Sündüz Keles

According to our database, Sündüz Keles authored at least 24 papers between 2002 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of four.

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., October, 2023

AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver.

Chenyang Dong, Siqi Shen, Sündüz Keles

Bioinform., April, 2023

2022

scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data.

Siqi Shen, Ye Zheng, Sündüz Keles

Bioinform., 2022

2019

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

2018

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

Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium Workshops, 2018

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

GLANET: genomic loci annotation and enrichment tool.

Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan

Bioinform., 2017

2016

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

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, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles

PLoS Comput. Biol., 2015

atSNP: transcription factor binding affinity testing for regulatory SNP detection.

Chandler Zuo, Sunyoung Shin, Sündüz Keles

Bioinform., 2015

2014

A statistical framework for power calculations in ChIP-seq experiments.

Chandler Zuo, Sündüz Keles

Bioinform., 2014

CNV-guided multi-read allocation for ChIP-seq.

Qi Zhang, Sündüz Keles

Bioinform., 2014

2013

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

2012

Normalization of ChIP-seq data with control.

Kun Liang, Sündüz Keles

BMC Bioinform., 2012

Detecting differential binding of transcription factors with ChIP-seq.

Kun Liang, Sündüz Keles

Bioinform., 2012

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, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles

PLoS Comput. Biol., 2011

eQTL Mapping for Functional Classes of <i>Saccharomyces cerevisiae</i> Genes with Multivariate Sparse Partial Least Squares Regression.

Dongjun Chung, Sündüz Keles

Proceedings of the Handbook of Statistical Bioinformatics., 2011

2009

Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming.

Héctor Corrada Bravo, Stephen J. Wright, Kevin H. Eng, Sündüz Keles, Grace Wahba

Proceedings of the Twelfth International Conference on Artificial Intelligence and Statistics, 2009

2008

CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure.

Pei Fen Kuan, Hyonho Chun, Sündüz Keles

Proceedings of the Biocomputing 2008, 2008

2006

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

2004

Regulatory motif finding by logic regression.

Sündüz Keles, Mark J. van der Laan, Chris Vulpe

Bioinform., 2004

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

Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures.

Sündüz Keles, Mark J. van der Laan, James M. Robins

Proceedings of the Advances in Survival Analysis, 2003

2002

Identification of regulatory elements using a feature selection method.

Sündüz Keles, Mark J. van der Laan, Michael B. Eisen

Bioinform., 2002