Sündüz Keles

Publication Activity (10 Years)

Years Active: 2002-2023
Publications (10 Years): 9

Top Topics

Systematic Evaluation

Genetic Variation

Transcriptional Regulatory

Regulatory Elements

Top Venues

J. Comput. Biol.

Publications

Chenyang Dong, Siqi Shen, Sündüz Keles
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver. Bioinform. 39 (4) (2023)
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)
Siqi Shen, Ye Zheng, Sündüz Keles
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinform. 38 (14) (2022)
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) (2019)
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)
Burçak Otlu, Can Firtina, Sündüz Keles, Oznur Tastan
GLANET: genomic loci annotation and enrichment tool. Bioinform. 33 (18) (2017)
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) (2017)
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 (2016)
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)
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)
Chandler Zuo, Sunyoung Shin, Sündüz Keles
atSNP: transcription factor binding affinity testing for regulatory SNP detection. Bioinform. 31 (20) (2015)
Chandler Zuo, Sündüz Keles
A statistical framework for power calculations in ChIP-seq experiments. Bioinform. 30 (6) (2014)
Qi Zhang, Sündüz Keles
CNV-guided multi-read allocation for ChIP-seq. Bioinform. 30 (20) (2014)
Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia 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)
Kun Liang, Sündüz Keles
Detecting differential binding of transcription factors with ChIP-seq. Bioinform. 28 (1) (2012)
Kun Liang, Sündüz Keles
Normalization of ChIP-seq data with control. BMC Bioinform. 13 (2012)
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)
Héctor Corrada Bravo, Stephen J. Wright, Kevin H. Eng, Sündüz Keles, Grace Wahba
Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. AISTATS (2009)
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)
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) (2006)
Sündüz Keles, Mark J. van der Laan, Chris Vulpe
Regulatory motif finding by logic regression. Bioinform. 20 (16) (2004)
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) (2003)
Sündüz Keles, Mark J. van der Laan, Michael B. Eisen
Identification of regulatory elements using a feature selection method. Bioinform. 18 (9) (2002)