Software

TCF: Tensor Clustering Framework

References:

  1. 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.

  2. 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.

  3. 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.

SpolGen: Spoligoforest generator

References:

  1. 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.

  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.

UBF: Unified Biclustering Framework

References:

  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