Identification of regulatory elements using a feature selection method. - Sündüz Keles; Mark J. van der Laan; Michael B. Eisen (Bioinform., 2002)

Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures. - Sündüz Keles; Mark J. van der Laan; James M. Robins (Advances in Survival Analysis, 2003)

Loss-based estimation with cross-validation: applications to microarray data analysis. - Sandrine Dudoit; Mark J. van der Laan; Sündüz Keles; Annette M. Molinaro; Sandra E. Sinisi; Siew Leng Teng (SIGKDD Explor., 2003)

Regulatory motif finding by logic regression. - Sündüz Keles; Mark J. van der Laan; Chris Vulpe (Bioinform., 2004)

Multiple Testing Methods For ChIP - Chip High Density Oligonucleotide Array Data. - Sündüz Keles; Mark J. van der Laan; Sandrine Dudoit; Simon E. Cawley (J. Comput. Biol., 2006)

CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure. - Pei Fen Kuan; Hyonho Chun; Sündüz Keles (Pacific Symposium on Biocomputing, 2008)

Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. - Héctor Corrada Bravo; Stephen J. Wright 001; Kevin H. Eng; Sündüz Keles; Grace Wahba (AISTATS, 2009)

eQTL Mapping for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression. - Dongjun Chung; Sündüz Keles (Handbook of Statistical Bioinformatics, 2011)

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. - Dongjun Chung; Pei Fen Kuan; Bo Li 015; Rajendran Sanalkumar; Kun Liang 001; Emery H. Bresnick; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2011)

Detecting differential binding of transcription factors with ChIP-seq. - Kun Liang 001; Sündüz Keles (Bioinform., 2012)

Normalization of ChIP-seq data with control. - Kun Liang 001; Sündüz Keles (BMC Bioinform., 2012)

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data. - Dongjun Chung; Dan Park; Kevin Myers; Jeffrey Grass; Patricia J. Kiley; Robert Landick; Sündüz Keles (PLoS Comput. Biol., 2013)

CNV-guided multi-read allocation for ChIP-seq. - Qi Zhang; Sündüz Keles (Bioinform., 2014)

A statistical framework for power calculations in ChIP-seq experiments. - Chandler Zuo; Sündüz Keles (Bioinform., 2014)

atSNP: transcription factor binding affinity testing for regulatory SNP detection. - Chandler Zuo; Sunyoung Shin; Sündüz Keles (Bioinform., 2015)

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. - Xin Zeng; Bo Li 015; Rene Welch; Constanza Rojo; Ye Zheng; Colin N. Dewey; Sündüz Keles (PLoS Comput. Biol., 2015)

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. - Qi Zhang; Xin Zeng; Samuel G. Younkin; Trupti Kawli; Michael P. Snyder; Sündüz Keles (BMC Bioinform., 2016)

GLANET: genomic loci annotation and enrichment tool. - Burçak Otlu; Can Firtina; Sündüz Keles; Öznur Tastan (Bioinform., 2017)

A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. - Chandler Zuo; Kailei Chen; Sündüz Keles (J. Comput. Biol., 2017)

atSNPInfrastructure, a Case Study for Searching Billions of Records While Providing Significant Cost Savings over Cloud Providers. - Christopher Harrison; Sündüz Keles; Rebecca Hudson; Sunyoung Shin; Inês Dutra (IPDPS Workshops, 2018)

atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. - Sunyoung Shin; Rebecca Hudson; Christopher Harrison; Mark Craven; Sündüz Keles (Bioinform., 2019)

scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. - Siqi Shen; Ye Zheng; Sündüz Keles (Bioinform., 2022)

AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver. - Chenyang Dong; Siqi Shen; Sündüz Keles (Bioinform., 2023)

MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing. - Ali Osman Berk Sapci; Shan Lu; Shuchen Yan; Ferhat Ay; Öznur Tastan; Sündüz Keles (Bioinform., 2023)