Xiaoning Qian , Ph.D.

*Email: <xqian, cse.usf.edu>


Assistant Professor

Dept. of Computer Science & Engineering

University of South Florida

4202 E Fowler Ave, ENB 118

Tampa, FL 33620


Office:   ENB 317

Phone:   +1-813-974-9653

Fax:   +1-813-974-5456



Brief Biography

    I am currently in the Department of Computer Science & Engineering at the University of South Florida. Before joining the department, I was in the Bioinformatics Training Program at the Department of Statistics, Texas A&M University.   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 Unviersity.



·  Special Issue on Genomic Signal Processing (GSP) -- Journal of Biological Systems (JBS)

   The aim of this special issue is to present the latest research advances in the broad area of GSP. Detailed information about the special issue can be found in the following CFP [Call for Paper]:
    - Submission Deadline: July 1st, 2012;
    - Lead Guest Editor: Edward R. Dougherty (Texas A&M);
    - Guest Editors: Byung-Jun Yoon (Texas A&M), Xiaoning Qian (USF), Ranadip Pal (Texas Tech);
    - Journal Website: http://www.worldscinet.com/jbs/

·  IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'12)

   GENSIPS'12 will provide a forum for signal processing researchers, bioinformaticians, computational biologists, biomedical engineers, and biostatisticians to exchange ideas and discuss the challenges confronting computational bioinformatics and systems biology communities due to the high modality of disparate high-throughput data, high variability of data acquisition, high dimensionality of biomedical data, and high complexity of genomics and proteomics.:
    - Paper Submission Deadline: August 1st, 2012 [Call for Paper].

Research Interests

·  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.

New: 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 and brief research statements.


    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 (New):  Spring 2013

·         Introduction to Bayesian learning methods in statistical learning


Current Graduate Students

    - Amin Ahmadi Adl (PhD student 2011 – present);
    - Meng Lv (PhD student 2010 – present);
    - Shaogang Ren (PhD student 2012 – present);
    - Seyed Javad Sajjadi (PhD student 2010 – present, co-advising with Dr. Bo Zeng);
    - Yijie Wang (PhD student 2010 – present);
    - Bhargava Kondaveeti (MS student 2010 – present).

Selected Publications

·         Yijie Wang and Xiaoning Qian,
"A novel subgradient-based optimization algorithm for blockmodel functional module identification
," [New]
11th Asia Pacific Bioinformatics Conference, 2013.

·         Shaogang Ren, Bo Zeng, and Xiaoning Qian,
"Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints
," [New]
11th Asia Pacific Bioinformatics Conference, 2013.

·         Meng Lu, Jianhua Z. Huang, and Xiaoning Qian,
"Supervised logistic principal component analysis for pathway based genome-wide association studies
," [New]
ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012.

·         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, Sayed Mohammad Ebrahim Sahraeian, and Byung-Jun Yoon,
"Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores
," [Paper]
BMC Bioinformatics, 12(Suppl 10), S6, 2011.

·         Xiaoning Qian and Byung-Jun Yoon,
"Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception
," [Paper]
BMC Bioinformatics 12(Suppl 1), S19: 10 pages, doi:10.1186/1471-2105-12-S1-S19, 2011.

·         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.

·         Ivan Ivanov,  Plamen Simeonov, Noushin Ghaffari,  Xiaoning Qian and Edward R. Dougherty,
Selection policy-induced reduction mappings for Boolean networks," [Paper]
IEEE Transactions on Signal Processing, 58(9): 4871--4882, 2010.

·         Noushin Ghaffari,  Ivan Ivanov,  Xiaoning Qian and Edward R. Dougherty,
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks,"[Paper]
Bioinformatics, 26(12): 1556--1563, 2010.

·         Xiaoning Qian and Byung-Jun Yoon,
Effective identification of conserved pathways in biological networks using hidden Markov models," [Paper]
PLoS ONE 4(12): e8070. Doi:10.1371/journal.pone.0008070, 2009.

·         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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