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Author: Xiaoning Qian

Easton Li Xu, Xiaoning Qian, Qilian Yu, Han Zhang, Shuguang Cui, "Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application", BMC Genomics, 19(Suppl 4): 170, 9 pages, doi: 10.1186/s12864-018-4552-x, 2018.  (Journal Publication)  [More Details]  [Online]

Yijie Wang and Xiaoning Qian, "Finding Low-Conductance sets with Dense interactions (FLCD) for better protein complex prediction", BMC Systems Biology, 11(S3): 22, 11 pages, doi: 10.1186/s12918-017-0405-5, 2017.  (Journal Publication)  [More Details]  [Online]

SiamakZamaniDadaneh, Xiaoning Qian, Mingyuan Zhou, "BNP-Seq: Bayesian nonparametric differential expression analysis of sequencing count data", Journal of the American Statistical Association, in press, DOI: 10.1080/01621459.2017.1328358, 2017  (Journal Publication)  [More Details]  [Online]

ShahinBoluki, Mohammad ShahrokhEsfahani, Xiaoning Qian, Edward R. Dougherty, "Constructing pathway-based priors within a Gaussian Mixture Model for Bayesian regression and classification", IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, DOI: 10.1109/TCBB.2017.2778715, 2017  (Journal Publication)  [More Details]  [Online]

MeltemApaydin, Liang Xu, Bo Zeng, Xiaoning Qian, "Robust mutant strain design by pessimistic optimization", BMC Genomics, 18(S6): 677, 12 pages, doi: 10.1186/s12864-017-4025-7, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "CUFID-query: accurate network querying through estimation of network flow between query and target networks based on random walk", BMC Bioinformatics, 18(Suppl 14):500, 2017  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Xiaoning Qian, and Byung-Jun Yoon, "Effective computational detection of piRNAs using n-gram models and support vector machine", BMC Bioinformatics, 18(Suppl 14):517. 2017.  (Journal Publication)  [More Details]  [Online]

Chun-Chi Chen, Noushin Ghaffari, Xiaoning Qian, and Byung-Jun Yoon, "Optimal hybrid sequencing and assembly: feasibility conditions for accurate genome reconstruction and cost minimization strategy", Computational Biology and Chemistry, 69, pp. 153–163, 2017  (Journal Publication)  [More Details]  [Online]

AseemPandey, Sheng Li Ding, Qing-Ming Qin, Rahul Gupta, Gabriel Gomez, Furong Lin, Xue-huaFeng, Luciana Fachini da Costa, Sankar P. Chaki, MadhuKatepalli, Elizabeth Case, Erin van Schaik, TabasumSidiq, Omar Khalaf, Angela Arenas, Koichi Kobayashi, James E. Samuel, Gonzalo Rivera, Robert C. Alaniz, Sing-Hoi Sze, Xiaoning Qian, Allison Rice-Ficht, William Russell, Thomas A. Ficht, Paul de Figueiredo, "Global reprogramming of host kinase signaling in response to fungal infection", Cell Host & Microbe, 21(5): 637–649.e1–e6, 2017. (Cover Page)  (Journal Publication)  [More Details]  [Online]

Yijie Wang and Xiaoning Qian, "Stochastic block coordinate Frank-Wolfe algorithm for large-scale biological network alignment,", EURASIP Journal on Bioinformatics and Systems Biology, 2016: 9, 9 pages, doi: 10.1186/s13637-016-0041-1, 2016.  (Journal Publication)  [More Details]  [Online]

Xiaoning Qian and Edward R. Dougherty, "Bayesian regression with network prior: Optimal Bayesian filtering perspective", IEEE Transactions on Signal Processing, 64(23):6243-6253, 2016.  (Book Chapter)  [More Details]  [Online]

SiamakZamaniDadanehand Xiaoning Qian, "Bayesian module identification from multiple noisy networks", EURASIP Journal on Bioinformatics and Systems Biology, 2016:5, 11 pages, doi: 10.1186/s13637-016-0038-9, 2016.  (Book Chapter)  [More Details]  [Online]

Meng Lu, Jianhua Z. Huang, Qian, "Sparse Exponential Family Principal Component Analysis", Pattern Recognition, 60: 681-691, 2016.  (Journal Publication)  [More Details]  [Online]

Hyundoo Jeong, Xiaoning Qian, and Byung-Jun Yoon, "Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model", BMC Bioinformatics, 17(Suppl 13):395, 2016.  (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]

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]

Byung-Jun Yoon, Xiaoning Qian, and Edward R. Dougherty, "Quantifying the objective cost of uncertainty in complex dynamical systems", IEEE Transactions on Signal Processing, vol. 61, no. 9, pp. 2256-2266, May 2013  (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]

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]

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]