterns and Mining of Epigenetic Markers During Genomic Reprogramming in SCNT Embryos. Front Cell Dev Biol. 2020 Sep 2;8:570107. doi: 10.3389/fcell.2020.570107. PMID: 32984351; PMCID: PMC7492385. (2020 IF: 6.081)

· Pengfei Liang, Wuritu Yang, Xing Chen, Chunshen Long, Lei Zheng, Hanshuang Li, Yongchun Zuo*. Machine Learning of Single-Cell Transcriptome Highly Identifies mRNA Signature by Comparing F-Score Selection with DGE Analysis. Mol Ther Nucleic Acids. 2020 Jun 5;20:155-163. doi: 10.1016/j.omtn.2020.02.004. Epub 2020 Feb 13. PMID: 32169803; PMCID: PMC7066034. (2019 IF: 7.032)

· Hanshuang Li, Mingmin Song, Wuritu Yang, Pengbo Cao, Lei Zheng, Yongchun Zuo*. A Comparative Analysis of Single-Cell Transcriptome Identifies Reprogramming Driver Factors for Efficiency Improvement. Mol Ther Nucleic Acids. 2020 Mar 6;19:1053-1064. doi: 10.1016/j.omtn.2019.12.035. Epub 2020 Jan 14. PMID: 32045876; PMCID: PMC7015826. (2019 IF: 7.032)

2019

· Hanshuang Li, Na Ta, Chunshen Long, Qiutang Zhang, Siyu Li, Shuai Liu, Lei Yang, Yongchun Zuo*. The spatial binding model of the pioneer factor Oct4 with its target genes during cell reprogramming. Comput Struct Biotechnol J. 2019 Sep 11;17:1226-1233. doi: 10.1016/j.csbj.2019.09.002. PMID: 31921389; PMCID: PMC6944736. (2018IF: 4.720)

· Dongyang Liu, Guangpeng Li, Yongchun Zuo*. Function determinants of TET proteins: the arrangements of sequence motifs with specific codes. Brief Bioinform. 2019 Sep 27;20(5):1826-1835. doi: 10.1093/bib/bby053. PMID: 29947743. (2019 IF: 13.994)

· Chunshen Long, Wei Li, Pengfei Liang, Shuai Liu, Yongchun Zuo*. Transcriptome Comparisons of Multi-Species Identify Differential Genome Activation of Mammals Embryogenesis. IEEE Access, 7, 7794-7802. (2018 IF: 4.098) ESI 1%高被引论文

· Yongchun Zuo*, Yu Chang, Shenghui Huang, Lei Zheng, Lei Yang, Guifang Cao*. iDEF-PseRAAC: Identifying the Defensin Peptide by Using Reduced Amino Acid Composition Descriptor. Evol Bioinform Online. 2019 Jul 31;15:1176934319867088. doi: 10.1177/1176934319867088. PMID: 31391777; PMCID: PMC6669840. (2018 IF: 2.203)

· Bosu Hu, Lei Zheng, Chunshen Long, Mingmin Song, Tao Li, Lei Yang, Yongchun Zuo*. EmExplorer: a database for exploring time activation of gene expression in mammalian embryos. Open Biol. 2019 Jun 28;9(6):190054. doi: 10.1098/rsob.190054. Epub 2019 Jun 5. PMID: 31164042; PMCID: PMC6597754. (2018IF: 3.890)

· Lei Zheng, Shenghui Huang, Nengjiang Mu, et al. Yongchun Zuo*. RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. Database (Oxford). 2019 Jan 1;2019:baz131. doi: 10.1093/database/baz131. PMID: 31802128; PMCID: PMC6893003. (2019 IF: 2.593)

Before

· Guangqi Gao, Meng Xu, Chunling Bai, Yulan Yang, Guangpeng Li, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong Chi Zhang, Jun Yin*, Yongchun Zuo*, Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage colouration. GigaScience, 2018, 7(10) 1-14. (2017 IF: 7.267).

· Rongsong Luo, Chunling Bai, Lei Yang, Zhong Zheng, Guanghua Su, Guangqi Gao, Zhuying Wei, Yongchun Zuo*, Guangpeng Li*, DNA methylation subpatterns at distinct regulatory regions in human early embryos, Open Biol. 2018, 8: 180131. (2017 IF: 3.286).

· Wang SY, Huo HY, Su DQ, Lu QZ, Chen XW, Yang L, Zuo YC*, Lv YL, Characterize the difference between TMPRSS2-ERG and non-TMPRSS2-ERG fusion patients by clinical and biological characteristics in prostate cancer, Gene, 2018 679:186-194. (2017 IF: 2.498).

· Lei Yang, Shiyuan Wang, Qi Zhang, Yi Pan, Yingli Lv, Xiaowen Chen, Yongchun Zuo* and Dapeng Hao, Clinical significance of immune microenvironment in ovarian cancer patients. Mol. Omics, 2018, 14, 341-351. (2016 IF: 2.781).

· Luqiang Zhang, Qianzhong Li*, Wen Jin, Yongchun Zuo, Shuchun Guo. Genome-wide analysis of H3K36me3 and its regulations to cancer-related genes expression in human cell lines. Biosystems 2018, 171(2018) 59-65, (2017 IF: 1.619).

· Mengye Lu, Shuai Liu, Arun Kumarsangaiah, Yunpeng Zhou, Zheng Pan, Yongchun Zuo, Nucleosome Positioning with Fractal Entropy Increment of Diversity in Telemedicine. IEEE Access, 2018, 6：33451-33459. (2017 IF: 3.557).

· Zuo YC*, Su GH, Cheng L, Liu K, Feng Y, Wei ZY, Bai CL, Cao GF, Li GP*, Coexpression analysis identifies nuclear reprogramming barriers of somatic cell nuclear transfer embryos, Oncotarget, 2017, 8(39) 65847-65859 (2016 IF: 5.168).

· Huo HY, Li T, Wang SY, Lv YL, Zuo YC*, Yang L*, Prediction of presynaptic and postsynaptic neurotoxins by using Pseudo amino acid composition and motif features, Scientific Reports, 7: 5827 (2016 IF: 4.259).

· Yang L, Wang SY, Zhou M, Chen XW, Jiang W, Zuo YC*, lv YL, Molecular classification of prostate adenocarcinoma by the integrated somatic mutation profiles and molecular network. Scientific Reports, 2017, 7(1):738. (2016 IF: 4.259).

· Guo SC# , Zuo YC#, Zhang YF, Wu CY, Su WX, Jin W, Yu HF, An YL, Li QZ*. Large-scale transcriptome comparison of sunflower genes responsive to Verticillium dahliae. BMC Genomics. 2017. 18(1):42 (2015 IF: 3.867).

· Zuo YC*, Li Y, Chen YL, Li GP, Yan ZH, Yang L*. PseKRAAC: A flexible web server for generating pseudo K-tuple reduced amino acids composition. ,Bioinformatics. 2017, 33(1):122-124 (2016 IF:7.307).ESI 1%高被引.

· Che D, Wang Y, Bai W, Li L, Liu G, Zhang L, Zuo YC, Tao S, Hua J, Liao M*. Dynamic and modular gene regulatory networks drive the development of gametogenesis. Brief Bioinform. 2017 18(4):712-721. (2015 IF: 5.134).

· Zuo YC*, Su GH, Wang SS, Yang L, Liao MZ, Wei ZY, Bai CL, Li GP*. Exploring timing activation of functional pathway based on differential co-expression analysis in preimplantation embryogenesis, Oncotarget, 2016 7(45): 74120-74131. (2014 IF: 6.359).

· Yang L, Wang SY, Zhou M, Chen XW, Zuo YC*, Lv YL. Characterize the relationship between essential and TATA-containing genes for S. cerevisiae by network topologies in the perturbation sensitivity network. Genomics, 2016 108(3-4) 177-183. (2015 IF: 2.386).

· Yang L, Wang SY, Zhou M, Chen XW, Zuo YC, Lv YL. Characterization of BioPlex network by topological properties. J Theor Biol. 2016 409:148-154. (2015 IF: 2.049).

· Su WX, Li QZ*, Zhang LQ, Fan GL, Wu CY, Yan ZH, Zuo YC. Gene expression classification using epigenetic features and DNA sequence composition in the human embryonic stem cell line H1. Gene. 2016, 592(1):227–234 (2015 IF: 2.319).

· Zhang L, Xuan H, Zuo YC, Xu G, Wang P, Song Y, Zhang SH*. Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network. Funct Integr Genomics. 2016 16(3):243-51. (2015 IF: 2.265 ).

· Jia X, Sun C, Zuo YC, Li G, Li G, Ren L, Chen G. Integrating transcriptomics and metabolomics to characterise the response of Astragalus membranaceus Bge. var. mongolicus (Bge.) to progressive drought stress. BMC Genomics. 2016 17:188. (2014 IF: 3.986).

· Yang L, Wang S, Zhou M, Chen X, Zuo YC, Sun D, Lv Y.Comparative analysis of housekeepingand tissue-selective genes in Human based on network topologies andbiological properties. Molecular Genetics and Genomics, 2016 291(3):1227-41 (2014 IF: 2.728).

· Su WX, Li QZ*, Zuo YC, Zhang LQ. Association analysis between the distributions of histone modifications and gene expression in the human embryonic stem cell. Gene, 2016 575(1):90-100. (2014 IF: 2.019).

· Zuo YC*, Lv Y, Wei Z, Yang L, Li G, Fan G. iDPF-PseRAAAC : A web-server for identifying the defensin peptide family and subfamily using pseudo reduced amino acid alphabet composition. PLOS ONE, 2015 Dec 29;10(12):e0145541. (2014 IF: 3.234).

· Tai, DP, Liu, PX, Gao, J, Jin, MZ, Xu, T, Zuo, YC, Liang, H, Liu, DJ*. Generation of Arbas Cashmere Goat Induced Pluripotent Stem Cells Through Fibroblast Reprogramming. Cellular Reprogramming, 2015 17(4): 297-305. (2014 IF: 1.788).

· Yang L, Hao D, Wang J, Xing X, Lv Y, Zuo YC*, Jiang W*. Characterization of proteins in S. cerevisiae with subcellular localizations Molecular BioSystems, 2015, 11(5), 1360-9. (2014 IF: 3.210).

· Zuo YC*, Su WX, Zhang SH, Wang SS, Wu CY, Yang L*, Li GP*. Discrimination of membrane transporter protein types using K-nearest neighbor method derived from similarity distance of total diversity measure. Molecular BioSystems,2015 11(3):950-7. (2014 IF: 3.210).

· Yang L, Hao D, Lv Y, Zuo YC*, Jiang W. Genome-wide characterization of essential, toxicity-modulating and nophenotype genes in S. cerevisiae, GENE, 2015 559(1):1-8. (2014 IF: 2.019).

· Zuo YC, Gao Y, Su G, Bai C, Wei Z, Liu K, Li Q, Bou S1, Li GP.* Irregular transcriptome reprogramming probably causes thec developmental failure of embryos produced by interspecies somatic cell nuclear transfer between the Przewalski's gazelle and the bovine. BMC Genomics, 2014, 15:1113. (2013 IF: 4.041).

· Yang L, Wang J, Lv Y, Hao D, Zuo YC, Li X, Jiang W. Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae by network topologies and biological properties. Genomics. 2014 104(6B):562-71. (2013 IF: 2.793).

· Yang L, Wang J, Wang H, Lv Y, Zuo YC, Li X, Jiang W. Analysis and identification of essential genes in humans using topological properties and biological information Gene. 2014, 349:82-91. (2013 IF: 2.082).

· Fan GL*, Liu YL, Zuo YC*, Mei HX, Rang Y, Hou BY, Zhao Y. acACS: Improving the Prediction Accuracy of Protein Subcellular Locations and Protein Classification by Incorporating the Average Chemical Shifts Composition. The Scientific World Journal. 2014:864135, 1-9. (2013 IF: 1.73).

· Zuo YC*, Peng Y, Liu L, Chen W, Yang L, Fan GL. Predicting peroxidase subcellular location by hybridizing different descriptors of Chou' pseudo amino acid patterns. Anal Biochem. 2014 458:14-9. (2013 IF: 2.305).

· Yang L, Lv Y, Li T, Zuo YC*, Jiang W. Human proteins characterization with subcellular localizations. J Theor Biol. 2014 358C:61-73. (2013 IF: 2.303).

· Yang L, Wang J, Wang H, Lv Y, Zuo YC*, Jiang W*. Characterization of essential genes by topological properties in the perturbation sensitivity network. Biochem Biophys Res Commun. 2014 448(4):473-9. (2008 IF: 2.281).

· Zuo YC*, Zhang P, Liu L, Li T, Peng Y, Li G, Li QZ. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome. Chromosome Research ,2014 22(3):321-34. (2013 IF: 2.688).

· Huang X, Han X, Uyunbilig B, Zhang M, Duo S, Zuo YC, Zhao Y, Yun T, Tai D, Wang C, Li J, Li XL*, Li RF*. Establishment of Bovine Trophoblast Stem-Like Cells from In Vitro-Produced Blastocyst-Stage Embryos Using Two Inhibitors. Stem Cells Dev. 2014 23(13):1501-14. (2013 IF: 4.202).

· Feng P, Lin H, Chen W, Zuo YC, Predicting the types of J-proteins using clustered amino acids. BioMed Research International,2014, 935719. (2014 IF: 1.579).

· Yang L, Wang J, Wang H, Lv Y, Zuo YC*, Jiang W*. Analysis and identification of toxin targets by topological properties in protein–protein interaction network, Journal of Theoretical Biologys, 2014 349(2014)82–91. (2013 IF: 2.303).

· Liu L, Li QZ*, Lin H, Zuo YC. The effect of regions flanking target site on siRNA potency. Genomics 2013 102(4) 215-222. (2012 IF: 3.010).

· Fan GL, Li QZ*, Zuo YC. Predicting acidic and alkaline enzymes by incorporating the average chemical shift and gene ontology informations into the general form of Chou's PseAAC. Process Biochemistry 48 (2013) 1048–1053. (2012 IF: 2.414).

· Li T, Li QZ*, Liu S, Fan GL, Zuo YC, Peng Y. PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information, Bioinformatics, 2013, 29(6):678-85. (2012 IF: 5.323).

· Zuo YC*, Chen W, Fan GL, Li QZ. A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins. Amino Acids. 2013，44(2):573-80. (2012 IF: 3.914).

· Zuo YC*, Li QZ. The DNA geometric flexibility of promoter in model organism genomes, Procedia 2012 (2011)2732–2737. (EI, ISTP).

· Zuo YC, Li QZ*. Identification of TATA and TATA-less promoters in plant genomes by integrating diversity measure, GC-Skew and DNA geometric flexibility. 2011 Genomics. 97(3): 112-120. (2010 IF: 3.327).

· Zuo YC, Li QZ*. The hidden physical codes for modulating the prokaryotic transcription initiation. 2010 Physica A 2010 389(19) 4217–4223. (2009 IF: 1.562).

· Zuo YC, Li QZ*. Using K-minimum increment of diversity to predict secretory proteins of malaria parasite based on groupings of amino acids. 2010, Amino Acids. 2010(3) 38:859–867. (2008 IF: 4.132).

· Zuo YC, Li QZ*. Analysis of plant TATA and TATA-less promoters by using sequence and structure features. 2009，Progress in Biochemistry and Biophysics. 36(7): 863-871. (2008 IF: 0.211).

· Zuo YC, Li QZ*. . Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet. 2009, Peptides. 30(10) 1788–1793. (2008 IF: 2.565).

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