Publication

63. Siwen Wu, Kun Wang, Sisi Yuan, Tengfei Dou, Zhengchang Su, Changrong Ge, Junjing Jia. De novo assembly of four indigenous chicken genomes reveal loss of function as a major driving force in chicken domestication and evolution. https://www.researchsquare.com/article/rs-2019326/v1

62. Pengyu Ni, Siwen Wu and Zhengchang Su. Underlying causes for prevalent false positives and false negatives in STARR-seq data. https://www.biorxiv.org/content/10.1101/2023.03.03.530915v1

61. Jing Chen, Meng Niu, Jun-tao Guo, Zhengchang Su. Prevalent utilizations of exons as regulatory sequences are possible and unavoidable in the human genome. Nat Sci. 2023; e20220058. https://doi.org/10.1002/ntls.20220058

60. Yangqi Su, Chen Xu, Jonathan Shea, Darla DeStephanis and Zhengchang Su. Transcriptomic changes in single yeast cells under various stress conditions. BMC Genomics 24, 88 (2023). https://doi.org/10.1186/s12864-023-09184-w

59. Liu X, Yu T, Zhao X, Long C, Han R, Su Z, Li G. ARBic: an all-round biclustering algorithm for analyzing gene expression data. NAR Genom Bioinform. 2023 Jan 31;5(1):lqad009. https://doi:10.1093/nargab/lqad009 eCollection 2023 Mar. PMID: 36733402

58. Ni P, Moe J, Su Z. Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice. BMC Biol. 2022 Oct 5;20(1):221. https://doi:10.1186/s12915-022-01426-9 PMID: 36199141.

57. Jian Z, Zeng L, Xu T, Sun S, Yan S, Zhao S, Su Z, Ge C, Zhang Y, Jia J, Dou T. The intestinal microbiome associated with lipid metabolism and obesity in humans and animals. J Appl Microbiol. 2022 Nov;133(5):2915-2930. https://doi:10.1111/jam.15740 Epub 2022 Aug 8. PMID: 35882518.

56. Zhao L, Li X, Atwill ER, Aly SS, Williams DR, Su Z. Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line. BMC Microbiol. 2022 May 14;22(1):132. https://doi:10.1186/s12866-022-02549-3 .

55. Ni P, Su Z. PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. Database (Oxford). 2022 Apr 22;2022. https://doi:10.1093/database/baac024

54. Dou T, Yan S, Liu L, Wang K, Jian Z, Xu Z, Zhao J, Wang Q, Sun S, Talpur MZ, Duan X, Gu D, He Y, Du Y, Abdulwahid AM, Li Q, Rong H, Cao W, Su Z, Zhao G, Liu R, Zhao S, Huang Y, Te Pas MFW, Ge C, Jia J. Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens. BMC Genomics. 2022 Mar 2;23(1):173. https://doi:10.1186/s12864-022-08388-w

53. Jeamsripong S, Li X, Aly SS, Su Z, Pereira RV, Atwill ER. Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California. Antibiotics (Basel). 2021 Aug 26;10(9). https://doi:10.3390/antibiotics10091042

52. Ni P, Su Z. Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. NAR Genom Bioinform. 2021 Jun 17;3(2):lqab052. https://doi:10.1093/nargab/lqab052

51. Qinling Mei, Guojun Li, Zhengchang Su. Clustering single-cell RNA-seq data by rank constrained similarity learning. Bioinformatics, btab276, 2021. https://doi.org/10.1093/bioinformatics/btab276

50. X Liu, D Li, J Liu, Z Su, G Li. RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters. Bioinformatics. 2020 Jul 11;btaa630. https://doi:10.1093/bioinformatics/btaa630

49. Zhengtian Li, Irfan Ahmed, Zhiqiang Xu, Shuai Sun, Tao Li, Dahai Gu, Yong Liu, Xia Zhang, Shixiong Yan, Wenyuan Hu, Ziqing Jiang, Xiaohua Duan, Qihua Li, Lixian Liu, Hua Rong, Kun Wang, Alsoufi Mohammed Abdulwahid, Tengfei Dou, Shanrong Wang, Zhengchang Su, Changrong Ge, Marinus FW Te Pas, Junjing Jia, Ying Huang. Profiles of expression pattern and tissue distribution of host defense peptides genes in different chicken (Gallus gallus) breeds related to body weight. PLOS ONE. 2020, 15 (12), e0238675. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238675

48. Ma H, Li G, Su Z. KSP: an integrated method for predicting catalyzing kinases of phosphorylation sites in proteins. BMC Genomics. 2020 Aug 4;21(1):537. https://doi:10.1186/s12864-020-06895-2

47. Ni P, Su Z. Deciphering Epigenomic Code for Cell Differentiation Using Deep Learning. BMC Genomics. 2019 Sep 12;20(1):709. https://doi:10.1186/s12864-019-6072-8

46. Qi E, Wang D, Li Y, Li G, Su Z. Revealing Favorable and Unfavorable Residues in Cooperative Positions in Protease Cleavage Sites. Biochem Biophys Res Commun. 2019 Nov 19;519(4):714-720. https://doi:10.1016/j.bbrc.2019.09.056 Epub 2019 Sep 20.

45. Li Y, Ni P, Zhang S, Li G, Su Z. ProSampler: an ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. Bioinformatics. 2019 May 9. pii: btz290. https://doi:10.1093/bioinformatics/btz290

44. Zhang S, Liang Y, Wang X, Su Z, Chen Y. FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets. DNA Res. 2019 Apr 8. pii: dsz004. https://doi:10.1093/dnares/dsz004

43. Li X, Aly SS, Su Z, Pereira RV, Williams DR, et al. (2018) Phenotypic Antimicrobial Resistance Profiles of E. coli and Enterococcus from Dairy Cattle in Different Management Units on a Central California Dairy. Clin Microbiol 7: 311. https://doi:10.4172/2327-5073.1000311

42. Bo Gao, Yue Zhao, Yang Li, Juntao Liu, Guojun Li, Zhengchang Su. Prediction of driver modules via balancing exclusive coverages of mutations in cancer samples. Adv Sci (Weinh). 18 December 2018; https://doi:0.1002/advs.201801384

41. Hou Y, Gao B, Li G, Su Z. MaxMIF: A New Method for Identifying Cancer Driver Genes through Effective Data Integration. Adv Sci (Weinh). 2018 Jul 23;5(9):1800640. https://doi:10.1002/advs.201800640

40. Niu M, Tabari E, Ni P, Su Z. Towards a map of cis-regulatory sequences in the human genome. Nucleic Acids Res. 2018 Jun 20;46(11):5395-5409. https://doi:10.1093/nar/gky338

39. Junjing Jia, Irfan Ahmed, Lixian Liu, Yong Liu , Zhiqiang Xu , Xiaohua Duan , Qihua Li , Tengfei Dou , Dahai Gu , Hua Rong , Kun Wang , Zhengtian Li , Mir Zulqarnain Talpur , Ying Huang , Shanrong Wang , Shixiong Yan , Huiquan Tong , Sumei Zhao , Guiping Zhao , Marinus F. W. te Pas, Zhengchang Su, Changrong Ge. Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens. PLOS ONE. https://doi.org/10.1371/journal.pone.0195378 April 9, 2018.

38. Chen Xu and Zhengchang Su. Prediction of the cooperative cis-regulatory elements of broadly expressed neuronal genes in Caenorhabditis elegans. Proceedings of 10th International Symposium, ISBRA 2014, Zhangjiajie, China, June 28-30, 2014

37. Ehsan Tabari and Zhengchang Su. PorthoMCL: Parallel orthology prediction using MCL for the realm of massive genome availability. Big Data Analytics. 2017; 2:4. https://doi:10.1186/s41044-016-0019-8 . Google Scholar citations: 18.

36. Chen Xu and Zhengchang Su. Identification of cell types from single-cell transcriptome using a novel clustering method. Bioinformatics 2015 (btv088) (pdf)

35. Chen Xu and Zhengchang Su. Identification of genes driving lineage divergence from single-cell gene expression data in C. elegans. Developmental biology. 2014 Sep 15;393(2):236-44. (pdf)

34. Meng Niu, Ehsan Tabari and Zhengchang Su. De novo prediction of cis-regulatory modules through integrative analysis of a large number of ChIP datasets BMC Genomics. 2014 Dec 2;15:1047. (pdf)

33. Shan Li, Xia Dong and Zhengchang Su. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics. 2013, 14:520 (pdf)

32. Shaoqiang Zhang, Lifen Jiang Chuanbin Du and Zhengchang Su. A Novel Information Contents Based Similarity Metric for Comparing TFBS Motifs. 2012 IEEE International Conference on Systems Biology (ISB) (pdf)

31. Shaoqiang Zhang, Huazhi Su, Guojun Li, Zhengchang Su, A simulated annealing heuristic for resource allocation and scheduling with precedence constraints, Journal of Information & Computational Science. 2011,Vol.8 (9) :1541-1550.

30. Shaoqiang Zhang, Huazhi Sun, Guojun Li, Zhengchang Su. A Simulated Annealing Algorithm for Resource Allocation and Scheduling with Precedence Constraints in the GLECLUBS/eGLECLUBS Pipelines. cse, pp.421-426, 2011. 14th IEEE International Conference on Computational Science and Engineering, 2011.

29. Shaoqiang Zhang, Shan Li, Meng Niu, Phuc Pham and Zhengchang Su. MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC Bioinformatics 2011, 12:238 (pdf)

28. Shan Li, Minli Xu and Zhengchang Su. Computational analysis of LexA regulons in Cyanobacteria. BMC Genomics 2010, 11:527. (pdf)

27. Xu M, Su Z. A novel alignment-free method for comparing transcription factor binding site motifs. PLoS One. 2010;5(1):e8797. (pdf)

26. Zhang S, Li S, Pham PT, Su Z. Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. BMC Bioinformatics. 2010;11:397. PMCID: 2920276. (pdf)

25. Shaoqiang Zhang, MinLi Xu, Shan Li, and Zhengchang Su. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Research, 2009. doi:10.1093/nar/gkp248. (PMID: 19383880)

24. Minli Xu and Zhengchang Su. Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes. BMC Genomics. 2009 Jan 15;10:23. (PMID: 19146659)

23. Zhengchang Su Guojun Li and Ying Xu. Prediction of regulons through comparative genomics analyses. In Computational methods for understanding bacterial and archaeal genomes. Ying Xu and J. Peter Gogarten (eds). Imperial Colleger Press. 2008. p259-279.

22. Zhengchang Su, Victor Olman and Ying Xu. Computational prediction of Pho regulons in Cyanobacteria. BMC Genomics. 2007 Jun 8;8:156. (PMID: 17559671)

21. P. Dam, V Olman, K. Harris, Z. Su, Ying Xu, Operon prediction using both genome-specific and general genome information, Nucleic Acids Research, 2007;35(1):288-98. (PMID: 17170009)

20. T. Tran, Phuongan Dam, Zhengchang Su, Farris Poole, Michael Adams, G. Tong Zhou, Ying Xu. Operon prediction in Pyrococcus furiosus.Nucleic Acids Res. 2007;35(1):11-20. (PMID: 17148478)

19. Zhenchang Su , Phuongan Dam, Xin Chen, Victor Olman, Tao Jiang, Brian Plaenik and Ying Xu. Computational inference and experimental validation of nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH8102. Nucleic Acids Research. 2006; 34(3):1050-65. (PMID: 16473855)

18. Andrea Catte, James Patterson; Gilbert Weinstein; Zhengchang Su; Ling Li; Jianguo Chen; Martin Jones; Marcela Aliste; Stephen Harvey; Jere Segrest . Novel Minimal Surface Conformations of Nascent High Density Lipoproteins through Molecular Dynamics. Biophysical Journal. 2006; 90(12):4345-60. (pdf)

17. H. Wu, F. Mao, Z. Su, V Olman, Ying Xu, Prediction of functional modules based on gene distributions in microbial genomes. Genome Inform.2005;16(2):247-59. (pdf)

16. Zhengchang Su, Victor Olman, Fenglou Mao, and Ying Xu. Comparative genomics analysis of ntcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Research. 2005, 33(16): 5156-5171. (pdf)

15. Jinling Huang, Zhengchang Su and Ying Xu, The evolution of Microbial phosphonate Degradation Pathways. Journal of Molecular Evolution. 2005; 61(5):682-90. (pdf)

14. Fenglou Mao, Zhengchang Su, Victor Olman, Phuongan Dam, Zhijie Liu, Ying Xu. Mapping of Orthologous Genes in the Context of Biological Pathways: an Application of Integer Programming. Proceedings of National Academy of Sciences U S A . 2005; 103(1):129-34. (pdf)

13. Hongwei Wu, Zhengchang Su, Victor Olman and Ying Xu. Prediction of functional gene modules based on comparative genome analysis and gene otology application, Nucleic Acids Research. 2005;33(9):2822-37. (pdf)

12. Zhengchang Su, Xiaochuan Guo, Richard L. Shoemaker, Richard B. Marchase, and J. Edwin Blalock. A Store-operated Nonselective Cation Channel in Human Lymphocytes. Cellular and Molecular Neurobiology. 2005; 25(3-4):625-47. (pdf)

11. Phuongan Dam and Zhengchang Su and Victor Olman Ying Xu. In sillco reconstruction of the carbon fixation pathway in Synechococcus sp. WH8102. Journal of Biological Systems. 2004; 12:97-125. (pdf)

10. Xin Chen, Zhengchang Su, Ying Xu, Tao Jiang. Computational prediction of operons in Synechococcus sp. WH8102. Genome Informatices 2004; 15(2):211-222. (pdf)

9. Victor Olman, Hanchun Peng, Zhengchang Su, Ying Xu. Mapping of Microbial Pathways through Constrained Mapping of Orthologous Genes. Proceedings of CSB 2004 Conference. p363-370. (pdf)

8. Zhengchang Su, Richard L. Shoemaker Richard B. Marchase and J. Edwin Blalock. Ca2+ dependent inactivation of monovalent cation current through Ca2+ release activated Ca channels. Biophys J. 2004;86(2):805-14. (pdf)

7. X. Chen, Z. Su, P. Dam, B. Palenik, Y. Xu and T. Jiang. Operon prediction by comparative genomics. Nucleic Acid Research. 2004; 19;32(7):2147-57. (pdf)

6. Zhenchang Su , Phuongan Dam, Xin Chen Vicor Olman, Tao Jiang, Brian Plaenik and Ying Xu. Computational inference of regulatory pathway in microbes. An application to phosphorus assimilation pathway. Genome Informatics 2003; 14:1-10. (pdf)

5. Zhengchang Su, Douglas S. Barker, Peter Csutora, Theresa Chang, Richard L. Shoemaker, Richard B. Marchase and J. Edwin Blalock. Regulation of Ca2+ release activated Ca2+ channel by INAD and Calcium influx factors. Am J Physiol Cell Physiol. 2003;284(2):C497-505. (pdf)

4. Zhengchang Su, Peter Csutora, Dacia Hunton, Richard L. Shoemaker, Richard B. Marchase, and J. Edwin Blalock A Store-operated Non-selective Cation Channel in Lymphocytes is Activated Directly by Ca2+ Influx Factor (CIF) and Diacylglycerol. American Journal of Physiology. 2001;280(5):C1284-92. (pdf)

3. Manion MK, Su Z, Villain M, Blalock JE. A new type of Ca(2+) channel blocker that targets Ca(2+) sensors and prevents Ca(2+)-mediated apoptosis. FASEB Journal. 2000;14(10):1297-306. (pdf)

2. Villain M, Jackson PL, Manion MK, Dong WJ, Su Z, Fassina G, Johnson TM, Sakai TT, Krishna NR, Blalock JE. De novo design of peptides targeted to the EF hands of calmodulin. Journal of Biological Chemistry 2000; 275(4):2676-85. (pdf)

1. Csutora P, Su Z, Kim HY, Bugrim A, Cunningham KW, Nuccitelli R, Keizer JE, Hanley MR, Blalock JE, Marchase RB. Calcium influx factor is synthesized by yeast and mammalian cells depleted of organellar calcium stores. Proceedings of National Academy of Sciences U S A. 1999;96(1):121-6. (pdf)