Publications (Google Scholar)

[By type] [By year]

Journal Publications

  1. Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets
    S. Salem, C. Ozcaglar
    BioData Mining, 2014.

  2. TB-vis: Visualizing TB patient-pathogen relationships
    K. P. Bennett, C. Ozcaglar, J. Ranganathan, S. Raghavan, J. Katz, D. Croft, B. Yener, A. Shabbeer
    Tuberculosis, 2013.

  3. Crossing minimization within graph embeddings
    A. Shabbeer, C. Ozcaglar, K. P. Bennett
    arXiv, 2012.

  4. Inferred spoligoforest topology unravels spatially bimodal distribution of mutations in the DR region
    C. Ozcaglar, A. Shabbeer, N. Kurepina, N. Rastogi, B. Yener, K. P. Bennett
    IEEE Transactions on NanoBioscience, 2012.

  5. Epidemiological models of Mycobacterium tuberculosis complex infections
    C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, K. P. Bennett
    Mathematical Biosciences, 2012.
    Most accessed paper of Mathematical Biosciences journal between March 2012 and December 2012.

  6. TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex
    A. Shabbeer, L. S. Cowan, C. Ozcaglar, N. Rastogi, S. L. Vandenberg, B. Yener, K. P. Bennett
    Infection, Genetics and Evolution, 2012.

  7. Web tools for molecular epidemiology of tuberculosis
    A. Shabbeer, C. Ozcaglar, B. Yener, K. P. Bennett
    Infection, Genetics and Evolution, 2012.
    Most accessed paper of Infection, Genetics and Evolution journal between December 2011 and June 2012.

  8. Sublineage structure analysis of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors
    C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, K. P. Bennett
    BMC Genomics, 2011.

Conference and Workshop Publications

  1. MFMS: Maximal frequent module set mining from multiple human gene expression datasets
    S. Salem, C. Ozcaglar
    ACM SIGKDD International Workshop on Data Mining in Bioinformatics (BIOKDD), Chicago, August 2013.

  2. Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using spoligoforests
    C. Ozcaglar, A. Shabbeer, N. Kurepina, B. Yener, K. P. Bennett
    IEEE BIBM, Atlanta, November 2011.

  3. Visualization of tuberculosis patient and Mycobacterium tuberculosis complex genotype data via host-pathogen maps
    K. P. Bennett, C. Ozcaglar, J. Ranganathan, S. Raghavan, J. Katz, D. Croft, B. Yener, A. Shabbeer
    IEEE BIBM Workshop on Computational Advances in Molecular Epidemiology, Atlanta, November 2011.

  4. Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages
    M. Aminian, A. Shabbeer, K. Hadley, C. Ozcaglar, S. Vandenberg, K. P. Bennett
    ACM BCB, Chicago, August 2011.

  5. Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors
    C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, K. P. Bennett
    IEEE BIBM, Hong Kong, December 2010.

  6. Optimal embedding of heterogeneous graph data with edge crossing constraints
    A. Shabbeer, C. Ozcaglar, M. Gonzalez, K. P. Bennett
    NIPS Workshop on Challenges of Data Visualization, Whistler, BC, Canada, 2010.

  7. Multiple-biomarker tensor analysis for tuberculosis lineage identification
    C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, K. P. Bennett
    NIPS Workshop on Tensors, Kernels and Machine Learning, Whistler, BC, Canada. 2010.

  8. MetPetDB: The unique aspects of metamorphic geochemical data and their influence on data model, user interface and collaborations
    J. M. Pyle, F. S. Spear, S. Adali, B. Szymanski, S. Pearce, A. Waters, Z. Linder, C. Ozcaglar
    Geological Society of America Abstracts with Programs, Denver, 2007.

Technical Reports

  1. Host-pathogen association analysis of tuberculosis patients via Unified Biclustering Framework
    C. Ozcaglar, B. Yener, K. P. Bennett
    Rensselaer Polytechnic Institute, TR-12-05, 2012.

  2. A clustering framework for Mycobacterium tuberculosis complex strains using multiple-biomarker tensors
    C. Ozcaglar, A. Shabbeer, S. Vandenberg, B. Yener, K. P. Bennett
    Rensselaer Polytechnic Institute, TR-10-08, 2010.

  3. MetPetDB: A database for metamorphic geochemistry
    F. S. Spear, J. M. Pyle, S. Adali, B. Szymanski, A. Waters, Z. Linder, C. Ozcaglar, S. Pearce
    Rensselaer Polytechnic Institute, TR-08-14, 2008.

Theses

  1. Algorithmic data fusion methods for tuberculosis
    Ph.D. thesis, 2012.

  2. Classification of email messages into topics using Latent Dirichlet Allocation
    M.S. thesis, 2008.

Working Papers

  1. Ensampling Methods.
    C. Ozcaglar, S. Salem.