Sündüz Keles

27 papers A 1B 1Misc 1Journal 21Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data.
Bioinform.
Shuyang Chen, Sündüz Keles
2024 J jnl
Integrative annotation scores of variants for impact on RNA binding protein activities.
Bioinform.
Jingqi Duan, Audrey P. Gasch, Sündüz Keles
2023 J jnl
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver.
Bioinform.
Chenyang Dong, Siqi Shen, Sündüz Keles
2023 J jnl
MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.
Bioinform.
Ali Osman Berk Sapci, Shan Lu, Shuchen Yan, Ferhat Ay, Öznur Tastan, Sündüz Keles
2022 J jnl
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data.
Bioinform.
Siqi Shen, Ye Zheng, Sündüz Keles
2019 J jnl
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding.
Bioinform.
Sunyoung Shin, Rebecca Hudson, Christopher Harrison, Mark Craven, Sündüz Keles
2018 — conf
atSNPInfrastructure, a Case Study for Searching Billions of Records While Providing Significant Cost Savings over Cloud Providers.
IPDPS Workshops
Christopher Harrison, Sündüz Keles, Rebecca Hudson, Sunyoung Shin, Inês Dutra
2017 J jnl
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.
J. Comput. Biol.
Chandler Zuo, Kailei Chen, Sündüz Keles
2017 J jnl
GLANET: genomic loci annotation and enrichment tool.
Bioinform.
Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan
2016 B conf
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.
RECOMB
Chandler Zuo, Kailei Chen, Sündüz Keles
2016 J jnl
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.
BMC Bioinform.
Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Keles
2015 J jnl
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.
PLoS Comput. Biol.
Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles
2015 J jnl
atSNP: transcription factor binding affinity testing for regulatory SNP detection.
Bioinform.
Chandler Zuo, Sunyoung Shin, Sündüz Keles
2014 J jnl
A statistical framework for power calculations in ChIP-seq experiments.
Bioinform.
Chandler Zuo, Sündüz Keles
2014 J jnl
CNV-guided multi-read allocation for ChIP-seq.
Bioinform.
Qi Zhang, Sündüz Keles
2013 J jnl
dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data.
PLoS Comput. Biol.
Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia J. Kiley, Robert Landick, Sündüz Keles
2012 J jnl
Detecting differential binding of transcription factors with ChIP-seq.
Bioinform.
Kun Liang, Sündüz Keles
2012 J jnl
Normalization of ChIP-seq data with control.
BMC Bioinform.
Kun Liang, Sündüz Keles
2011 J jnl
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data.
PLoS Comput. Biol.
Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles
2011 — ch.
eQTL Mapping for Functional Classes of
Handbook of Statistical Bioinformatics
Dongjun Chung, Sündüz Keles
2009 A conf
Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming.
AISTATS
Héctor Corrada Bravo, Stephen J. Wright, Kevin H. Eng, Sündüz Keles, Grace Wahba
2008 Misc conf
CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure.
Pacific Symposium on Biocomputing
Pei Fen Kuan, Hyonho Chun, Sündüz Keles
2006 J jnl
Multiple Testing Methods For ChIP - Chip High Density Oligonucleotide Array Data.
J. Comput. Biol.
Sündüz Keles, Mark J. van der Laan, Sandrine Dudoit, Simon E. Cawley
2004 J jnl
Regulatory motif finding by logic regression.
Bioinform.
Sündüz Keles, Mark J. van der Laan, Chris Vulpe
2003 — ch.
Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures.
Advances in Survival Analysis
Sündüz Keles, Mark J. van der Laan, James M. Robins
2003 J jnl
Loss-based estimation with cross-validation: applications to microarray data analysis.
SIGKDD Explor.
Sandrine Dudoit, Mark J. van der Laan, Sündüz Keles, Annette M. Molinaro, Sandra E. Sinisi, Siew Leng Teng
2002 J jnl
Identification of regulatory elements using a feature selection method.
Bioinform.
Sündüz Keles, Mark J. van der Laan, Michael B. Eisen