Publications
- N. Thieme, K. P. Bennett, Time to reactivation of latent tuberculosis infection varies by lineage. Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 493-494, 2016.
- M. Aminian, D. Couvin, A. Shabbeer, K. Hadley, S. Vandenberg, N. Rastogi, K. P. Bennett,
Predicting Mycobacterium tuberculosis Complex Clades Using Knowledge-Based Bayesian Networks. Biomedical Research International, 2014.
- Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Nalin Rastogi, Bulent Yener, Kristin P. Bennett,
Inferred spoligoforest topology unravels spatially bimodal distribution of mutations in the DR region. IEEE Transactions on NanoBioscience, 11 (3), 191-202, 2012.
- Amina Shabbeer, Cagri Ozcaglar, Bulent Yener, Kristin P. Bennett,
Web tools for molecular epidemiology of tuberculosis.
Infection, Genetics and Evolution, 12(4), pp. 767-781, June 2012.
- Amina Shabbeer, Lauren S. Cowan, Cagri Ozcaglar, Nalin Rastogi, Scott L. Vandenberg, Bulent Yener, Kristin P. Bennett
TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex. Infection, Genetics and Evolution, 12(4), pp. 789-797, June 2012.
- Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett, Epidemiological models of Mycobacterium tuberculosis complex infections. Mathematical Biosciences, 236(2), pp. 77-96, April 2012.
- Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Bulent Yener, Kristin P. Bennett,
Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using spoligoforests.
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), pp. 75 - 82, November 2011.
- Kristin P. Bennett, Cagri Ozcaglar, Janani Ranganathan, Srivatsan Raghavan, Jacob Katz, Dan Croft, Bulent Yener, and Amina Shabbeer,
Visualization of tuberculosis patient and Mycobacterium tuberculosis complex genotype data via host-pathogen maps.
IEEE BIBM Workshop on Computational Advances in Molecular Epidemiology, pp. 124 - 129, November 2011.
- Minoo Aminian, Amina Shabbeer, Kane Hadley, Cagri Ozcaglar, Scott Vandenberg, Kristin P. Bennett,
Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), pp. 201-208, August 2011.
- Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett,
Sublineage structure analysis of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors. BMC Genomics, 12(Suppl 2), p. S1, July 2011.
- Amina Shabbeer, Cagri Ozcaglar, Michael Gonzalez, Kristin P. Bennett,
Optimal embedding of heterogeneous graph data with edge crossing constraints. NIPS Workshop on Challenges of Data Visualization, p. 17, 2010.
- Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett,
Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors.
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), pp. 543 - 548, 2010.
- Gautam Kunapuli, Kristin P. Bennett, Amina Shabbeer, Richard Maclin, Jude Shavlik,
Online knowledge-based support vector machines.
European Conference on Machine Learning (ECML), pp. 145-161, 2010.
- Minoo Aminian, Amina Shabbeer, Kristin P Bennett,
A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages.
BMC Bioinformatics, 11(Suppl 3), p. S4, 2010.
- Minoo Aminian, Amina Shabbeer, Kristin P Bennett,
Determination of major lineages of Mycobacterium tuberculosis complex using Mycobacterial Interspersed Repetitive Units.
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), 2009.
- Inna Vitol, Jeffrey Driscoll, Barry Kreiswirth, Natalia Kurepina, Kristin P. Bennett,
Identifying Mycobacterium tuberculosis complex strain families using spoligotypes.
Infection, Genetics and Evolution, 6 (6), pp. 491-504, 2006.
- C. Ozcaglar, A. Shabbeer, N. Kurepina, B. Yener, K. P. Bennett,
Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using Spoligoforests. Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine, 75-82, 2011.
- C. Ozcaglar, B. Yener, B, K. P. Bennett,
Host-pathogen association analysis of tuberculosis patients via unified biclustering framework.
Tech. Rep., Dept. Comp. Sci., Rensselaer Polytechnic Inst., Troy, NY, Tech. Rep. 12-05, 2012.
- L. Yao, Probabilistic modeling of genome evolution and disease spread of tuberculosis. PhD Thesis 3684122, Rensselaer Polytechnic Institute, 2014.
- J. Blondin, Probabilistic models for phylogenetic classification of Mycobacterium tuberculosis complex genotyping data. MS Thesis 1540431, Rensselaer Polytechnic Institute, 2013.
- A. Shabbeer, Nonconvex nonsmooth optimization for bioinformatics. PhD Thesis 3613308, Rensselaer Polytechnic Institute, 2013.
- I. Vitol, Mathematical models for Mycobacterium tuberculosis complex genotyping and patient data. PhD Thesis 3220218, Rensselaer Polytechnic Institute, 2006.
- C. Ozcaglar, Algorithmic data fusion methods for tuberculosis. PhD Thesis 3533351, Rensselaer Polytechnic Institute, 2012.
