PUBLICATIONS (over 1,170 Citations, h-index 14 by google scholar)

Link to my Google Scholar profile

  1. Brandon S. Razooky, Youfang Cao, Alan S. Perelson, Michael L. Simpson, Leor S. Weinberger (2017) Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean. PLoS Biology. 15(10):e2000841. (*Main contributor in modeling) (PDF)
  2. Jieling Zhao, Youfang Cao, Luisa A. DiPietro, and Jie Liang (2017). Dynamic cellular finite element method for modeling large scale cell migration and proliferation under the control of mechanical and biochemical cues: A study of reepithelialization. Journal of the Royal Society Interface. 14:20160959. (PDF)
  3. Jenna B. Honeycutt, William O. Thayer, Caroline E. Baker, Ruy M. Ribeiro, Steven M. Lada, Youfang Cao, Rachel A. Cleary, Michael G. Hudgens, Douglas D. Richman & J. Victor Garcia (2017). HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy. Nature Medicine. 23(5):638-643. (PDF)
  4. Youfang Cao, Anna Terebus and Jie Liang (2016). State space truncation with quantified errors for accurate solutions to discrete chemical master equation. Bulletin of Mathematical Biology. 78:617–661. (PDF)
  5. Youfang Cao, Anna Terebus and Jie Liang (2016). Accurate Chemical Master Equation solution using multi-finite buffers. SIAM: Multiscale Modeling and Simulation. 14(2): 923–963. (PDF)
  6. Youfang Cao, Anna Terebus and Jie Liang (2016), Modeling stochastic gene regulatory networks using direct solutions of chemical master equation and rare event sampling. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks. IGI Global. (PDF) (Book Chapter)
  7. Amber Ismael, Wei Tian, Nicholas Waszczak, Xin Wang, Youfang Cao, Dmitry Suchkov, Eli Bar, Metodi V. Metodiev, Jie Liang, Robert A. Arkowitz, and David E. Stone (2016). Gβ promotes receptor polarization and chemotropism by inhibiting receptor phosphorylation, Science Signaling. 9(423): ra38. (PDF) (*Main contributor in modeling)
  8. Jie Liang, Youfang Cao, Gamze Gursoy, Hammad Naveed, Anna Terebus and Jieling Zhao (2015), Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells. Critical Reviews in Biomedical Engineering, 43 (4), 323-346. (PDF)
  9. Sema Kachalo, Hammad Naveed, Youfang Cao, Jieling Zhao, and Jie Liang (2015). Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern. PLoS One. 10(5): e0126484. (PDF)
  10. Anna Terebus, Youfang Cao and Jie Liang (2014). Exact Computation of Probability Landscape of Stochastic Networks of Single Input and Coupled Toggle Switch Modules. Conf Proc IEEE Eng Med Biol Soc. 5228-5231. (PDF) (Peer-reviewed conference paper)
  11. Wei Tian, Youfang Cao, Amber Ismael, David Stone and Jie Liang (2014). Roles of Regulated Internalization in the Polarization of Cell Surface Receptors. Conf Proc IEEE Eng Med Biol Soc. 1166-1169. (PDF) (Peer-reviewed conference paper)
  12. Youfang Cao and Jie Liang (2013). Adaptively biased sequential importance sampling for rare events in reaction networks with comparison with exact solutions from finite buffer dCME method. Journal of Chemical Physics 139, 025101. (PDF)
  13. Youfang Cao, Hammad Naveed, Claire Liang and Jie Liang (2013). Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. Conf Proc IEEE Eng Med Biol Soc. 5550-5553. (PDF)
  14. Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen and Qing Nie (2012). Modeling spatial population dynamics of stem cell lineage in tissue growth. Conf Proc IEEE Eng Med Biol Soc. 5502–5505. (PDF)
  15. Hongyuan Zhu, Tianqi Chen, Xue Lei, Wei Tian, Youfang Cao and Ping Ao (2012). Understand the noise of CI expression in phage λ lysogeny. Control Conference (CCC), 31st Chinese, 7432-7436. (Peer-reviewed conference paper)
  16. Xiaojun Zhang, Siqing Yue, Huihui Zhong, Weiying Hua, Ruijia Chen, Youfang Cao, Liping Zhao (2011). A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis. Applied Microbiology and Biotechnology, 91(2), 425-434.
  17. Chenhong Zhang, Menghui Zhang, Shengyue Wang, Ruijun Han, Youfang Cao, Weiying Hua, Yuejian Mao, Xiaojun Zhang, Xiaoyan Pang, Chaochun Wei, Guoping Zhao, Yan Chen and Liping Zhao (2010). Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. The ISME Journal 4:232–241. Highly Cited: 389 (PDF)
  18. Youfang Cao, Hsiao-Mei Lu and Jie Liang (2010). Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proceedings of the National Academy of Sciences USA, 107(43), 18445–18450. (PDF)
  19. Youfang Cao and Jie Liang (2010). Nonlinear Langevin model with product stochasticity for biological networks: the case of the Schnakenberg model. Journal of Systems Science and Complexity, 23:896–905. (PDF)
  20. Youfang Cao and Jie Liang (2009). Nonlinear coupling for improved stochastic network model: A study of Schnakenberg model. The Third International Symposium on Optimization and Systems Biology (OSB’09) ORSC & APORC 379–386. (PDF) (Peer-reviewed conference paper)
  21. Youfang Cao and Jie Liang (2008). Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability. BMC Systems Biology 2:30. (PDF)
  22. Youfang Cao, Hsiao-Mei Lu, and Jie Liang (2008). Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda. Conf Proc IEEE Eng Med Biol Soc. 611–614. (PDF) (Peer-reviewed conference paper)
  23. Youfang Cao and Jie Liang (2007). An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules. Conf Proc IEEE Eng Med Biol Soc. 4599-4602. (PDF) (Peer-reviewed conference paper)
  24. Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang and Kexuan Tang (2006). Prediction of protein structural class with Rough Sets. BMC Bioinformatics 7:20. Highly Cited: 138 (PDF)
  25. Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, Yulei Zhang, Guifang Wei, Junjian He, Yunfang Wang and Liping Zhao (2005). Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC Bioinformatics 6:190. (PDF)
  26. Lida Zhang, Kaijing Zuo, Fei Zhang, Youfang Cao, Jiang Wang, Yidong Zhang, Xiaofen Sun, Kexuan Tang (2006). Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics 7(1), 323.
  27. Lida Zhang, Shunwu Yu, Youfang Cao, Jiang Wang, Kaijing Zuo, Jie Qin, Kexuan Tang (2006). Distributional gradient of amino acid repeats in plant proteins. Genome 49 (8), 900-905.
  28. Kai-Jing Zuo, Jie Qin, Jing-Ya Zhao, Hua Ling, Li-Da Zhang, Youfang Cao, Ke-Xuan Tang (2007). Over-expression GbERF2 transcription factor in tobacco enhances brown spots disease resistance by activating expression of downstream genes. Gene 391(1-2), 80-90.
  29. Jin Wang, Kai-Jing Zuo, Jie Qin, Lida Zhang, Lan Su, Junrong Liu, Hua Ling, Jing-Ya Zhao, Youfang Cao, Ke-Xuan Tang (2007). Isolation and bioinformatics analyses of a COR413-like gene from Gossypium barbadense. Acta Physiologiae Plantarum 29(1), 1-9.
  30. Yidong Zhang, Zeyun Wang, Lida Zhang, Youfang Cao, Danfeng Huang, Kexuan Tang (2006). Molecular cloning and stress-dependent regulation of potassium channel gene in Chinese cabbage (Brassica rapa ssp. Pekinensis). Journal of Plant Physiology 163(9), 968-978.
  31. Jie Qin, Kaijing Zuo, Jingya Zhao, Hua Ling, Youfang Cao, Chengxiang Qiu, Fupeng Li, Xiaofen Sun and Kexuan Tang (2006). Overexpression of GbERF confers alteration of ethylene-responsive gene expression and enhanced resistance to Pseudomonas syringae in transgenic tobacco. Journal of Biosciences 31(2):255–263.
  32. Yidong Zhang, Zeyun Wang, Lida Zhang, Youfang Cao, Danfeng Huang, Kexuan Tang (2006). Molecular cloning and stress-dependent regulation of a glutamine synthetase gene in Chinese cabbage. Russian Journal of Plant Physiology 53 (2), 231-237.
  33. Jiang Wang, Lida Zhang, Kai-Jing Zuo, Hong-Mei Qian, Youfang Cao, Kexuan Tang (2006). Cloning and Expressional Studies of the Voltage‐dependent Anion Channel Gene from Brassica rapa L. Journal of Integrative Plant Biology 48 (2), 197-203.
  34. Guoan Shen, Yongzhen Pang, Weisheng Wu, Zhongxiang Deng, Lingxia Zhao, Youfang Cao, Xiaofen Sun, Kexuan Tang (2006). Cloning and characterization of a flavanone 3-hydroxylase gene from Ginkgo biloba. Bioscience Reports 26(1), 19-29.
  35. Lingxia Zhao, Jingfu Li, Yourong Chai, Guoyin Kai, Youfang Cao, Xiaofen Sun, Kexuan Tang (2006). Investigation on Genetic Relationship and Cross Compatibility of S. lycopersicoides and Lycopersicon. Pakistan Journal of Biological Sciences 9, 1160-1168.
  36. Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, Kexuan Tang (2004). Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20 (7), 1081.
  37. Jie Qin, Jingya Zhao, Kaijing Zuo, Youfang Cao, Hua Ling, Xiaofen Sun, Kexuan Tang (2004). Isolation and characterization of an ERF-like gene from Gossypium barbadense. Plant Science 167(6):1383–1389.
  38. Zhugang Li, Lingxia Zhao, Guoyin Kai, Shunwu Yu, Youfang Cao, Yongzhen Pang, Xiaofen Sun, Kexuan Tang (2004). Cloning and expression analysis of a water stress-induced gene from Brassica oleracea. Plant Physiology and Biochemistry 42 (10), 789-794.
  39. Dongqin Tang, Hongmei Qian, Shunwu Yu, Youfang Cao, Zhihua Liao, Lingxia Zhao, Xiaofen Sun, Danfeng Huang, Kexuan Tang (2004). cDNA cloning and characterization of a new stress-responsive gene BoRS1 from Brassica oleracea var. acephala. Physiologia Plantarum 121(4):578-585.
  40. Lingxia Zhao, Lixin Jin, Zhugang Li, Youfang Cao, Chengxiang Qiu, Dongqin Tang, Hongmei Qian, Kexuan Tang (2004). Cloning and DNA sequence Analysis of Element Responsive to Ethylene in E8 Promoter of the Tomato. Acta Horticulturae Sinica 31 (2), 204-208.
  41. Jingya Zhao, Kaijing Zuo, Jin Wang, Youfang Cao, Lida Zhang, Kexuan Tang (2003). cDNA cloning and characterization of a cotton peptide methionine sulfoxide reductase (cMsrA). Mitochondrial DNA 14 (4), 303-310.
  42. Yingchun Chen, Youfang Cao, Liping Zhao (2002). Non-random nature of genomic DNA amplification of E. coli K-12 MG1655 via ERIC-PCR. Microbiology China (Chinese) 29 (6), 28-32.
  43. Youfang Cao, Liping Zhao (2001). Computational analysis of the distribution of ERIC (IRU) in different bacterial genomes. Journal of Shanxi University (Natural Science Edition) (in Chinese) 25 (4), 354-357.