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List of works by Piero Carninci

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing

scientific article

A Novel Control System for Polymerase Chain Reaction Using a RIKEN GS384 Thermalcycler

scientific article published on 01 December 1997

A Transcriptional Switch Point During Hematopoietic Stem and Progenitor Cell Ontogeny

scientific article published on 16 November 2016

A code for transcription initiation in mammalian genomes

scientific article

A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells.

scientific article published on 29 October 2013

A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs

scientific article

A damaged genome's transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

scientific article

A discontinuous buffer system increasing resolution and reproducibility in DNA sequencing on high voltage horizontal ultrathin-layer electrophoresis.

scientific article published in October 1995

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

scientific article published on 22 July 2015

A fast method for high-quality genomic DNA extraction from whole human blood

scientific article published on 01 September 1991

A field guide to cultivating computational biology

scientific article published on 08 October 2021

A framework for integrating the songbird brain

scientific article (publication date: December 2002)

A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner

scientific article published on 31 January 2020

A method for similarity search of genomic positional expression using CAGE.

scientific article published on 28 April 2006

A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes

scientific article (publication date: 10 October 2006)

A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription

article

A promoter-level mammalian expression atlas

scientific article

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

scientific article

A resource for transcriptomic analysis in the mouse brain

scientific article

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

article

A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence.

scientific article published on January 1990

A simple physical model predicts small exon length variations

scientific article published on 28 April 2006

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

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

Altruistic functions for selfish DNA.

scientific article

Amphioxus functional genomics and the origins of vertebrate gene regulation

scientific article published in Nature

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs

scientific article published on 22 July 2020

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 splice variants of the human protein disulfide isomerase (P4HB) gene

scientific article published on 04 November 2020

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)

Analysis of the mouse transcriptome for genes involved in the function of the nervous system.

scientific article

Annotating non-coding transcription using functional genomics strategies.

scientific article

Antisense RNAs during early vertebrate development are divided in groups with distinct features

scientific article published on 01 April 2021

Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases

scientific article published on 04 January 2019

Antisense transcription in the mammalian transcriptome

scientific article (publication date: 2 September 2005)

Antisense transcripts with rice full-length cDNAs

scientific article

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

scientific article published on 14 December 2015

Arabidopsis encyclopedia using full-length cDNAs and its application

scientific article published in 2001

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

scholarly article published in Scientific Data

Automated filtration-based high-throughput plasmid preparation system

scientific article published on May 1999

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

scientific article

Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis

scientific article

Beyond the FANTOM4.

scientific article

Biased allelic expression in human primary fibroblast single cells

scientific article

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

scientific article published on 29 August 2019

Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

scientific article

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

scientific article published in Nature Communications

CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks

scientific article

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

scientific article

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors.

scientific article

CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts.

scientific article

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

scientific article published on 24 December 2014

CAGE: cap analysis of gene expression

scientific article published in March 2006

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

scientific article

CTAB-urea method purifies RNA from melanin for cDNA microarray analysis

scientific article

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

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

scientific article published on 01 February 2019

Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones

scientific article

Characterization of novel transcripts of human papillomavirus type 16 using cap analysis gene expression technology

scientific article

Characterization of piRNAs across postnatal development in mouse brain.

scientific article published on 26 April 2016

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.

scientific article published on 27 January 2013

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

scientific article

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

scientific article published on 6 November 2011

Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method

scientific article

Clusters of internally primed transcripts reveal novel long noncoding RNAs

scientific article published on 28 April 2006

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice

scientific article published on July 2003

Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data

scientific article

Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries

scientific article

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

scientific article

Comparative transcriptomics of primary cells in vertebrates

scientific article published on 27 July 2020

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

scientific article

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

scientific article

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation

scientific article

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

scientific article

Complex Loci in human and mouse genomes

scientific article

Complexity of Mammalian Transcriptome Analyzed by RNA Deep Sequencing

Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana

scientific article published in December 2003

Comprehensive characterisation of transcriptional activity during influenza A virus infection reveals biases in cap-snatching of host RNA sequences

scientific article published on 11 March 2020

Comprehensive sequence analysis of translation termination sites in various eukaryotes

scientific article published in October 2002

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).

scientific article published on 12 January 2005

Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes

scientific article

Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library.

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

Constructing ORFeome resources with removable termination codons

scientific article published on 01 July 2006

Constructing the landscape of the mammalian transcriptome

scientific article published on 01 May 2007

Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags

scientific article published on 01 August 2004

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

scientific article published in June 2003

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

scientific article

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

scientific article

Correction: Cytoskeletal Rearrangements in Synovial Fibroblasts as a Novel Pathophysiological Determinant of Modeled Rheumatoid Arthritis

scientific article

Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes

scientific article

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

scientific article published on 10 February 2016

Corrigendum: DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs

scientific article published on 13 April 2017

Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

scientific article published in January 2020

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

scholarly article published in Nature Genetics

Corrigendum: Tiny RNAs associated with transcription start sites in animals

scholarly article published in Nature Genetics

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

scientific article

Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis

scientific article

DEIVA: a web application for interactive visual analysis of differential gene expression profiles

scientific article

DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs

scientific article published on 27 February 2017

Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq

scientific article published on 11 March 2021

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

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

DeepCAGE: Genome-Wide Mapping of Transcription Start Sites

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

scientific article

Definition of Promotome-Transcriptome Architecture Using CAGEscan

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

scholarly article

Detecting expressed genes using CAGE.

scientific article

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer

scientific article

Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray

scientific article

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

scientific article published on 27 March 2014

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

scientific article published on 28 April 2006

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

scientific article

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

scientific article (publication date: 3 July 2011)

Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome

scientific article

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

scientific article published on 6 January 2018

Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches

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

Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes

scientific article published in 2022

Diversity and dynamics of the Drosophila transcriptome

scientific article

Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells

scientific journal article

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

scientific article published on 10 January 2020

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

scientific article published on 03 September 2013

Dynamic usage of transcription start sites within core promoters

scientific article published on January 2006

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

scientific article published on 13 February 2019

Empirical analysis of transcriptional activity in the Arabidopsis genome

scientific article (publication date: 31 October 2003)

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

scientific article published on March 2013

Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins

scientific article published on 2 June 2015

Epi-drivers and cancer-testis genes

article

Epigenetic regulation of critical period plasticity in visual cortex

article by Judy C.G. Sng et al published January 2007 in Neuroscience Research

Evolutionary turnover of mammalian transcription start sites

scientific article published on 10 May 2006

Expanded ENCODE delivers invaluable genomic encyclopedia

scientific article published on 01 July 2020

Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine

scientific article published on 30 August 2015

Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease

scientific article

Extra-long first-strand cDNA synthesis

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

FREP: a database of functional repeats in mouse cDNAs

scientific article

FXYD6, a Na,K-ATPase Regulator, Is Expressed in Type II Taste Cells

scientific article published on 13 June 2011

From CAGE to DeepCAGE: High-Throughput Transcription Start Site and Promoter Identification for Gene Network Analysis

article

From identification to validation to gene count.

scientific article

From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond

scientific article published on 30 March 2018

Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis

scientific article

Functional annotation of a full-length Arabidopsis cDNA collection

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

G alpha14 is a candidate mediator of sweet/umami signal transduction in the posterior region of the mouse tongue

scientific article

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Gene discovery in genetically labeled single dopaminergic neurons of the retina

scholarly article

Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray

scientific article

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

scientific article

Generation of full-length cDNA libraries: focus on plants

scientific article

Genetic control of the innate immune response

scientific article

Genetics, gene expression and bioinformatics of the pituitary gland

scientific article

Genome Network and FANTOM3: assessing the complexity of the transcriptome

scientific article (publication date: April 2006)

Genome sequence and analysis of the Japanese morning glory Ipomoea nil.

scientific article

Genome-Wide Technologies to Study RNA-Chromatin Interactions

scientific article published on 27 May 2020

Genome-wide analysis of cancer/testis gene expression

scientific article

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

scientific article

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

scientific article

Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.

scientific article

Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality

scientific article published on 21 March 2007

Genomics approach to abscisic acid- and gibberellin-responsive genes in rice

scientific article published in December 2003

HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells

scientific article published on 8 May 2015

Heterotachy in mammalian promoter evolution

scientific article published on 28 April 2006

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 efficiency selection of full-length cDNA by improved biotinylated cap trapper.

scientific article published on February 1997

High sensitivity TSS prediction: estimates of locations where TSS cannot occur

scientific article

High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper

scientific article

High-efficiency full-length cDNA cloning by biotinylated CAP trapper

scientific article

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

scientific article

High-throughput verification of transcriptional starting sites by Deep-RACE.

scientific article

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

scientific article

Hunting hidden transcripts.

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of antisense long noncoding RNAs that function as SINEUPs in human cells

scientific article published on 20 September 2016

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation

scientific article published on 7 February 2018

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

scientific article published on 18 September 2019

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library

scientific article

Increased specificity of reverse transcription priming by trehalose and oligo-blockers allows high-efficiency window separation of mRNA display

scientific article published on March 1999

Inducing human retinal pigment epithelium-like cells from somatic tissue

scientific article

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data

scientific article

Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

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

scientific article

Is sequencing enlightenment ending the dark age of the transcriptome?

scientific article published on 01 October 2009

Isoforms of the Erythropoietin receptor in dopaminergic neurons of the Substantia Nigra

scientific article

Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline

scientific article

LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C

scientific article published on 10 February 2021

LOCATE: a mouse protein subcellular localization database

scientific article

Landscape of transcription in human cells

scientific article (publication date: 6 September 2012)

Large-scale clustering of CAGE tag expression data

scientific article

Large-scale collection and characterization of promoters of human and mouse genes.

scientific article

Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas

scientific article

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

scientific article published on 3 October 2017

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

scientific article

Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs

scientific article

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

scientific article

Look for methods, not conclusions

scientific article published on 05 December 2019

MOIRAI: a compact workflow system for CAGE analysis

scientific article

Machine-driven parameter screen of biochemical reactions

scientific article published on 06 February 2020

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

scientific article published on 8 May 2007

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

scientific article

Mapping of 19032 mouse cDNAs on mouse chromosomes

scientific article published in January 2002

Meeting Report: 14th International Mouse Genome Conference

Meeting report: The Human Genome Meeting (HGM) 2019 in Seoul, Korea

scientific article published on 01 August 2019

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

scientific article

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

scientific article

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

scientific article

Mice and men: their promoter properties

scientific article published on 28 April 2006

Mice in the ENCODE spotlight

scientific article published in Nature

MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis

scientific article published on 25 September 2019

Molecular mechanisms of pituitary organogenesis: In search of novel regulatory genes.

scientific article

Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray

article

Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray

scientific article

Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray

article

Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray

scientific article

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray

scientific article

Monitoring transcription initiation activities in rat and dog.

scientific article

Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson's Disease

scholarly article by Matthew N Z Valentine et al published 5 April 2019 in Scientific Data

Multifaceted mammalian transcriptome

scientific article published on 28 May 2008

Multiple tissue-specific promoters control expression of the murine tartrate-resistant acid phosphatase gene

scientific article (publication date: 27 March 2003)

Multiplicity of 5' cap structures present on short RNAs

scientific article

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

scientific article published on 02 September 2019

NMDA receptor regulation prevents regression of visual cortical function in the absence of Mecp2.

scientific article published on December 2012

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

scientific article

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes

scientific article

New approach for an analysis of full-length cDNA library

scientific article published on December 1, 1997

Non-coding RNA transcription: turning on neighbours

scientific article published on September 2008

Noncoding RNA transcription beyond annotated genes

scientific article

Noncoding RNA: The Major Output of Gene Expression

article

Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes

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)

Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

scientific article

On biased distribution of introns in various eukaryotes

scientific article

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

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

scientific article

Paradigm shifts in genomics through the FANTOM projects

scientific article published on 8 August 2015

Placental expression profiling in preeclampsia: local overproduction of hemoglobin may drive pathological changes

scientific article

Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types

scientific article

Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid

scientific article published on 23 April 2018

Profiling transcription initiation in human aged brain using deep-CAGE.

scientific article published on 21 November 2011

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 architecture of mouse olfactory receptor genes

scientific journal article

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

Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

scientific article

Pseudo-messenger RNA: phantoms of the transcriptome

scientific article published on 28 April 2006

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

scientific article published on 24 February 2020

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

scientific article

RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer

scientific article published in November 2000

RNA Dust: Where are the Genes?

scientific article published on 7 May 2010

RNA dust: where are the genes?

scientific article published on 07 March 2010

RNA extraction from sorted neuronal subtypes

Rapidly evolving human promoter regions

scientific article published in November 2008

Recombination of repeat elements generates somatic complexity in human genomes

scientific article published in 2022

Recounting the FANTOM CAGEAssociated Transcriptome

scientific article published on 20 February 2020

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

Regional differences in gene expression and promoter usage in aged human brains.

scientific article

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

scientific article

Removal of polyA tails from full-length cDNA libraries for high-efficiency sequencing

scientific article

SCPortalen: human and mouse single-cell centric database

scientific article published on 17 October 2017

SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson's Disease

scientific article published on 16 August 2019

SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies

scientific article published on 02 November 2020

SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia

scientific article published on 01 November 2019

SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells.

scientific article published on 13 May 2015

SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation

scientific article

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

STAP cells are derived from ES cells

scientific article published in September 2015

Safety and efficacy of the Russian COVID-19 vaccine: more information needed

scientific article published on 21 September 2020

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

scientific article published in March 2018

Simple and rapid preparation of plasmid template by a filtration method using microtiter filter plates

scientific article published on March 1997

Simplified ontologies allowing comparison of developmental mammalian gene expression

scientific article

Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

scientific article published on 28 September 2016

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

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians

scientific article published on 12 November 2019

Site-specific DICER and DROSHA RNA products control the DNA-damage response

scientific article

Small RNAs derived from snoRNAs

scientific article (publication date: July 2009)

Solution structure of a BolA-like protein from Mus musculus

scientific article

Solution structure of the RWD domain of the mouse GCN2 protein

scientific article published on August 2004

Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)

scientific article

Somatic retrotransposition alters the genetic landscape of the human brain

scientific article (publication date: 30 October 2011)

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

scientific article

Splicing bypasses 3' end formation signals to allow complex gene architectures

scientific article

Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.

scientific article published on 16 February 2018

Structure by Sequencing: Discovery of Hidden Messages in the Noncoding RNA Fraction

scientific article published on 01 October 2012

Subcellular Localization of Mammalian Type II Membrane Proteins

scientific article published on 01 May 2006

Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts

scientific article published in September 2003

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching

scientific article published on 24 November 2012

Synthetic in vitro transcribed lncRNAs (SINEUPs) with chemical modifications enhance target mRNA translation

scientific article published on 04 October 2020

Systematic analysis of transcription start sites in avian development

scientific article published on 5 September 2017

Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping

scientific article published on 16 April 2014

Tag-based approaches for transcriptome research and genome annotation

scientific article

Tagging mammalian transcription complexity

scientific article published on 21 July 2006

Target-enrichment sequencing for detailed characterization of small RNAs

scientific article published on 22 March 2018

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia

scientific article

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

scientific article published on 25 February 2015

Telomerase reverse transcriptase regulates microRNAs

scientific article

Temporal dynamics and transcriptional control using single-cell gene expression analysis

scientific article

The DT40 web site: sampling and connecting the genes of a B cell line

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