Publications

    1. S. N. Sahu, J. Lewis, I. Patel, S. Bozdag, J. H. Lee, R. Sprando, H. N. Cinar, "Genomic analysis of stress response against arsenic in Caenorhabditis elegans", in preparation.

    2. S. Bozdag, A. Li, G. Riddick, Y. Kotliarov, M. Baysan, F. M. Iwamoto, M. C. Cam, S. Kotliarova, H. A. Fine, "Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels", under review.

    3. M. Baysan, S. Bozdag, M. C. Cam, S. Kotliarova, S. Ahn, J. Walling, J. K. Killian, H. Stevenson, H. A. Fine, "G-CIMP status prediction of glioblastoma samples using mRNA expression data", under review.

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

    5. S. Wuchty, A. Vazquez, S. Bozdag, P. O. Bauer, "Genome-wide Associations of Signaling Pathways in Glioma Subtypes", under review.

    6. S. Wuchty, D. Arjona, S. Bozdag, P. O. Bauer, "The role of cancer-related miRs in networks of miR-gene interactions", NAR, in press.

    7. S. N. Sahu, J. Lewis, I. Patel, S. Bozdag, J. H. Lee, J. E. LeClerc, H. N. Cinar, "Genomic Analysis of Immune Response against Vibrio cholerae Hemolysin in Caenorhabditis elegans", PLoS ONE 2012 7(5): e38200.

    8. 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.

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

    10. 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, 3:11.

    11. 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, 10:582.

    12. S. Bozdag, T. J. Close, S. Lonardi, "A compartmentalized approach to the assembly of physical maps", BMC Bioinformatics 2009, 10:217.

    13. 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 148-161.

    14. 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.


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.