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List of works by Sündüz Keleş

A Hierarchical Framework for State-Space Matrix Inference and Clustering.

scientific article

A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets

scientific article

A Statistical Framework for the Analysis of ChIP-Seq Data

scientific article

A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions

scientific article published on 19 June 2009

A phylogenetic mixture model for the evolution of gene expression

scientific article published on 14 July 2009

A single C. elegans PUF protein binds RNA in multiple modes

scientific article published on 15 April 2009

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

scientific article published on May 10, 2013

A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets

scientific article published on April 2008

An empirical Bayes test for allelic-imbalance detection in ChIP-seq.

scientific article

Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny

scientific article published on 10 January 2020

Angiogenesis Induced by Signal Transducer and Activator of Transcription 5A (STAT5A) Is Dependent on Autocrine Activity of Proliferin ⬇️

scientific article published on December 23, 2011

Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data

scientific article published on 12 August 2016

Asymptotic optimality of likelihood-based cross-validation

scientific article published on 22 March 2004

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

scholarly article

Author Correction: Perspectives on ENCODE

scholarly article

Autophagy driven by a master regulator of hematopoiesis

scientific article

Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes

scientific article published on 26 March 2020

Bioinformatic analysis of neural stem cell differentiation

scientific article

CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure

scientific article

CNV-guided multi-read allocation for ChIP-seq

scientific article

CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data

scientific article

CTCF loss mediates unique DNA hypermethylation landscapes in human cancers

scientific article published on 05 June 2020

Chemical-genomic dissection of the CTD code.

scientific article

Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity

scientific article

Cistrome Control of Hematopoieitic Stem/Progenitor Cell Function ⬇️

scholarly article

Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories

scientific article published on 01 November 2020

Correction to: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny

scientific article published on 01 April 2020

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

scientific article published on September 2017

Detecting differential binding of transcription factors with ChIP-seq ⬇️

scientific article published on November 3, 2011

Differential Sox10 genomic occupancy in myelinating glia

scientific article

Differentially methylated plasticity genes in the amygdala of young primates are linked to anxious temperament, an at risk phenotype for anxiety and depressive disorders

scientific article

Discovering How Heme Controls Genome Function Through Heme-omics

scientific article published on 01 June 2020

Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy

scientific article

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data

scientific article

Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22

scientific article published on 15 December 2011

Divergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding Pocket ⬇️

scientific article published on December 28, 2011

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators ⬇️

scientific article published on February 21, 2012

Dynamic regulation of Schwann cell enhancers after peripheral nerve injury

scientific article

Effects of sleep and wake on oligodendrocytes and their precursors

scientific article published on September 2013

Epigenetic and genetic mechanisms in red cell biology

scientific article published on May 2014

Epstein-Barr Virus Nuclear Antigen 3 (EBNA3) Proteins Regulate EBNA2 Binding to Distinct RBPJ Genomic Sites

scientific article published on 30 December 2015

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

scientific article published on January 2009

Exploratory and confirmatory gene expression profiling of mac1Delta.

scientific article

Expression profiling of GABAergic motor neurons in Caenorhabditis elegans

scientific article published in February 2005

Expression quantitative trait loci mapping with multivariate sparse partial least squares regression

scientific article published on 06 March 2009

Framework for kernel regularization with application to protein clustering

scientific article

FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection

scientific article published on 11 July 2020

FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation

scientific article published on 11 November 2019

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis

scientific article

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia

scientific article published on August 2017

GATA Switches as Developmental Drivers ⬇️

scientific article published on July 29, 2010

GATA factor-regulated solute carrier ensemble reveals a nucleoside transporter-dependent differentiation mechanism

scientific article published on 28 December 2020

GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism

scientific article published on 16 August 2018

GLANET: Genomic Loci ANnotation and Enrichment Tool.

scientific article

Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies ⬇️

scientific article published on 31 January 2019

Genetic Determinants of the Definitive Hematopoietic Stem/Progenitor Cell Compartment ⬇️

scholarly article

Genetic framework for GATA factor function in vascular biology

scientific article

Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.

scientific article

Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress

scientific article

Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve

scientific article

Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism

scientific article published on 30 September 2015

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome

scientific article

Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points.

scientific article published on 09 May 2014

Identification of Estrogen Receptor Dimer Selective Ligands Reveals Growth-Inhibitory Effects on Cells That Co-Express ERα and ERβ ⬇️

scientific article published on February 7, 2012

Identification of regulatory elements using a feature selection method.

scientific article published in September 2002

Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons.

scientific article published on 15 December 2015

In silico pooling of ChIP-seq control experiments

scientific article

Increases in Central Aortic Impedance Precede Alterations in Arterial Stiffness Measures in Type 1 Diabetes

scientific article published on 08 August 2007

Integrating quantitative information from ChIP-chip experiments into motif finding

scientific article published on 28 May 2007

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq

scientific article published on 12 July 2016

Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes

scientific article

Locus-wide identification of Egr2/Krox20 regulatory targets in myelin genes

scientific article published on 4 November 2010

Mechanisms of erythrocyte development and regeneration: implications for regenerative medicine and beyond.

scientific article published on 10 January 2018

Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome

scientific article

Mixture modeling for genome-wide localization of transcription factors

scientific article published on March 2007

Mixture models with multiple levels, with application to the analysis of multifactor gene expression data

scientific article

Molecular hallmarks of endogenous chromatin complexes containing master regulators of hematopoiesis

scientific journal article

Multiple testing methods for ChIP-Chip high density oligonucleotide array data

scientific article

Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data

scientific article

Normalization of ChIP-seq data with control ⬇️

scientific article published on August 10, 2012

Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription

scientific article published on 14 December 2006

O2 availability impacts iron homeostasis in Escherichia coli

scientific article published on 30 October 2017

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments

scientific article published on 21 September 2020

PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans

scholarly article

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.

scientific article published on 20 October 2015

Predicting gene expression in massively parallel reporter assays: A comparative study

scientific article published on 21 February 2017

RNA-Binding Protein IGF2BP1 in Cutaneous Squamous Cell Carcinoma

scientific article published on 14 November 2016

Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells

scientific article published on 14 June 2016

Regulatory motif finding by logic regression

scientific article published on 27 May 2004

Research resource: global identification of estrogen receptor β target genes in triple negative breast cancer cells

scientific article published on 26 August 2013

Residual‐based tree‐structured survival analysis ⬇️

scientific article published on January 30, 2002

Rho directs widespread termination of intragenic and stable RNA transcription.

scholarly article

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins

scientific article published on 12 June 2020

Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress

scientific article

Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer

scientific article published on 11 February 2019

Sparse partial least squares classification for high dimensional data

scientific article

Sparse partial least squares regression for simultaneous dimension reduction and variable selection

scientific article

Statistical analysis of ChIP-seq data with MOSAiCS.

scientific article

Supervised detection of conserved motifs in DNA sequences with cosmo

scientific article published on 23 February 2007

Supervised detection of regulatory motifs in DNA sequences

scientific article published on 25 August 2003

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

scientific article

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

scientific article published on 01 March 2021

The bone morphogenetic protein 1/Tolloid-like metalloproteinases

scientific article published on 18 May 2007

Transcription of histone gene cluster by differential core-promoter factors

scientific article

Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes

scientific article

Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase

scientific article published on 15 April 2019

atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding

scientific article published on 01 August 2019

atSNP: transcription factor binding affinity testing for regulatory SNP detection

scientific article

atSNPInfrastructure, a case study for searching billions of records while providing significant cost savings over cloud providers

scientific article published on 01 May 2018

dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data

scientific article

iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies

scientific article published on 22 July 2019

jMOSAiCS: joint analysis of multiple ChIP-seq datasets ⬇️

scientific article published on April 29, 2013

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