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Topic: Regulatory Networks

Fangjun Li, Cheng Cheng, Fuhao Cui, Marcos VV de Oliveira, Xiao Yu, Xiangzong Meng, Aline C Intorne, Kevin Babilonia, Maoying Li, Bo Li, Sixue Chen, Xianfeng Ma, Shunyuan Xiao, Yi Zheng, Zhangjun Fei, Richard P Metz, Charles D Johnson, Hisashi Koiwa, Wenxian Sun, Zhaohu Li, Gonçalo A de Souza Filho, Libo Shan, Ping He, "Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity", Cell Host & Microbe doi:10.1016/j.chom.2014.10.018  (Journal Publication)  [More Details]  [Online]

Yijie Wang, Xiaoning Qian, , "A novel subgradient-based optimization algorithm for blockmodel functional module identification", BMC Bioinformatics, 14(Suppl 2):S23, 2013  (Journal Publication)  [More Details]  [Online]

Shaogang Ren, Bo Zeng, Xiaoning Qian, "Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints", BMC Bioinformatics, 14(Suppl 2):S17, 2013  (Journal Publication)  [More Details]  [Online]

Rezaei Yousefi, Datta, A. ; Dougherty, E., "Optimal Intervention in Markovian Gene Regulatory Networks with Random-Length Therapeutic Response to Antitumor Drug", Biomedical Engineering, IEEE Transactions on , vol.60, no.12, pp.3542,3552, Dec. 2013  (Journal Publication)  [More Details]  [Online]

Qian X, Dougherty ER., "Validation of gene regulatory network inference based on controllability", Front Genet. 2013 Dec 12;4:272.   (Journal Publication)  [More Details]  [Online]

Mohammadmahdi R. Yousefi, Edward R. Dougherty, "Intervention in gene regulatory networks with maximal phenotype alteration", Bioinformatics first published online April 29, 2013 doi:10.1093/bioinformatics/btt242  (Journal Publication)  [More Details]  [Online]

Mohammad Shahrokh Esfahania, Jason Knighta, Amin Zollanvaria, Byung-Jun Yoona, Edward R. Dougherty, "Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification", Pattern Recognition Volume 46, Issue 10, October 2013, Pages 2783–2797  (Journal Publication)  [More Details]  [Online]

Kahle JJ, Souroullas GP, Yu P, Zohren F, Lee Y, Shaw CA, Zoghbi HY, Goodell MA., "Ataxin1L is a regulator of HSC function highlighting the utility of cross-tissue comparisons for gene discovery", PLoS Genet. 2013 Mar;9(3):e1003359. doi: 10.1371/journal.pgen.1003359  (Journal Publication)  [More Details]  [Online]

D.C. Martins, Jr., E.A. de Oliveira, U.M. Braga-Neto, R.F. Hashimoto and R.M. Cesar, Jr., "Signal Propagation in Bayesian Networks and its Relationship with Intrinsically Multivariate Predictive Variables", Information Sciences, Vol. 225, Mar 2013, pp. 18-34, doi:10.1016/j.ins.2012.10.027.  (Journal Publication)  [More Details]

Nounou HN, Nounou MN, Meskin N, Datta A, Dougherty ER., "Fuzzy Intervention in Biological Phenomena", IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1819-25.   (Journal Publication)  [More Details]  [Online]

Knight, J., Datta, A., and Dougherty, E. R., "Generating Stochastic Gene Regulatory Networks Consistent With Pathway Information and Steady-State Behavior", IEEE Transactions on Biomedical Engineering, Vol. 59, No. 6, 1701-1710, 2012  (Journal Publication)  [More Details]  [Online]

Byung-Jun Yoon, Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, "Comparative analysis of biological networks using Markov chains and hidden Markov models", IEEE Signal Processing Magazine, Special Issue on Genomic and Proteomic Signal Processing in Biomolecular Pathways, 29(1): 22--34, 2012.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Edward R Dougherty, "Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 9, No. 1, 123-136, January, 2012  (Journal Publication)  [More Details]  [Online]

Zhao, C., Ivanov, I., Bittner, M. L., and Dougherty, E. R., "Pathway Regulatory Analysis in the Context of Bayesian Networks Using the Coefficient of Determination", Biological Systems, Vol. 19, No. 4, 651-682, December, 2011  (Journal Publication)  [More Details]  [Online]

Nader Meskin, Hazem N. Nounou, Mohamed N. Nounou, Aniruddha Datta, Edward R. Dougherty, "Intervention in Biological Phenomena Modeled by S-Systems", IEEE Trans. Biomed. Engineering 58(5): 1260-1267 (2011)  (Journal Publication)  [More Details]  [Online]

Ghaffari, N., Ivanov, I., Qian, X., and Dougherty, E. R., "A CoD-Based Stationary Control Policy for Intervening in Large Gene Regulatory Networks", BMC Bioinformatics 2011, 12(Suppl 10):S10doi:10.1186/1471-2105-12-S10-S10  (Journal Publication)  [More Details]  [Online]

Esfahani, M. S., Yoon, B-J., and Dougherty, E. R., "Probabilistic Reconstruction of the Tumor Progression Process in Gene Regulatory Networks in the Presence of Uncertainty", BMC Bioinformatics, 12(Suppl 10):S9, October, 2011  (Journal Publication)  [More Details]  [Online]

Dougherty ER., "Validation of gene regulatory networks: scientific and inferential", Briefings in Bioinformatics, 2011 May;12(3):245-52  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Noushin Ghaffari, Ivan Ivanov and Edward R. Dougherty, "State reduction for network intervention in probabilistic Boolean networks", Bioinformatics, 26(24): 3098--3104, 2010  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian, Ivan Ivanov, Noushin Ghaffari and Edward R. Dougherty, "Intervention in gene regulatory networks via greedy control policies based on long-run behavior", BMC Systems Biology, 3(61): 16 pages, 2009.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "On the long-run sensitivity of probabilistic Boolean network", Journal of Theoretical Biology, 257(4): 560--577, 2009  (Journal Publication)  [More Details]  [Online]

Dougherty ER, Brun M, Trent JM, Bittner ML., "Conditioning-based modeling of contextual genomic regulation", IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):310-20  (Journal Publication)  [More Details]  [Online]

Chao Sima, Jianping Hua and Sungwon Jung, "Inference of Gene Regulatory Networks Using Time-Series Data: A Survey", Current Genomics - CURR GENOMICS , vol. 10, no. 6, pp. 416-429, 2009  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian , Sing-Hoi Sze, Byung-Jun Yoon, "Querying pathways in protein interaction networks based on hidden Markov models", Journal of Computational Biology, 16(2):145--157, 2009  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "Effect of function perturbation on the steady state distribution of genetic regulatory networks: optimal structural intervention", IEEE Transactions on Signal Processing, 56(10):4966--4976, 2008.  (Journal Publication)  [More Details]  [Online]