Publications

Journal publications

1. 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, 2012.
   
2. Epidemiological models of Mycobacterium tuberculosis complex infections
   Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, Kristin P. Bennett
   Mathematical Biosciences, 2012.
   Most accessed paper of Mathematical Biosciences journal between March 2012 and December 2012.
   
3. 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.
   
4. 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.
   
5. Web tools for molecular epidemiology of tuberculosis
   Amina Shabbeer, Cagri Ozcaglar, Bulent Yener, Kristin P. Bennett
   Infection, Genetics and Evolution, 2012.
   Most accessed paper of Infection, Genetics and Evolution journal between December 2011 and June 2012.
   
6. 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

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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

1. Host-pathogen association analysis of tuberculosis patients via Unified Biclustering Framework
   Cagri Ozcaglar, Bulent Yener, Kristin P. Bennett
   Rensselaer Polytechnic Institute. TR-12-05, 2012.
2. 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.
3. 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

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

• SAL++: Seeded spectral clustering with attributes and links
  Cagri Ozcaglar, Saeed Salem.
  
• DIQB: Density-invariant quasi-biclustering
  Cagri Ozcaglar, Kristin P. Bennett, Bulent Yener.
  
• Crossing minimization within graph embeddings
  Amina Shabbeer, Cagri Ozcaglar, Kristin P. Bennett.