Publications

  1. A. Li, S. Bozdag, S. Wuchty, J. C. Zenklusen, H. A. Fine, “GliomaPredict: A Clinically Useful Tool For Assigning Glioma Patients to Specific Molecular Subtypes”, BMC Medical Informatics and Decision Making, 2010, 10:38 PDF

  2. S. Bozdag, A. Li, S. Wuchty, H. A. Fine, “FastMEDUSA: A parallelized tool to infer gene regulatory networks”, Bioinformatics, 2010, 26 (14) 1792-1793 PDF

  3. Y. Kotliarov, S. Bozdag, H. Chen, S. Wuchty, J. C. Zenklusen, H. A. Fine, “CNAReporter: A computational tool for the generation of clinical reports of genomic alterations”, BMC Medical Genomics 2010, 3:11PDF

  4. T. J. Close, P. R. Bhat, S. Lonardi, Y. Wu, N. Rostoks, L. Ramsay, A. Druka, N. Stein, J. T. Svensson, S. Wanamaker, S. Bozdag, M. L. Roose, M. J. Moscou, S. Chao, R. Varshney, P. Szucs, K. Sato, P. M. Hayes, D. E. Matthews, A. Kleinhofs, G. J. Muehlbauer, J. DeYoung, D. F. Marshall, K. Madishetty, R. D. Fenton, P. Condamine, A. Graner and R. Waugh, "Development and implementation of high-throughput SNP genotyping in barley", BMC Genomics, 2009, 10:582PDF

  5. S. Bozdag, T. J. Close, S. Lonardi, “A compartmentalized approach to the assembly of physical maps”, BMC Bioinformatics, 2009, 10:217 PDF

  6. S. Bozdag, T. J. Close, S. Lonardi, “Computing the minimal tiling path from a physical map by integer linear programming”, Proceedings of Workshop on Algorithms in Bioinformatics (WABI’08), pp 148-161PDF

  7. S. Bozdag, T. J. Close, S. Lonardi, “A compartmentalized approach to the assembly of physical maps”, Proceedings of IEEE International Symposium on Bioinformatics & Bioengineering (BIBE'07), pp. 218-225, Boston, MA, 2007 PDF (acceptance rate: 13%)

  8. S. Bozdag, T. J. Close, S. Lonardi, “Selecting the minimal tiling path from a physical map via integer linear programming”, under review.

  9. S. N. Sahu, I. Patel, J. Lewis, S. Bozdag, H. N. Cinar, “Genomic Analysis of Immune Response against Vibrio cholerae Hemolysin in Caenorhabditis elegans”, in preparation.

  10. S. Bozdag, A. Li, M. Baysan, G. Riddick, Y. Kotliarov H. A. Fine, "Age-specific genetic and epigenetic signatures in glioblastoma", in preparation.


Abstracts & Posters

  1. A. Li, S. Bozdag, S. Wuchty, J. C. Zenklusen, H. A. Fine, “GliomaPredict: A clinically useful tool for assigning glioma patients to specific molecular subtypes”, Poster in 3rd joint conference on Systems Biology, Regulatory Genomics, and DREAM – Reverse Engineering Challenges, 2010.

  2. S. Bozdag, A. Li, S. Wuchty, H. A. Fine, “Inferring gene regulatory networks via parallel programming”, Poster in 3rd joint conference on Systems Biology, Regulatory Genomics, and DREAM – Reverse Engineering Challenges, 2010.

  3. T. J. Close, M. Luo, S. Lonardi, M. Alpert, D. Duma, S. Bozdag, A. Farmer, G. D. May, S. A. Jackson, ,Y. Ma, Y. Q. Gu, ,J. Wu, ,F. M. You, N. Diop, S. Wanamaker, R. D. Fenton, M. P. Timko, P. A. Roberts, J. D. Ehlers, “Genome Resources for Cowpea Genotype IT97K-499-35”, Poster in Plant and Animal Genomics XIX Conference, 2011

  4. S. Bozdag, T. J. Close, S. Lonardi, “A graph-theoretic approach to compute minimal tiling path from a physical map”, Proceedings of LSS Computational Systems Bioinformatics Conference (CSB’09) PDF.

  5. T. J. Close, S. Lonardi, M.C. Luo, J. Dolezel, P. Bhat, K. Madishetty, J. T. Svensson, J. Zheng, Y. Wu, S. Bozdag, J. Resnik, S. Wanamaker, R.D. Fenton, M. Moscou, P. Condamine, E. L Rodriguez, M. L Roose, Y. Ma, F. You, J. Bartos, H. Simkova, N. Rostoks, L. Ramsay, D.F. Marshall, R. Waugh, N. Stein, A. Graner, R. Varshney, K. Sato, R. Wing, A. Schulman, …, B. Steffenson, “Coupling ESTs, SNPs, BACs, Mapping Populations, Flow-Sorting And Synteny To Access The Barley Genome”, Poster in Plant and Animal Genomes XVII Conference, 2009

  6. S. Bozdag, T. J. Close, S. Lonardi, “A Compartmentalized Approach to the Assembly of the Physical Maps”, Poster in Plant and Animal Genomes XVI Conference, 2008.

  7. Y. Ma, H. Witt, R. Naderi, F. M. You, C. X. Wang, K. Madishetty, J. T. Svensson, J. Zheng, P. Condamine, R. Ashgar, S. Wanamaker, P. Bhat, M. Moscou, E. Rodriguez, H. Walia, J. Resnik, S. Bozdag, G. J. Muehlbauer, S. Lonardi, T. J. Close, M.C. Luo, “Updates on Contig Assembly with Gene-Containing BACs of Barley”, Poster in Plant and Animal Genomes XVI Conference, 2008.

  8. K. Madishetty, P. Condamine, M. Moscou, J. T. Svensson, J. Zheng, S. Wanamaker, P. Bhat, E. Rodriguez, H. Walia, S. Bozdag, J. Resnik, H. Le, S. Heinen, G. H. Muehlbauer, M.C. Luo, T. Jiang, S. Lonardi, H. Witt, F. You, T. J. Close, “Progress on physical mapping of the gene-space of barley”, Abstract in Plant and Animal Genomes XV Conference, 2007.

  9. Y. Ma, H. Witt, R. Naderi, F. M. You, C. X. Wang, K. Madishetty, J. T. Svensson, J. Zheng, P. Condamine, R. Ashgar, S. Wanamaker, P. Bhat, M. Moscou, E. Rodriguez, H. Walia, J. Resnik, S. Bozdag, G. J. Muehlbauer, S. Lonardi, T. J. Close, M.C. Luo, “Contig assembly of gene-containing BACs of barley”, Poster in Plant and Animal Genomes XV Conference, 2007.

  10. J. T. Svensson, K. Madishetty, J. Zheng, Jin Xu, P. Condamine, R. Ashgar, S. Wanamaker, P. Bhat, M. Moscou, E. Rodriguez, H. Walia, J. Resnik, H. Le, S. Bozdag, H. Witt, F. You, N. Rostoks, R. Waugh, N. Stein, R. Varshney, A. Graner, M.C. Luo, X. Cui, T. Jiang, S. Lonardi, T. J. Close, “Connecting the barley genetic and physical maps for 1000 abiotic stress genes”, Abstract in Plant and Animal Genomes XIV Conference, 2006.