Research

I'm working on the following research areas:

• Multiple-biomarker tensors to cluster M. tuberculosis complex strains into sublineages.
• Non-deterministic tensor decomposition.
• Visualization: spoligoforests and host-pathogen graphs.
• Epidemiological models of M. tuberculosis complex infections.

Publications

Journal publications

• Inferred spoligoforest topology unravels spatially bimodal distribution of mutations in the DR region
  Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Nalin Rastogi, Bulent Yener, Kristin P. Bennett
  IEEE Transactions on NanoBioscience, accepted, in preparation.
• Epidemiological models of Mycobacterium tuberculosis complex infections
  Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
  Mathematical Biosciences, 2012.
• TB-Lineage: An online tool for classification and analysis of strains of Mycobacterium tuberculosis complex
  Amina Shabbeer, Lauren S. Cowan, Cagri Ozcaglar, Nalin Rastogi, Scott L. Vandenberg, Bulent Yener, Kristin P. Bennett
  Infection, Genetics and Evolution, 2012.
• Incorporating biology rules of thumb into Bayesian Networks
  Minoo Aminian, Amina Shabbeer, Kane Hadley, Cagri Ozcaglar, Scott Vandenberg, Kristin P. Bennett
  Journal of Bioinformatics and Computational Biology (JBCB), in press, 2012.
• Web tools for molecular epidemiology of tuberculosis
  Amina Shabbeer, Cagri Ozcaglar, Bulent Yener, Kristin P. Bennett
  Infection, Genetics and Evolution, 2011.
• Sublineage structure analysis of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors
  Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
  BMC Genomics, 2011.

Conference and workshop publications

• Data-driven insights into deletions of Mycobacterium tuberculosis complex chromosomal DR region using spoligoforests
  Cagri Ozcaglar, Amina Shabbeer, Natalia Kurepina, Bulent Yener, Kristin P. Bennett
  IEEE BIBM, Atlanta, November 2011.
• Visualization of tuberculosis patient and Mycobacterium tuberculosis complex genotype data via host-pathogen maps
  Kristin P. Bennett, Cagri Ozcaglar, Janani Ranganathan, Srivatsan Raghavan, Jacob Katz, Dan Croft, Bulent Yener, Amina Shabbeer
  IEEE BIBM Workshop on Computational Advances in Molecular Epidemiology, Atlanta, November 2011.
• Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages
  Minoo Aminian, Amina Shabbeer, Kane Hadley, Cagri Ozcaglar, Scott Vandenberg, Kristin P. Bennett
  ACM BCB, Chicago, August 2011.
• Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors
  Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
  IEEE BIBM, Hong Kong, December 2010.
• Multiple-biomarker tensor analysis for tuberculosis lineage identification
  Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
  NIPS Workshop on Tensors, Kernels and Machine Learning. Whistler, BC, Canada. 2010.
• Optimal Embedding of Heterogeneous Graph Data with Edge Crossing Constraints
  Amina Shabbeer, Cagri Ozcaglar, Michael Gonzalez, Kristin P. Bennett
  NIPS Workshop on Challenges of Data Visualization, Whistler, BC, Canada, 2010.
• MetPetDB: The Unique Aspects of Metamorphic Geochemical Data and Their Influence on Data Model, User Interface and Collaborations
  Joseph M. Pyle, Frank S. Spear, Sibel Adali, Boleslaw Szymanski, Shawn Pearce, Anthony Waters, Zak Linder, Cagri Ozcaglar
  Geological Society of America Abstracts with Programs, Denver, 2007.

Technical reports

• A clustering framework for Mycobacterium tuberculosis complex strains using multiple-biomarker tensors
  Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
  Rensselaer Polytechnic Institute. TR-10-08, 2010.
• MetPetDB: A database for metamorphic geochemistry
  Frank S. Spear, Joseph M. Pyle, Sibel Adali, Boleslaw Szymanski, Anthony Waters, Zak Linder, Cagri Ozcaglar, Shawn Pearce
  Rensselaer Polytechnic Institute. TR-08-14, 2008.

Theses

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

Working papers

• Crossing minimization within graph embeddings
  Amina Shabbeer, Cagri Ozcaglar, Kristin P. Bennett
  Submitted to Journal of Machine Learning Research.
• Distance and time matter: Spatio-temporal attributes of tuberculosis patients via Unified Matrix-Tensor Clustering Framework
  Cagri Ozcaglar, Bulent Yener, Kristin P. Bennett