List of works - Kyoung-Jae Won

5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation

scientific article

A stationary wavelet entropy-based clustering approach accurately predicts gene expression

scientific article published on 10 November 2014

A wavelet approach to detect enriched regions and explore epigenomic landscapes.

scientific article

A wavelet-based method to exploit epigenomic language in the regulatory region

scientific article published on 04 October 2013

AMPK-SKP2-CARM1 signalling cascade in transcriptional regulation of autophagy

scientific article published on 15 June 2016

ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis.

scientific article published on 25 June 2015

Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation

scientific article

An evolutionary method for learning HMM structure: prediction of protein secondary structure

scientific article

An iPSC line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression.

scientific article published on 20 June 2013

An integrated approach to identifying cis-regulatory modules in the human genome.

scientific article

Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARγ-driven enhancers

scientific article

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type.

scientific article

DNA hypermethylation induced by Epstein-Barr virus in the development of Epstein-Barr virus-associated gastric carcinoma

scientific article published on 4 August 2017

Deacetylase-independent function of HDAC3 in transcription and metabolism requires nuclear receptor corepressor

scientific article

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus.

scientific article

Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue

scientific article published on 14 May 2018

EBF2 determines and maintains brown adipocyte identity

scientific journal article

EBF2 promotes the recruitment of beige adipocytes in white adipose tissue.

scientific article published on 14 November 2015

EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex

scientific article published on 20 April 2017

EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1

scientific article

Ebf2 is a selective marker of brown and beige adipogenic precursor cells

scientific article

Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation.

scientific article published on 17 November 2016

Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets.

scientific article published on 26 December 2013

Evolving fisher kernels for biological sequence classification.

scientific article published on 24 February 2012

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo.

scientific article published in July 2015

Genome-wide prediction of transcription factor binding sites using an integrated model.

scientific article

Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo

scientific article published on 8 May 2015

Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells.

scientific article

HEART DEVELOPMENT. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts

scientific article

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

scientific article published on 4 February 2016

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

scientific article

Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge.

scientific article

LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells.

scientific article published on 12 December 2016

Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology

scientific article published on 04 June 2020

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

scientific article

Modeling promoter grammars with evolving hidden Markov models.

scientific article published on 05 June 2008

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data

scientific article

PKCα-LSD1-NF-κB-Signaling Cascade Is Crucial for Epigenetic Control of the Inflammatory Response

scientific article

PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program.

scientific article

PRDM16 represses the type I interferon response in adipocytes to promote mitochondrial and thermogenic programing

scientific article published on 13 April 2017

Prdm16 is required for the maintenance of brown adipocyte identity and function in adult mice

scientific journal article

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

scientific article

Prenatal Choline Supplementation Diminishes Early-Life Iron Deficiency-Induced Reprogramming of Molecular Networks Associated with Behavioral Abnormalities in the Adult Rat Hippocampus

scientific article published on 10 February 2016

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.

scientific article

RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking

scientific article

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription.

scientific article published on 8 February 2018

Shared nucleotide flanks confer transcriptional competency to bZip core motifs

scientific article published on 01 September 2018

Single Cell RNA-Sequencing for the Study of Atherosclerosis

scientific article published on 30 July 2019

Single cell transcriptomic profiling of mouse pancreatic progenitors

scientific article published on 23 December 2016

Single-Cell Transcriptomics of the Human Endocrine Pancreas.

scientific article published on 30 June 2016

Targeting ACLY sensitizes castration-resistant prostate cancer cells to AR antagonism by impinging on an ACLY-AMPK-AR feedback mechanism.

scientific article

Targeting PPARγ in the epigenome rescues genetic metabolic defects in mice.

scientific article published on 27 February 2017

The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

scientific article published on 17 November 2015

The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling.

scientific article published on 21 March 2016

The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure.

scientific article

Threshold-Dependent Cooperativity of Pdx1 and Oc1 in Pancreatic Progenitors Establishes Competency for Endocrine Differentiation and β-Cell Function

scientific article published on 8 June 2016

Training HMM structure with genetic algorithm for biological sequence analysis

article

Transcriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation.

scientific article published on 11 August 2015

Transcriptomic analysis reveals novel mechanisms mediating islet dysfunction in the intrauterine growth restricted (IUGR) rat.

scientific article published on 4 January 2018

Zfp423 binds autoregulatory sites in p19 cell culture model.

scientific article

List of works by Kyoung-Jae Won

5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation

A stationary wavelet entropy-based clustering approach accurately predicts gene expression

A wavelet approach to detect enriched regions and explore epigenomic landscapes.

A wavelet-based method to exploit epigenomic language in the regulatory region

AMPK-SKP2-CARM1 signalling cascade in transcriptional regulation of autophagy

ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis.

Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation

An evolutionary method for learning HMM structure: prediction of protein secondary structure

An iPSC line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression.

An integrated approach to identifying cis-regulatory modules in the human genome.

Anti-diabetic rosiglitazone remodels the adipocyte transcriptome by redistributing transcription to PPARγ-driven enhancers

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type.

DNA hypermethylation induced by Epstein-Barr virus in the development of Epstein-Barr virus-associated gastric carcinoma

Deacetylase-independent function of HDAC3 in transcription and metabolism requires nuclear receptor corepressor

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus.

Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue

EBF2 determines and maintains brown adipocyte identity

EBF2 promotes the recruitment of beige adipocytes in white adipose tissue.

EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex

EBNA2 Drives Formation of New Chromosome Binding Sites and Target Genes for B-Cell Master Regulatory Transcription Factors RBP-jκ and EBF1

Ebf2 is a selective marker of brown and beige adipogenic precursor cells

Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation.

Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets.

Evolving fisher kernels for biological sequence classification.

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo.

Genome-wide prediction of transcription factor binding sites using an integrated model.

Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo

Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells.

HEART DEVELOPMENT. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells

Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis

Histone deacetylase 3 prepares brown adipose tissue for acute thermogenic challenge.

LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells.

Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

Modeling promoter grammars with evolving hidden Markov models.

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data

PKCα-LSD1-NF-κB-Signaling Cascade Is Crucial for Epigenetic Control of the Inflammatory Response

PRDM16 binds MED1 and controls chromatin architecture to determine a brown fat transcriptional program.

PRDM16 represses the type I interferon response in adipocytes to promote mitochondrial and thermogenic programing

Prdm16 is required for the maintenance of brown adipocyte identity and function in adult mice

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

Prenatal Choline Supplementation Diminishes Early-Life Iron Deficiency-Induced Reprogramming of Molecular Networks Associated with Behavioral Abnormalities in the Adult Rat Hippocampus

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.

RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription.

Shared nucleotide flanks confer transcriptional competency to bZip core motifs

Single Cell RNA-Sequencing for the Study of Atherosclerosis

Single cell transcriptomic profiling of mouse pancreatic progenitors

Single-Cell Transcriptomics of the Human Endocrine Pancreas.

Targeting ACLY sensitizes castration-resistant prostate cancer cells to AR antagonism by impinging on an ACLY-AMPK-AR feedback mechanism.

Targeting PPARγ in the epigenome rescues genetic metabolic defects in mice.

The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

The Nuclear Receptor Rev-erbα Regulates Adipose Tissue-specific FGF21 Signaling.

The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure.

Threshold-Dependent Cooperativity of Pdx1 and Oc1 in Pancreatic Progenitors Establishes Competency for Endocrine Differentiation and β-Cell Function

Training HMM structure with genetic algorithm for biological sequence analysis

Transcriptomic Profiling and H3K27me3 Distribution Reveal Both Demethylase-Dependent and Independent Regulation of Developmental Gene Transcription in Cell Differentiation.

Transcriptomic analysis reveals novel mechanisms mediating islet dysfunction in the intrauterine growth restricted (IUGR) rat.

Zfp423 binds autoregulatory sites in p19 cell culture model.