Xiaoning Qian , Ph.D.

*Email: <xqian, ece.tamu.edu>

Assistant Professor

Dept. of Electrical & Computer Engineering

Texas A&M University

MS 3128, TAMU

College Station, TX 77843


Office:   Wisenbaker Engineering Research Center (WERC) 205J

Phone:   +1-979-845-6268



Brief Biography

    I am currently in the Department of Electrical & Computer Engineering at Texas A&M University . Before joining the department, I was in the Department of Computer Science & Engineering at the University of South Florida (USF).   I worked on biomedical image segmentation and shape-based image databases using statistical shape analysis in the Image Processing and Analysis Group (IPAG) at Yale University. I received my Ph.D. degree from Yale University.



·  I am organizing the Bio-Seminar for Biomedical Imaging, Sensing & Genomic Signal Processing in the Department of Electrical & Computer Engineering at Texas A&M. If you will be around College Station, I would certainly love to have you to give a talk and meet with our faculty and students.

·  My first edited book ``Emerging Research in the Analysis and Modeling of Gene Regulatory Networks'' can be found at Amazon.

Publication Errata

    The convergence proof in the recent retracted conference paper---Y Wang and X Qian, "Stochastic Coordinate Descent Frank-Wolfe Algorithm for Large-Scale Biological Network Alignment" in Proceedings of 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP'2014)---is not correct. Please consult the full paper at arXiv.


Research Interests

·  Bayeisan learning & experimental design:
    - Bayesian learning and analytic methods for large-scale data in life and materials science;
    - Bayesian computation for optimal experimental design with model and data uncertainty.

·  Bioinformatics:
    - Analysis and intervention in biological networks;
    - Functional data analysis on genomic and proteomic datasets.

·  Biomedical image processing and analysis:
    - Image segmentation and robust boundary finding;
    - Shape-based similarity retrieval in multimedia databases.

I am currently recruiting for graduate students. Research Assistantship (RA) positions will be offered to outstanding students who are hard-working and motivated. Interested candidates should email their CVs, transcripts, and brief research statements. [Note] I apologize but I may not have time to reply to all the inquiry emails. However, I do reply to the students who have applied for admissions to our department if you have all the requested documents in your inquiry emails.



    ECEN 303.501 Random Signals and Systems:  Fall 2013, 2014, 2015; Spring 2017

·         Introduction to fundamental concepts of probability theory and their applications in engineering problems

    ECEN 489.500 SPTP: At the Interface of Engineering and Life Sciences :  Spring 2015, 2016, 2017, 2018

·         Overview of electrical and computer engineering principles that are being applied to various areas in life sciences to address emerging grand challenges

    ECEN 765.600 Machine Learning with Networks :  Spring 2014, 2015; Fall 2016, 2017

·         Introduction to basics of machine learning, focusing on state-of-the-art research with structured data


    CISE 6930.002 Computational Molecular Biology:  Spring 2010

·         Introduction to major topics in bioinformatics and computational biology

    CISE 4930.007/6930.002 Data Mining in Bioinformatics:  Spring 2011

·         Introduction to basic data mining and machine learning techniques and their applications

    GMS 7930 Bioinformatics (I & II):  Fall 2011, 2012

·         Introduction to basic topics in bioinformatics (lead lecturer: Dr. Vladimir N. Uversky)

    CISE 4930.007/6930.002 Biological Network Analysis:  Spring 2012

·         Introduction to basic methods to analyze topology and dynamics of network systems

    CISE 6930.002 Machine Learning:  Spring 2013

·         Introduction to Bayesian learning methods in statistical learning


Current Students

    - Siamak Zamani Dadaneh (PhD student 2014 – present);
    - Chung-Chi "Charles" Tsai (PhD student 2014 – present);
    - Meltem Apaydin (PhD student 2015 – present);
    - Kai He (PhD student 2015 – present);
    - Ehsan Hajiramezanali (PhD student 2016 – present);
    - Guang Zhao (PhD student 2016 – present);
    - Randy Ardywibowo (PhD student 2017 – present; REU student 2016 – 2017);

    - Xiaoqian Jia (MS student 2017 – present);
    - Fan Liu (MS student 2017 – present);
    - Xueting Liu (MS student 2017 – present);

    - Dario Avendano Ovalle (Undergraduate researcher 2017 – present);


    - Seyed Javad Sajjadi (PhD – defended summer 2014, co-advising with Dr. Bo Zeng; Current employment: Data scientist at Precima, Inc.; LoyaltyOne);
    - Yijie Wang (PhD – defended summer 2015; First employment: Post-doc at NIH/NCBI);
    - Amin Ahmadi Adl (PhD – defended summer 2015; Current employment: Data scientist at Microsoft);
    - Meng Lv (PhD – defended fall 2015; First employment: Assistant professor at Tianjin University);
    - Shaogang Ren (PhD – defended fall 2017);
    - Zhou Wang (MS – defended fall 2016; First employment: FactSet Research System).

Selected Recent Publications

    Please check my Google Scholoar page for a more complete list of publications.

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

·         Siamak Zamani Dadaneh and Xiaoning Qian,
"Bayesian module identification from multiple noisy networks
," [Paper]
EURASIP Journal on Bioinformatics and Systems Biology, 2016:5, 2016.

·         Meltem Apaydin, Bo Zeng, Xiaoning Qian,
"Is OptKnock a reliable strategy for desirable mutants?
," [Paper]
Workshops on Machine Learning in Computational Biology (MLCB) & Machine Learning in Systems Biology (MLSB) 2015, A Workshop at the Annual Conference on Neural Information processing Systems (NIPS 2015), Montreal, Canada, December, 2015.

·         Shaogang Ren, Shuai Huang, John Onofrey, Xenophon Papademetris, Xiaoning Qian,
"A scalable algorithm for structured kernel feature selection
," [Paper]
Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics (AISTATS), 781-789, San Diego, CA, May, 2015.

·         Yijie Wang and Xiaoning Qian,
"Functional module identification in protein interaction networks by interaction patterns
," [Paper]
Bioinformatics, 30(1): 81-93, 2014.

·         Meng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, and Xiaoning Qian,
"Supervised categorical principal component analysis for genome-wide association analyses
," [Paper]
BMC Genomics, 15(Suppl 1):S10, 2014.

·         Byung-Jun Yoon, Xiaoning Qian, Edward R Dougherty,
"Quantifying the objective cost of uncertainty in complex dynamic systems
," [Paper]
IEEE Transactions on Signal Processing, 61(9): 2256-2266, 2013.

·         Yijie Wang and Xiaoning Qian,
"A novel subgradient-based optimization algorithm for blockmodel functional module identification
," [Paper]
BMC Bioinformatics, 14(Suppl 2): S23, 2013.

·         Shaogang Ren, Bo Zeng, and Xiaoning Qian,
"Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints
," [Paper]
BMC Bioinformatics, 14(Suppl 2):S17, 2013.

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

·         Xiaoning Qian and Edward R Dougherty,
"Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior
," [Paper]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(1): 123--136, 2012.

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

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

·         Xiaoning Qian and Edward R. Dougherty,
On the long-run sensitivity of probabilistic Boolean networks," [Paper]
Journal of Theoretical Biology, 257(4): 560-577, 2009.

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

·         Xiaoning Qian , Matthew P. Brennan, Donald P. Dione, Wawrzyniec L. Dobrucki, Marcel P. Jackowski, Christopher K. Breuer, Albert J. Sinusas, Xenophon Papademetris,
A nonparametric vessel detection method for complex vascular structures," [Paper]
Medical Image Analysis, 13(1): 49-61, 2009.

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


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