Zuo Yongchun, Ph.D.  Principal Investigator of Bioinformatics.  He is oneprofessor of State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock in Inner Mongolia University.

Professor Zuo focuses on the computational biology researches, including computational biologyand development omics. Computational biologyinvolves identification of important regulatory regions, such as enhancers, promoter and TFBSs from genomic sequences by combining machine learning methods and expression omics data. For omics ofdevelopment and reprogramming, we mainly focus on the regulation mechanism of embryonic development and cell reprogramming process for animals. Recently, we successfully performed systematic comparisons based on differential co-expression analysis for preimplantation embryo development, and deciphered the spatiotemporal patterns of gene expression in cloned embryos. In addition,he also focuses on the regulation mechanism of reprogramming for cloned animals,bioinformatics analysis of cloned animals by somatic nuclear transfer based on RNA-seq technologyand investigationof transgene on adult stem cell characteristics.

Contact Way: 0471-5227683，  Email：yongchunzuo@163.comor yczuo@imu.edu.cn

Research Group Website: http://bioinfor.imu.edu.cn

Research areas: 

Welcome to the Bioinformatics Lab ofInner Mongolia University. Our research interests mainly focus on:

1.       Computational biology research:In this direction, we focus on the identification of important regulatory elements, such as enhancers, promoter and TFBSs from genomic sequences by integratingmachine learning methods, feature selection techniques and expression omics data. In this area, we have published over 20 peer-reviewed papers in international journals. The K-MID(Amino Acids 2010, 38:859–867), KNN-ID(Amino Acids. 2013, 44(2):573-80; Mol Biosyst. 2015 11(3):950-7), Protein Block and PseKRAAC method have been firstly developed and extensively used in bioinformatics area(Peptides. 2009, 30(10)1788–1793; Plos one, 2015 10(12):e0145541; Bioinformatics. 2017, 33(1):122-124).

2.       Computational genomicsresearch:In this direction, we focus on the codons optimizationof gene between different species, nucleotide synthesis of optimized gene, and redesign of regulatory functional elements based on computational genomics. In this area, a set of bioinformatics-based methods for the transformation of exogenous gene codons and tissue-specific expression regulatory elements was developed, and two National Invention Patents have been approved in the past years (Number：ZL201310344833.5 and ZL201410123506.1).

3.       Bigdata of development and cell reprogramming:For development omics, we mainly focus on the regulation mechanism of embryonic development and cell reprogramming process for animals. Recently, we have successfully performed systematic comparisons based on differential co-expression analysis for preimplantation embryo development, and deciphered the spatiotemporal patterns of gene expression in cloned embryos(Oncotarget,2016 7(45):74120-74131; Oncotarget, 2017). Besides, we are also interested in investigating the effect of transgene on adult stem cell characteristics and animal development by using computational methods（BMC Genomics. 2016 17:188; Brief Bioinform. 2017 18(4):712-721.）. In this area, a series of high-quality studies are being published.

Publications( ^#Equal contribution. * Corresponding author)

2016-Now:

(51). Song, MM, Feng Y, Cao PB, Zheng L, Chen X, Yang L, Zuo YC*, Epigenetic marker identification of cell reprogramming based on genome-wide DNA methylation analysis, Epigenomics, 2018, Under Review . 
(50). 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, Under Review .
(49).  Mengye Lu, Shuai Liu, Arun Kumarsangaiah, Yunpeng Zhou, Zheng Pan, Yongchun Zuo, Nucleosome Positioning with Fractal Entropy Increment of Diversity in Telemedicine. 2018,  IEEE Access, DOI 10.1109/ACCESS.2017.2779850. (2016 IF: 3.244).. 
(48).  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). 
(47).  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). 
(46).  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). 
(45).  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).
(44).  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 High Cited Paper. 
(43).  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)
(42).  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).
(41). 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).
(40). Yang L, Wang SY, Zhou M, Chen XW, Zuo YC, Lv YL*. Characterization of BioPlex network by topological properties. J Theor Biol.  409:148-154. (2015 IF: 2.049). 
(39). 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)
(38). 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 )
(37). 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)
(36). 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)
(35). 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).
(34). 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).

2011-2015:
 (33). 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).  
 (32). 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).
 (31). 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).  
 (30). 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).  
 (29). 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). 
 (28). 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).  
 (27). 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).  
 (26). 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).  
 (25).  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). 
 (24).  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). 
 (23). 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).  
 (22).  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). 
 (21).  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). 
 (20). 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). 
 (19). 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,  349(2014)82–91 Journal of Theoretical Biologys, 349(2014)82–91. (2013 IF: 2.303).  
 (18). 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).  
 (17). 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).  
 (16). 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).
 (15). Uyunbilig B, Gu T, He  ZY, Wu X, Li GP,Li QZ, Ding XY, Zuo  YC*, Wang X*, Analysis of Transcription  Factors Regulated Stem Cell Differentiation by ChIP-Seq. Chinese Journal  of Cell Biology 2013, 35(6): 870–879  
 (14). 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).
 (13). Zuo YC*, Li QZ. The DNA geometric flexibility of promoter in  model organism genomes, Procedia 11  (2011)2732–2737. (EI, ISTP).
 (12). Chen W, Lin H, Feng PM, Ding  C, Zuo YC, Chou KC. iNuc-PhysChem: A Sequence-Based Predictor  for Identifying Nucleosomes via Physicochemical Properties. PLoS  One. 2012;7(10):e47843. (2011 IF: 4.092) ESI High Cited Paper.
 (11). 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).
 (10).  Zuo YC, Li QZ*. The DNA Geometric Flexibility Property around the Transcription  Initiation in Model Organism Genomes. 2011 International Conference on  Bioscience, Biochemistry and Bioinformatics 2011,  314-318.(EI, ISTP).
 (9). Zuo YC, Li QZ*. The positional distribution of TATA-box and TC-element in the transcription  start region. 2011 International Biophysics Congress (17th IBC)  2011, 588-589. (EI, ISTP).

Before 2010:
 (8). 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).
 (7). 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).
 (6).  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).
 (5).  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).
 (4).  Zuo YC, Li QZ*. Predicting plant Pol-Ⅱ promoter based on  subsequence increment of overlap content diversity. 2009 2nd  International Conference On Biomedical Engineering and Informatics, Vol  (3) 1494-1498. (EI, ISTP) .
 (3).  Zuo YC, Li QZ*. Using Six Physical Structural Parameters to Describe the Plant  Transcription Initiation. 2009 Proceedings of the International  Conference of Genomics, Vol (1) 91-92. (EI, ISTP) .
 (2). Yang L, Li QZ*, Zuo YC. Prediction of human  transcription factor binding sites by using an improved position correlation  scoring function. Journal of Inner Mongolia University, 2009,  40(1):60-67.
 (1). Yang L, Li QZ*, Zuo YC. Prediction of presynaptic and postsynaptic  neurotoxins using hybrid approach and pseudo amino acid composition. 2009  2nd International Conference On Biomedical Engineering and  Informatics, Vol (3) 1504-1507. (EI, ISTP).