Sündüz Keleş

Q: What Schools Are Affiliated With Sündüz Keleş

Sündüz Keleş is affiliated with the following schools: University of California, Berkeley, University of Wisconsin–Madison

Sündüz Keleş's AcademicInfluence.com Rankings

Sündüz Keleş

Mathematics

#7862

World Rank

#10673

Historical Rank

Statistics

#1025

World Rank

#1125

Historical Rank

mathematics Degrees

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Mathematics

Why Is Sündüz Keleş Influential?

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According to Wikipedia, Sündüz Keleş is a Turkish statistician specializing in statistical methods in genomics. She is a professor of statistics and of biostatistics and medical informatics at the University of Wisconsin–Madison. Her research has included the development of the FreeHi-C system for generating synthetic Hi-C data.

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Sündüz Keleş's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Sparse partial least squares regression for simultaneous dimension reduction and variable selection (2010) (743)
Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. (2009) (344)
Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma (2010) (274)
GATA Switches as Developmental Drivers* (2010) (250)
The bone morphogenetic protein 1/Tolloid-like metalloproteinases. (2007) (235)
Asymptotic Optimality of Likelihood-Based Cross-Validation (2004) (208)
Rho directs widespread termination of intragenic and stable RNA transcription (2009) (185)
Effects of Sleep and Wake on Oligodendrocytes and Their Precursors (2013) (172)
Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity. (2012) (172)
Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding (2013) (164)
Chemical-genomic dissection of the CTD code (2010) (162)
Sparse Partial Least Squares Classification for High Dimensional Data (2010) (162)
Identification of regulatory elements using a feature selection method (2002) (128)
A Statistical Framework for the Analysis of ChIP-Seq Data (2011) (118)
Autophagy Driven by a Master Regulator of Hematopoiesis (2011) (112)
Transcription of histone gene cluster by differential core-promoter factors. (2007) (106)
Expression Quantitative Trait Loci Mapping With Multivariate Sparse Partial Least Squares Regression (2009) (104)
Expression Profiling of GABAergic Motor Neurons in Caenorhabditis elegans (2005) (104)
Normalization of ChIP-seq data with control (2012) (98)
Genetic framework for GATA factor function in vascular biology (2011) (97)
Dynamic Regulation of Schwann Cell Enhancers after Peripheral Nerve Injury* (2015) (92)
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data (2011) (91)
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (2007) (83)
Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve (2012) (80)
Perspectives on ENCODE (2020) (79)
Detecting differential binding of transcription factors with ChIP-seq (2012) (78)
Recurrent events analysis in the presence of time‐dependent covariates and dependent censoring (2004) (77)
Differential Sox10 genomic occupancy in myelinating glia (2015) (77)
Identification of Estrogen Receptor Dimer Selective Ligands Reveals Growth-Inhibitory Effects on Cells That Co-Express ERα and ERβ (2012) (75)
Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis (2008) (66)
Multiple Testing Methods For ChIP - Chip High Density Oligonucleotide Array Data (2006) (66)
Integromic Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes (2015) (66)
atSNP: transcription factor binding affinity testing for regulatory SNP detection (2015) (66)
Regulatory motif finding by logic regression (2004) (65)
Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators (2012) (64)
jMOSAiCS: joint analysis of multiple ChIP-seq datasets (2013) (60)
Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes. (2020) (60)
Mechanisms of erythrocyte development and regeneration: implications for regenerative medicine and beyond (2018) (59)
Framework for kernel regularization with application to protein clustering. (2005) (59)
Residual‐based tree‐structured survival analysis (2002) (57)
O2 availability impacts iron homeostasis in Escherichia coli (2017) (56)
Novel TRF1/BRF target genes revealed by genome‐wide analysis of Drosophila Pol III transcription (2007) (50)
Research resource: global identification of estrogen receptor β target genes in triple negative breast cancer cells. (2013) (49)
Exploratory and Confirmatory Gene Expression Profiling of mac1Δ* (2004) (48)
Mixture Modeling for Genome‐Wide Localization of Transcription Factors (2007) (47)
A single C. elegans PUF protein binds RNA in multiple modes. (2009) (45)
Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons (2015) (45)
Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress (2016) (43)
Locus‐wide identification of Egr2/Krox20 regulatory targets in myelin genes (2010) (42)
Divergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding Pocket* (2011) (40)
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets (2008) (39)
Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome (2016) (38)
Epstein-Barr Virus Nuclear Antigen 3 (EBNA3) Proteins Regulate EBNA2 Binding to Distinct RBPJ Genomic Sites (2015) (38)
Differentially Methylated Plasticity Genes in the Amygdala of Young Primates Are Linked to Anxious Temperament, an at Risk Phenotype for Anxiety and Depressive Disorders (2014) (37)
Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22. (2012) (34)
Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase (2019) (34)
Predicting gene expression in massively parallel reporter assays: A comparative study (2017) (34)
Supervised Detection of Regulatory Motifs in DNA Sequences (2003) (34)
CMARRT: A Tool of Analysis of CHIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure (2007) (33)
Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. (2015) (31)
Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome. (2015) (31)
Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells (2016) (30)
GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism. (2018) (27)
Mixture models with multiple levels, with application to the analysis of multifactor gene expression data. (2008) (25)
Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer (2019) (25)
Loss-based estimation with cross-validation: applications to microarray data analysis (2003) (24)
Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress (2016) (23)
Statistical analysis of ChIP-seq data with MOSAiCS. (2013) (23)
Epstein-Barr Virus Infection Promotes Epithelial Cell Growth by Attenuating Differentiation-Dependent Exit from the Cell Cycle (2019) (22)
Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points. (2014) (22)
GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. (2017) (21)
CTCF loss mediates unique DNA hypermethylation landscapes in human cancers (2020) (21)
Transient Genotype-by-Environment Interactions Following Environmental Shock Provide a Source of Expression Variation for Essential Genes (2010) (21)
Angiogenesis Induced by Signal Transducer and Activator of Transcription 5A (STAT5A) Is Dependent on Autocrine Activity of Proliferin* (2011) (20)
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions (2009) (19)
Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis (2015) (18)
Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies (2019) (18)
The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms. (2016) (17)
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding (2018) (17)
Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq (2016) (17)
dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data (2013) (16)
Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories (2020) (16)
CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data (2008) (15)
A Phylogenetic Mixture Model for the Evolution of Gene Expression (2009) (14)
A statistical framework for power calculations in ChIP-seq experiments (2014) (13)
Asymptotically optimal model selection method with right censored outcomes (2004) (13)
Discovering How Heme Controls Genome Function Through Heme-omics. (2020) (13)
Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming (2009) (12)
GLANET: genomic loci annotation and enrichment tool (2017) (12)
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping (2015) (12)
Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder (2019) (11)
Bioinformatic analysis of neural stem cell differentiation. (2007) (11)
CNV-guided multi-read allocation for ChIP-seq (2014) (10)
An Introduction to the ‘spls’ Package, Version 1.0 (2008) (10)
Integrating quantitative information from ChIP-chip experiments into motif finding. (2008) (10)
MOSAiCS-HMM: A Model-Based Approach for Detecting Regions of Histone Modifications from ChIP-Seq Data (2014) (9)
FreeHi-C simulates high fidelity Hi-C data for benchmarking and data augmentation (2019) (9)
Epigenetic and genetic mechanisms in red cell biology (2014) (9)
The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition (2021) (9)
Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny (2020) (8)
Comments on: Augmenting the bootstrap to analyze high dimensional genomic data (2008) (8)
GATA factor-regulated solute carrier ensemble reveals a nucleoside transporter-dependent differentiation mechanism (2020) (8)
RNA-Binding Protein IGF2BP1 in Cutaneous Squamous Cell Carcinoma. (2017) (7)
Identification of direct transcriptional targets of NFATC2 that promote β-cell proliferation. (2021) (7)
SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins (2020) (7)
PKM2‐TMEM33 axis regulates lipid homeostasis in cancer cells by controlling SCAP stability (2021) (7)
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection (2016) (6)
An empirical Bayes test for allelic‐imbalance detection in ChIP‐seq (2018) (6)
Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures (2003) (5)
Normalization and De-noising of Single-cell Hi-C Data with BandNorm and 3DVI (2021) (4)
Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data (2016) (3)
A Linear Mixed Effects Clustering Model for Multi-species Time Course Gene Expression Data 1 (2008) (3)
Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D (2022) (3)
eQTL Mapping for Functional Classes of Saccharomyces cerevisiae Genes with Multivariate Sparse Partial Least Squares Regression (2011) (3)
A Hierarchical Semi-Markov Model for Detecting Enrichment with Application to ChIP-Seq Experiments (2009) (3)
In Silico Pooling of ChIP-seq Control Experiments (2014) (2)
FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection. (2020) (2)
Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer (2022) (2)
RNA-Binding Protein IGF 2 BP 1 in Cutaneous Squamous Cell Carcinoma (2017) (2)
A Hierarchical Framework for State-Space Matrix Inference and Clustering. (2015) (2)
Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data (2014) (2)
Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders (2021) (2)
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants (2021) (2)
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data (2021) (2)
Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments (2017) (2)
PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments (2019) (1)
Declined presentation hematopoietic signaling mechanism revealed from a stem/progenitor cell cistrome (2015) (1)
iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies (2019) (1)
Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies (2018) (1)
Kernel Regularization and Dimension Reduction (2006) (1)
Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks (2023) (1)
Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data (2017) (1)
Multiple Tests of Association with Biological (2006) (1)
jMOSAiCS: joint analysis of multiple ChIP-seq datasets (2013) (1)
atSNPInfrastructure, a Case Study for Searching Billions of Records While Providing Significant Cost Savings over Cloud Providers (2018) (1)
Processed data and analysis results for 104 RBPs (2020) (1)
Unbiased screen of RNA tailing enzymes at single-nucleotide resolution reveals a poly(UG) polymerase required for genome integrity and RNA silencing (2018) (1)
MLG: multilayer graph clustering for multi-condition scRNA-seq data (2021) (1)
TRAID-seq: Unbiased analysis of RNA tailing enzyme activity at single-nucleotide resolution (2019) (1)
Biometrics , 1 – 17 Mixed Effects Tests of Covariance Structure in Neutral Evolution Inference (2012) (0)
Latent infection of B lymphocytes by Epstein-Barr virus (EBV) in vitro results in their immortalization (2015) (0)
Supplementary Materials for ‘ GLANET : Genomic Loci ANnotation and Enrichment Tool ’ (2017) (0)
crystal structure of FBF-2 in complex with gld-1 FBEa13 RNA (2012) (0)
Author response: Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies (2018) (0)
Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase (2019) (0)
Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue (2022) (0)
1008 – FROM GATA2 HUMAN GENETICS TO LEUKEMIA PREDISPOSITION-GENERATING NETWORKS (2022) (0)
Statistical Methods for Profiling 3-Dimensional Chromatin Interactions from Repetitive Regions of Genomes (2018) (0)
crystal structure of FBF-2 in complex with a mutant gld-1 FBEa13 RNA (2012) (0)
GATA2-Dependent Developmental and Regenerative Networks (2019) (0)
Exploratory and Confirmatory Gene Expression Profiling of mac1 (cid:1) * □ S (2004) (0)
FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation (2019) (0)
Genome analysis GLANET: genomic loci annotation and enrichment tool (2017) (0)
Abstract 4434: CTCF acts as a master regulator to direct epigenetic events important for tumor development and progression (2016) (0)
CSSP : ChIP-Seq Statistical Power (2013) (0)
SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins (2020) (0)
Correction to: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny (2020) (0)
Enhancer mechanisms governing developmental and regenerative hematopoietic programs (2017) (0)
Transcription and Chromatin Regulators Expression Dynamics but Are Linked to Occupancy Are Not Predictive of Gene Dynamic Changes in Nucleosome (2013) (0)
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver (2022) (0)
MuDCoD: Multi-Subject Community Detection in Personalized Dynamic Gene Networks from Single Cell RNA Sequencing (2021) (0)
mHi-C: robust leveraging of multi-mapping reads in Hi-C analysis (2018) (0)
ccosmo: A stand-along C program for the supervised detection of conserved motifs in DNA sequences. (2006) (0)
Joint tensor modeling of single cell 3D genome and epigenetic data with Muscle (2023) (0)
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation (2019) (0)
Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master 1 (2008) (0)
Declined Presentation: From a hematopoietic stem cell cistrome to novel regulators of hematopoiesis (2014) (0)
Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny (2020) (0)
Author Correction: Perspectives on ENCODE (2022) (0)
Correction to: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny (2020) (0)
SAMD14 enhancer-mediated hematopoietic stress signaling (2016) (0)
GATA/Heme Multi-Omics Reveals a Trace Metal-Dependent Erythrocyte Developmental Mechanism (2018) (0)
Normalization of ChIP-seq data with control (2012) (0)
Dozer: Debiased personalized gene co-expression networks for population-scale scRNA-seq data (2023) (0)
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants (2021) (0)
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes (2022) (0)
Genetic Determinants of the Definitive Hematopoietic Stem/Progenitor Cell Compartment (2012) (0)
Divergence of PUF protein specificity through variations in an RNA-binding pocket (2012) (0)
Abstract 2083: A single tyrosine in a PUF RNA binding protein controls its mRNA binding landscape and separates its distinct biological functions (2023) (0)
Bur1 kinase places new phosphorylation marks in RNA pol II CTD in the 3' region of genes (2010) (0)
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection (2016) (0)
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets (2016) (0)
CTCF loss mediates unique DNA hypermethylation landscapes in human cancers (2020) (0)
Enhancing motif finding models using multiple sources of genome-wide data (2011) (0)
cosmoweb: A web application for the supervised detection of conserved motifs in DNA sequences. (2006) (0)
Analysis of ChIP-seq Data with ‘ mosaics ’ Package : MOSAiCS and MOSAiCS-HMM (2010) (0)
Cistrome Control of Hematopoieitic Stem/Progenitor Cell Function (2015) (0)
Materials to “ A Non-Homogeneous Hidden Markov Model on First Order Differences for Automatic Detection of Nucleosome Positions ” (2008) (0)

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What Schools Are Affiliated With Sündüz Keleş?

Sündüz Keleş is affiliated with the following schools: