Piero Carninci

发表

Wavelet profiles: their application in Oryza sativa DNA sequence analysis

Shoshi Kikuchi, Nobuyuki Kawagashira, Yasuhiro Ohtomo, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

Two independent transcription initiation codes overlap on vertebrate core promoters

Nan Li, Boris Lenhard, Piero Carninci, 2014, Nature.

assay information of the mouse qualitycontrol samples for HeliScopeCAGE

Mariko Okada, Hans Clevers, Kim M. Summers, 2017 .

MOIRAI: a compact workflow system for CAGE analysis

Carsten O. Daub, Akira Hasegawa, Piero Carninci, 2014, BMC Bioinformatics.

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

Piero Carninci, Toshio Yamazaki, Silvia Zucchelli, 2018, PloS one.

Definition of Promotome–Transcriptome Architecture Using CAGEscan

Piero Carninci, Charles Plessy, Nicolas Bertin, 2012 .

LOCATE: a mouse protein subcellular localization database

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2005, Nucleic Acids Res..

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

Carsten O. Daub, Vladimir B. Bajic, Tom C. Freeman, 2016, bioRxiv.

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

Finn Drabløs, David J. Arenillas, Piero Carninci, 2016, Nucleic Acids Res..

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

Masaru Tomita, Kenichi Higo, Shoshi Kikuchi, 2005, Bioinform..

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

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2005, Nucleic Acids Res..

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

Piero Carninci, Yoshihide Hayashizaki, Hiroshi Arakawa, 2002, Nucleic Acids Res..

BMC Bioinformatics BioMed Central Methodology article Large-scale clustering of CAGE tag expression data

Takio Kurita, Martin C. Frith, Kazuro Shimokawa, 2007 .

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2016, Database J. Biol. Databases Curation.

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

Liang Yang, Vladimir B. Bajic, Jun Kawai, 2006, BMC Bioinformatics.

SCPortalen: human and mouse single-cell centric database

Sachi Kato, Akira Hasegawa, Hiroki Ura, 2017, Nucleic Acids Res..

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

Piero Carninci, Claudio Schneider, Stefano Gustincich, 1990, Nucleic Acids Res..

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

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

Piero Carninci, Yoshihide Hayashizaki, Robin Andersson, 2016, Database J. Biol. Databases Curation.

Assessment of Redundancy and Full-Length Rate of Full-Length Enriched cDNA Libraries

Piero Carninci, Yoshihide Hayashizaki, Hideaki Konno, 2000 .

ZENBU-reports: Interactive data visualization for whole genome analyses

Piero Carninci, Takeya Kasukawa, Michiel J. L. de Hoon, 2017 .

Profiling transcription initiation in human aged brain using deep-CAGE

Carsten O. Daub, Piero Carninci, Patrizia Rizzu, 2011, BMC Bioinformatics.

sample information of the human samples

Mariko Okada, Hans Clevers, Kim M. Summers, 2017 .

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

Alexander E. Kel, Kenta Nakai, Toshihisa Takagi, 2004, Silico Biol..

Results for 8,032 Multi-Protein TUs from the IPS Set

Piero Carninci, Takeya Kasukawa, J. Lynn Fink, 2006 .

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Carsten O. Daub, Mariko Okada, Piero Carninci, 2015, PLoS Comput. Biol..

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

Akira Hasegawa, Piero Carninci, Yoshihide Hayashizaki, 2018, Nucleic Acids Res..

Machine-driven parameter optimisation of biochemical reactions

Sachi Kato, Piero Carninci, Charles Plessy, 2019, bioRxiv.

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

Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, 2010, Nucleic Acids Res..

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

Norio Kobayashi, Piero Carninci, Yoshihide Hayashizaki, 2020, Nucleic Acids Res..

Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.

Shoshi Kikuchi, Kazuo Murakami, Jun Kawai, 2004, Physiological genomics.

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

Piero Carninci, Hideya Kawaji, Alistair R. R. Forrest, 2015, Nature Communications.

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

Shoshi Kikuchi, Kazuo Murakami, Jun Kawai, 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2009, Genome research.

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

Piero Carninci, Hideya Kawaji, Shuhei Noguchi, 2019, Journal of molecular biology.

Unexpected expression of α- and β-globin in mesencephalic dopaminergic neurons and glial cells

Isidro Ferrer, Piero Carninci, Kazuto Kobayashi, 2009, Proceedings of the National Academy of Sciences.

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, bioRxiv.

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

Piero Carninci, Timo Lassmann, Mitsuyoshi Murata, 2012, Nature Protocols.

Monitoring transcription initiation activities in rat and dog

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, Scientific Data.

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

Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, 2015, PloS one.

Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

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

Piero Carninci, Yoshihide Hayashizaki, Robin Andersson, 2016, Cancer research.

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Piero Carninci, Timo Lassmann, Justen Andrews, 2011, Genome research.

Genome-Wide Technologies to Study RNA–Chromatin Interactions

Piero Carninci, Masaki Kato, Piero Carninci, 2020, Non-coding RNA.

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

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, Scientific Data.

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

Masaru Tomita, Jun Kawai, Piero Carninci, 2010, BMC Genomics.

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

Piero Carninci, Alexander Dobin, Thomas R Gingeras, 2013, Genome research.

Simplified ontologies allowing comparison of developmental mammalian gene expression

Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, 2007, Genome Biology.

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

Shoshi Kikuchi, Jun Kawai, Piero Carninci, 2002, Genome research.

The Abundance of Short Proteins in the Mammalian Proteome

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, 2015, PLoS Comput. Biol..

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

Carsten O. Daub, Vladimir B. Bajic, Tom C. Freeman, 2016, bioRxiv.

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

Piero Carninci, Hideya Kawaji, Shuhei Noguchi, 2017, Scientific Data.

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

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2014, Genome research.

FANTOM5 CAGE profiles of human and mouse samples

Hiroshi Tanaka, Geoffrey J Faulkner, Sarah Klein, 2017, Scientific Data.

Insights into social insects from the genome of the honeybee Apis mellifera

Ying Wang, Michal Linial, Andrew G. Clark, 2006, Nature.

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

Shoshi Kikuchi, Kazuo Murakami, Jun Kawai, 2004, Molecular biology and evolution.

Constructing the landscape of the mammalian transcriptome

Piero Carninci, Piero Carninci, 2007, Journal of Experimental Biology.

Genome-wide analysis of cancer/testis gene expression

Oliver Hofmann, C. V. Jongeneel, Piero Carninci, 2008, Proceedings of the National Academy of Sciences.

Differential Use of Signal Peptides and Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

Antisense transcripts with rice full-length cDNAs

Shoshi Kikuchi, Kazuo Murakami, Jun Kawai, 2003, Genome Biology.

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

Geoffrey J Faulkner, Piero Carninci, Yoshihide Hayashizaki, 2017, PLoS genetics.

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

S. Q. Xie, Piero Carninci, Yoshihide Hayashizaki, 2015, Molecular systems biology.

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

Piero Carninci, Yoshihide Hayashizaki, Martin C Frith, 2014, BMC Genomics.

High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur

Vladimir B. Bajic, Jun Kawai, Piero Carninci, 2010, PloS one.

Additional data file 5

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2003 .

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

Piero Carninci, Yoshihide Hayashizaki, Akira Hasegawa, 2008, BioTechniques.

The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.

Piero Carninci, Yoshihide Hayashizaki, Reed George, 2002, Genome research.

Noncoding RNA transcription beyond annotated genes.

Piero Carninci, Yoshihide Hayashizaki, Piero Carninci, 2007, Current opinion in genetics & development.

Transcriptional network dynamics in macrophage activation.

Piero Carninci, Diego di Bernardo, Manuela Gariboldi, 2006, Genomics.

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

Piero Carninci, Jayson Harshbarger, Piero Carninci, 2017, BMC Genomics.

Subcellular Localization of Mammalian Type II Membrane Proteins

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, Traffic.

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

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2018, Open Biology.

A Simple Physical Model Predicts Small Exon Length Variations

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

The effect of genetic variation on promoter usage and enhancer activity

Piero Carninci, Olivier Delaneau, Alexandre Fort, 2017, Nature Communications.

The devil in the details of RNA-seq

Piero Carninci, Piero Carninci, A. Kratz, 2014, Nature Biotechnology.

Alternate transcription of the Toll-like receptor signaling cascade

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, Genome Biology.

Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Shoshi Kikuchi, Yoshiaki Nagamura, Mayu Yamamoto, 2007, PloS one.

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

Piero Carninci, Silvia Zucchelli, Stefano Gustincich, 2016, Scientific Reports.

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

Boris Lenhard, Piero Carninci, Uwe Strähle, 2013, Genome research.

Multifaceted mammalian transcriptome.

Piero Carninci, Yoshihide Hayashizaki, Jun Yasuda, 2008, Current opinion in cell biology.

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

Vladimir B. Bajic, Sebastian Schmeier, Piero Carninci, 2015, Nucleic acids research.

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

Carsten O. Daub, Philipp Kapranov, Thomas R. Gingeras, 2010, Nature Methods.

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

Geoffrey J Faulkner, Jun Kawai, Piero Carninci, 2006, Genome Biology.

Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome

Piero Carninci, Yoshihide Hayashizaki, Piero Carninci, 2006, PLoS genetics.

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

Masaru Tomita, Piero Carninci, Yoshihide Hayashizaki, 2002, Genome research.

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

Boris Lenhard, Piero Carninci, Yoshihide Hayashizaki, 2015, Nucleic acids research.

Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.

Wolfgang Huber, Hans Lehrach, Piero Carninci, 2007, Genomics.

The complexity of the mammalian transcriptome

Piero Carninci, Yoshihide Hayashizaki, Albin Sandelin, 2006, The Journal of physiology.

Heterotachy in Mammalian Promoter Evolution

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

Biased allelic expression in human primary fibroblast single cells.

Piero Carninci, Olivier Delaneau, Pedro G. Ferreira, 2015, American journal of human genetics.

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

Kazuro Shimokawa, Jun Kawai, Piero Carninci, 2004, FEBS letters.

Whole transcriptome analysis: what are we still missing?

Piero Carninci, Alka Saxena, Piero Carninci, 2011, Wiley interdisciplinary reviews. Systems biology and medicine.

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

Piero Carninci, Yoshihide Hayashizaki, Patrick McConnell, 2006, Proceedings of the National Academy of Sciences.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Boris Lenhard, Lusy Handoko, Piero Carninci, 2020, Genome research.

Evolutionary turnover of mammalian transcription start sites.

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, Genome research.

Solution structure of a BolA‐like protein from Mus musculus

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2004, Protein science : a publication of the Protein Society.

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.

Inanç Birol, Edwin Cuppen, Paul Flicek, 2010, Genome research.

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

Piero Carninci, Yoshihide Hayashizaki, Joost Boele, 2014, Proceedings of the National Academy of Sciences.

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

Geoffrey J Faulkner, Piero Carninci, Yoshihide Hayashizaki, 2008, Genomics.

Tag-based approaches for transcriptome research and genome annotation

Piero Carninci, Matthias Harbers, Piero Carninci, 2005, Nature Methods.

TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images

Yanhui Hu, Lukas Wagner, David E Hill, 2017 .

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

Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji, 2017, EBioMedicine.

Tagging mammalian transcription complexity.

Piero Carninci, Piero Carninci, 2006, Trends in genetics : TIG.

Paradigm shifts in genomics through the FANTOM projects

Piero Carninci, Jay W. Shin, Michiel de Hoon, 2015, Mammalian Genome.

Pseudo–Messenger RNA: Phantoms of the Transcriptome

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, PLoS genetics.

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

Kazuo Shinozaki, Piero Carninci, Yoshihide Hayashizaki, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Mapping of 19032 mouse cDNAs on mouse chromosomes

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2002, Journal of Structural and Functional Genomics.

RNA Dust: Where are the Genes?

Piero Carninci, Piero Carninci, 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

Hideyuki Okano, Piero Carninci, Yasushi Okazaki, 2019, Proceedings of the National Academy of Sciences.

Dynamic usage of transcription start sites within core promoters

Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, 2006, Genome Biology.

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

Boris Lenhard, Piero Carninci, Yoshihide Hayashizaki, 2007, Nature Reviews Genetics.

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

Masaru Tomita, Kenichi Higo, Shoshi Kikuchi, 2003, FEBS letters.

Antisense Transcription in the Mammalian Transcriptome RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium

Boris Lenhard, Martin C. Frith, Jun Kawai, 2005 .

George MW, Gene ER. Insights into social insects from the genome of the honeybee Apis mellifera. Nature

Ying Wang, Michal Linial, Peer Bork, 2006 .

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

Mathieu Blanchette, Nicholas M. Luscombe, Boris Lenhard, 2020, Nature Communications.