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List of works by Takeya Kasukawa

A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock

scientific article

A promoter-level mammalian expression atlas

scientific article

Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags

scientific article published in February 2004

Acute induction of Eya3 by late-night light stimulation triggers TSHβ expression in photoperiodism

scientific article

Alternate transcription of the Toll-like receptor signaling cascade

scientific article published on 17 February 2006

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

scientific article (publication date: 5 December 2002)

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

scholarly article published in Scientific Data

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

scientific article published in Nature Communications

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

scientific article

CDS annotation in full-length cDNA sequence

scientific article

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

scientific article

Cell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells

scientific article

Comparative transcriptomics of primary cells in vertebrates

scientific article published on 27 July 2020

Comprehensive analysis of the mouse metabolome based on the transcriptome

scientific article published on June 2003

Connecting sequence and biology in the laboratory mouse

scientific article

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

article

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

scholarly article published in Nature Genetics

Development and evaluation of an automated annotation pipeline and cDNA annotation system

scientific article

Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units

scientific article

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

scientific article

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

scientific article published on January 2006

EpiFactors: a comprehensive database of human epigenetic factors and complexes

scientific article

Establishment of Functional Genomics Pipeline in Epiblast-Like Tissue by Combining Transcriptomic Analysis and Gene Knockdown/Knockin/Knockout, Using RNA Interference and CRISPR/Cas9.

scientific article

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

scientific article

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

scientific article published on 19 November 2020

FANTOM-DB: database of functional annotation of RIKEN mouse cDNA clones

scientific article published on 01 February 2003

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

FREP: a database of functional repeats in mouse cDNAs

scientific article

Foxg1 coordinates the switch from nonradially to radially migrating glutamatergic subtypes in the neocortex through spatiotemporal repression

scientific article published on 21 March 2013

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

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Genome Annotation

scientific article published on January 2017

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Human blood metabolite timetable indicates internal body time

scientific article

Inducing human retinal pigment epithelium-like cells from somatic tissue

scientific article

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells

scientific article published on 01 December 2021

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

scientific article published on 3 October 2017

MaXML: mouse annotation XML.

scientific article published on 26 December 2003

Measurement of internal body time by blood metabolomics.

scholarly article

Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation

scientific article published on 03 February 2020

Monitoring transcription initiation activities in rat and dog.

scientific article

Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep

Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks

scientific article published on 21 September 2008

Quantitative expression profile of distinct functional regions in the adult mouse brain

scientific article

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

scientific article published on 24 February 2020

READ: RIKEN Expression Array Database.

scientific article published on January 2002

Recounting the FANTOM CAGEAssociated Transcriptome

scientific article published on 20 February 2020

SCPortalen: human and mouse single-cell centric database

scientific article published on 17 October 2017

STAP cells are derived from ES cells

scientific article published in September 2015

Self-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism

scientific article published on 7 November 2017

Single-cell gene profiling defines differential progenitor subclasses in mammalian neurogenesis.

scientific article published on September 2008

Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

Systematic Functional Annotation Workflow for Insects

scientific article published in 2022

Systematic analysis of transcription start sites in avian development

scientific article published on 5 September 2017

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

scientific article published on June 2003

The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers.

scientific article published on January 2017

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

scientific article published on 29 August 2017

The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression

scientific article published on 01 June 2020

The transcriptional landscape of the mammalian genome

scientific article

Thyrotrophin in the pars tuberalis triggers photoperiodic response.

scientific article published in March 2008

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

scientific article

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article

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

scientific article

Transcriptome tomography for brain analysis in the web-accessible anatomical space

scientific article

Transcriptomic landscape of the primitive streak.

scientific article published on 28 July 2010

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: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

[Physical simulation of the transcriptional network of mammalian circadian clocks]

scientific article published on 01 December 2009

[RTPS]

scientific article published on 01 December 2004

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

scientific article published on 08 May 2019

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