Sunduz Keles

Sunduz Keles

TEACHING

CV

Publications and submitted manuscripts:

S. Keleș, C. L. Warren, A. Z. Ansari (2007). CSITree: A regression tree appraoch for modeling binding properties of DNA binding molecules based on CSI-array data. Under review.

H. Shim and S. Keleș (2007). Integrating quantitative information from ChIP-chip experiments into motif finding. To appear in Biostatistics.

Y. Isogai, S. Takada, R. Tjian, S. Keleș (2007). Novel TRF1/BRF target genes revealed bu genome-wide analysis of Drosophila Pol III transcription. The EMBO Journal, Jan 10; 26(1): 79-89.

S. Dudoit, S. Keleș, and M. J. van der Laan (2006). Multiple tests of association with biological annotation metadata. [supp. website] Under review.

S. Keleș (2006). Mixture modeling for genome-wide localization of transcription factors. (Tech Rep 189). To appear in Biometrics.

S. Keleș, M. J. van der Laan, Sandrine Dudoit, and Simon E. Cawley (2006). Multiple Testing Methods for ChIP-Chip High Density Oligonucleotide Array Data. Journal of Computational Biology. 13(3): 579-613.

F. Lu, S. Keleș, S. Wright, and Wahba, G. (2005) A Framework for Kernel Regularization With Application to Protein Clustering. PNAS, 102 (35): 12332-12337.

H. Cinar, S. Keleș, and Y. Jin (2005). Expression Profiling of GABAergic Motor Neurons in Caenorhabditis elegans. Current Biology, 15 (4): 340 -346. (Journal website)

S. Keleș, M.J. van der Laan, and S. Dudoit (2004). Asymptotically optimal model selection method for regression on censored outcomes. Bernoulli, 10 (6): 1011-1037.

S. Keleș, M. J. van der Laan, and C. Vulpe (2004). Regulatory Motif Finding Using Logic Regression. Bioinformatics, 20 (16): 2799-2811. (Journal website)

M. J. van der Laan, S. Dudoit, and S. Keleș(2004). Asymptotic optimality of likelihood-based cross-validation. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3. (Journal website)

J. De Freitas, J. Kim, H. Poynton, T. Su, H. Wintz, T. Fox, P. Holman, A. Loguinov, S. Keleș, M.J. van der Laan, and C. Vulpe (2004). Exploratory and confirmatory gene expression profiling of mac1. Journal of Biological Chemistry, 2 (6): 4450-4458.

M. Miloslavsky, S.Keleș, M.J. van der Laan, and S. Butler (2004). Recurrent events analysis in the presence of time dependent covariates and dependent censoring. Journal of Royal Statistical Society Series B (Statistical Methodology), 66 (1): 239-257.

S. Keleș, M.J. van der Laan, and J.M. Robins (2004). Estimation of the bivariate survival function with right censored data structures. Handbook of Statistics, Volume 23: Advances in Survival Analysis, edited by N. Balakrishnan and C.R. Rao.

S. Dudoit, M. J. van der Laan, S. Keleș, A. M. Molinaro, S. E. Sinisi, and S. L. Teng (2003). Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding. SIGKDD Explotaions, 5 (2): 37-49.

S. Keleș, M.J. van der Laan, S. Dudoit, B. Xing, and M.B. Eisen (2003). Supervised detection of regulatory motifs in DNA sequences. Statistical Applications in Genetics and Molecular Biology, Vol. 2, No. 1, Article 5. (Journal website)

S. Keleș, M.J. van der Laan, and M. B. Eisen (2002). Identification of regulatory elements using a feature selection method. Bioinformatics, 18: 1167-1175. (Journal website)

S. Keleș, M.R. Segal (2002). Residual-based tree-structured survival analysis. Statistics in Medicine, 21: 313-326. (Journal website)

Dissertation:

S. Keleș (2003). Statistical methods for cis-regulatory motif detection in DNA sequences and Two censored data problems, Ph.D. dissertation.