List of works by Hideya Kawaji

A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny

scientific article published on 16 November 2016

A draft network of ligand-receptor-mediated multicellular signalling in human

scientific article published on 22 July 2015

A promoter-level mammalian expression atlas

scientific article

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

article

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

scientific article published on 10 July 2014

Abstract 2897: Recurrent transcriptome alterations across multiple cancer types

Alternate transcription of the Toll-like receptor signaling cascade

scientific article published on 17 February 2006

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An atlas of active enhancers across human cell types and tissues

scientific article

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An atlas of human long non-coding RNAs with accurate 5' ends.

scientific article

An integrated expression atlas of miRNAs and their promoters in human and mouse.

scientific article

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

scientific article published on 26 March 2014

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

scientific article published on 04 January 2019

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

scientific article published on 14 December 2015

Author Correction: Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

scholarly article published in Scientific Data

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

scientific article

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

scientific article

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

scientific article published on 24 December 2014

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

scientific article published on 9 June 2016

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

scientific article

CD157 Marks Tissue-Resident Endothelial Stem Cells with Homeostatic and Regenerative Properties.

scientific article published in February 2018

CDK1 dependent phosphorylation of hTERT contributes to cancer progression

scientific article published on 25 March 2020

CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells

scientific article published on 15 March 2019

Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites

scientific article published on 01 January 2020

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

scientific article

Capturing drug responses by quantitative promoter activity profiling

scientific article

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

scientific article

ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data

scientific article published on 09 November 2018

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

scientific article

Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset

scientific article published in 2021

Comparative transcriptomics of primary cells in vertebrates

scientific article published on 27 July 2020

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

scientific article

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

scientific article

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

scientific article published on 01 August 2018

Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis

article

Correction to: Relatively frequent switching of transcription start sites during cerebellar development

scientific article

Correction: Novel Small Noncoding RNAs in Mouse Spermatozoa, Zygotes and Early Embryos

scientific article published on 14 May 2013

Correction: discovery of molecular markers to discriminate corneal endothelial cells in the human body

scientific article published on 26 May 2015

Correlation of EGFR or KRAS mutation status with 18F-FDG uptake on PET-CT scan in lung adenocarcinoma

scientific article

Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human

scientific article published on 10 February 2016

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

scholarly article published in Nature Genetics

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

scientific article

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

scientific article published on 4 November 2015

DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C.

scientific article published on 19 May 2016

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

scientific article published on 27 March 2014

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

scientific article published on 6 January 2018

Discovery of molecular markers to discriminate corneal endothelial cells in the human body

scientific article published on 25 March 2015

Dynamic usage of transcription start sites within core promoters

scientific article published on January 2006

Effects of cytosine methylation on transcription factor binding sites

scientific article

Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells

scientific article published on 12 November 2019

Exploration of novel motifs derived from mouse cDNA sequences

scientific article

Exploration of small RNAs

scientific article

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

scientific article published on 19 November 2020

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

scientific article published on 19 April 2009

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies

scientific article published on 29 August 2017

FANTOM5 CAGE profiles of human and mouse samples

scientific article published on 29 August 2017

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

scientific article

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

scientific article published on 21 March 2016

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genome Annotation

scientific article published on January 2017

Genome annotation

scientific article published on January 2008

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Graph-based clustering for finding distant relationships in a large set of protein sequences

scientific article published in January 2004

Hidden layers of human small RNAs

scientific article

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

scientific article published on 23 December 2015

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor

scientific article

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

scientific article published on 26 March 2014

Identification of chromatin marks at TERRA promoter and encoding region.

scientific article published on 5 October 2015

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

scientific article published on 18 September 2019

Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity

article

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC.

scientific article published on 11 July 2017

Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

scientific article published in March 2014

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

scientific article published on 3 October 2017

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line

scientific article

Monitoring transcription initiation activities in rat and dog.

scientific article

Mouse proteome analysis

scientific article

NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

scientific article published on 02 September 2019

Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes

scientific article

Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung

scientific article

Novel small noncoding RNAs in mouse spermatozoa, zygotes and early embryos

scientific article

Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells

scientific article published on 16 October 2019

Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells

scientific article (publication date: 2011)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

scientific article published on 26 December 2016

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β

scientific article published in Scientific Reports

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

scientific article published on 16 July 2015

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis

scientific article published on 26 October 2017

Pseudo-messenger RNA: phantoms of the transcriptome

scientific article

RNA sequencing analysis revealed the induction of CCL3 expression in human intracranial aneurysms

scientific article published on 17 July 2019

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

scientific article

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing

scientific article

Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing

scientific article

Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas

scientific article published on 4 November 2017

SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes

scientific article

Selective Activation of Alternative Core Promoters by Wnt-Responsive Enhancers

article

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

scientific article published in March 2018

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer.

scientific article

Systematic analysis of transcription start sites in avian development

scientific article published on 5 September 2017

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

scientific article published on 25 February 2015

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

scientific article (publication date: 11 February 2013)

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 19 April 2009

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

scientific article published on 29 August 2017

The RIKEN integrated database of mammals

scientific article

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

scientific article published on 26 March 2014

The evolution of human cells in terms of protein innovation

scientific article

The frequent evolutionary birth and death of functional promoters in mouse and human

scientific article published on 30 July 2015

The transcriptional landscape of the mammalian genome

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcription and enhancer profiling in human monocyte subsets

scientific article published on 26 March 2014

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

scientific article

Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution.

scientific article

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response

scientific article

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

scientific article

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

scientific article

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

scientific article

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

scientific article published on 9 November 2015

Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

scientific article published on 20 September 2016

Unamplified cap analysis of gene expression on a single-molecule sequencer.

scientific article

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

scientific article published on 01 January 2019

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

scientific article published on 12 November 2010

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

scientific article

[Computational predictions of transcription factor binding sites]

scientific article published on 01 December 2004

dirHub: a trackHub configurator with directory structure projection

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

scientific article published on 08 May 2019

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