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2020 – today
- 2023
[j19]Chenyang Dong, Siqi Shen, Sündüz Keles:
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver. Bioinform. 39(4) (2023)- [j18]Ali Osman Berk Sapci
, Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Tastan, Sündüz Keles:
MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing. Bioinform. 39(10) (2023) - 2022
- [j17]Siqi Shen, Ye Zheng, Sündüz Keles:
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinform. 38(14): 3642-3644 (2022)
2010 – 2019
- 2019
- [j16]Sunyoung Shin, Rebecca Hudson, Christopher Harrison, Mark Craven, Sündüz Keles:
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. Bioinform. 35(15): 2657-2659 (2019) - 2018
- [c4]Christopher Harrison, Sündüz Keles, Rebecca Hudson, Sunyoung Shin, Inês Dutra:
atSNPInfrastructure, a Case Study for Searching Billions of Records While Providing Significant Cost Savings over Cloud Providers. IPDPS Workshops 2018: 497-506 - 2017
- [j15]Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan:
GLANET: genomic loci annotation and enrichment tool. Bioinform. 33(18): 2818-2828 (2017) - [j14]Chandler Zuo, Kailei Chen, Sündüz Keles:
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. J. Comput. Biol. 24(6): 472-485 (2017) - 2016
- [j13]Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Keles:
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. BMC Bioinform. 17: 96 (2016) - [c3]Chandler Zuo, Kailei Chen, Sündüz Keles:
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. RECOMB 2016: 19-36 - 2015
- [j12]Chandler Zuo, Sunyoung Shin, Sündüz Keles:
atSNP: transcription factor binding affinity testing for regulatory SNP detection. Bioinform. 31(20): 3353-3355 (2015) - [j11]Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles:
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j10]Chandler Zuo, Sündüz Keles:
A statistical framework for power calculations in ChIP-seq experiments. Bioinform. 30(6): 753-760 (2014) - [j9]Qi Zhang, Sündüz Keles:
CNV-guided multi-read allocation for ChIP-seq. Bioinform. 30(20): 2860-2867 (2014) - 2013
- [j8]Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia J. Kiley, Robert Landick, Sündüz Keles:
dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data. PLoS Comput. Biol. 9(10) (2013) - 2012
- [j7]Kun Liang, Sündüz Keles:
Detecting differential binding of transcription factors with ChIP-seq. Bioinform. 28(1): 121-122 (2012) - [j6]Kun Liang, Sündüz Keles:
Normalization of ChIP-seq data with control. BMC Bioinform. 13: 199 (2012) - 2011
- [j5]Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles:
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. PLoS Comput. Biol. 7(7) (2011) - [p2]Dongjun Chung, Sündüz Keles:
eQTL Mapping for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression. Handbook of Statistical Bioinformatics 2011: 283-298
2000 – 2009
- 2009
- [c2]Héctor Corrada Bravo, Stephen J. Wright, Kevin H. Eng, Sündüz Keles, Grace Wahba:
Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. AISTATS 2009: 41-48 - 2008
- [c1]Pei Fen Kuan, Hyonho Chun, Sündüz Keles:
CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure. Pacific Symposium on Biocomputing 2008: 515-526 - 2006
- [j4]Sündüz Keles, Mark J. van der Laan, Sandrine Dudoit, Simon E. Cawley:
Multiple Testing Methods For ChIP - Chip High Density Oligonucleotide Array Data. J. Comput. Biol. 13(3): 579-613 (2006) - 2004
- [j3]Sündüz Keles, Mark J. van der Laan, Chris Vulpe:
Regulatory motif finding by logic regression. Bioinform. 20(16): 2799-2811 (2004) - 2003
- [j2]Sandrine Dudoit, Mark J. van der Laan, Sündüz Keles, Annette M. Molinaro, Sandra E. Sinisi, Siew Leng Teng:
Loss-based estimation with cross-validation: applications to microarray data analysis. SIGKDD Explor. 5(2): 56-68 (2003) - [p1]Sündüz Keles, Mark J. van der Laan, James M. Robins:
Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures. Advances in Survival Analysis 2003: 143-173 - 2002
- [j1]Sündüz Keles, Mark J. van der Laan, Michael B. Eisen:
Identification of regulatory elements using a feature selection method. Bioinform. 18(9): 1167-1175 (2002)
Coauthor Index
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