Carninci, Piero

Landscape of transcription in human cells

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 5,187

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature

Genomics and Chromatin DynamicsCancer-related molecular mechanisms research

Cited by 2,550

Genome-wide analysis of mammalian promoter architecture and evolution

Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 1,350

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

Hon, C.-C., Ramilowski, J. A., Harshbarger, J., Bertin, N., Rackham, O. J. L., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T. M., Severin, J., et al. (2017) · Nature

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 1,007

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

Ramilowski, J. A., Goldberg, T., Harshbarger, J., Kloppmann, E., Lizio, M., Satagopam, V. P., Itoh, M., Kawaji, H., Carninci, P., Rost, B., et al. (2015) · Nature Communications

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 887

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 871

An atlas of combinatorial transcriptional regulation in mouse and man

Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 715

Somatic retrotransposition alters the genetic landscape of the human brain

Baillie, J. K., Barnett, M. W., Upton, K. R., Gerhardt, D. J., Richmond, T. A., De Sapio, F., Brennan, P. M., Rizzu, P., Smith, S., Fell, M., et al. (2011) · Nature

Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

Cited by 684

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

The FANTOM Consortium, de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Åström, G., Babina, M., Bertin, N., et al. (2017) · Nature Biotechnology

MicroRNA in disease regulationGenomics and Chromatin Dynamics

Cited by 561

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

Hashimoto, K., Kouno, T., Ikawa, T., Hayatsu, N., Miyajima, Y., Yabukami, H., Terooatea, T., Sasaki, T., Suzuki, T., Valentine, M., et al. (2019) · Proceedings of the National Academy of Sciences

T-cell and B-cell ImmunologySingle-cell and spatial transcriptomics

Cited by 343

FANTOM5 CAGE profiles of human and mouse samples

Noguchi, S., Arakawa, T., Fukuda, S., Furuno, M., Hasegawa, A., Hori, F., Ishikawa-Kato, S., Kaida, K., Kaiho, A., Kanamori-Katayama, M., et al. (2017) · Scientific Data

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 310

Two independent transcription initiation codes overlap on vertebrate core promoters

Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A. M., et al. (2014) · Nature

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 180

NMDA Receptor Regulation Prevents Regression of Visual Cortical Function in the Absence of Mecp2

Durand, S., Patrizi, A., Quast, K. B., Hachigian, L., Pavlyuk, R., Saxena, A., Carninci, P., Hensch, T. K., & Fagiolini, M. (2012) · Neuron

Genetics and Neurodevelopmental DisordersNeuroscience and Neuropharmacology Research

Cited by 172

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

Nepal, C., Hadzhiev, Y., Previti, C., Haberle, V., Li, N., Takahashi, H., Suzuki, A. M. M., Sheng, Y., Abdelhamid, R. F., Anand, S., et al. (2013) · Genome Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 127

Biased Allelic Expression in Human Primary Fibroblast Single Cells

Borel, C., Ferreira, P. G., Santoni, F., Delaneau, O., Fort, A., Popadin, K. Y., Garieri, M., Falconnet, E., Ribaux, P., Guipponi, M., et al. (2015) · The American Journal of Human Genetics

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 120

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

Kawaji, H., Lizio, M., Itoh, M., Kanamori-Katayama, M., Kaiho, A., Nishiyori-Sueki, H., Shin, J. W., Kojima-Ishiyama, M., Kawano, M., Murata, M., et al. (2014) · Genome Research

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 109

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

Rossiello, F., Aguado, J., Sepe, S., Iannelli, F., Nguyen, Q., Pitchiaya, S., Carninci, P., & d’Adda di Fagagna, F. (2017) · Nature Communications

Telomeres, Telomerase, and SenescenceDNA Repair Mechanisms

Cited by 105

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics

Genomics and Chromatin DynamicsZebrafish Biomedical Research Applications

Cited by 101

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

Centlow, M., Carninci, P., Nemeth, K., Mezey, E., Brownstein, M., & Hansson, S. R. (2008) · Fertility and Sterility

Pregnancy and preeclampsia studiesNeurological Complications and Syndromes

Cited by 86

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

Michelini, F., Jalihal, A. P., Francia, S., Meers, C., Neeb, Z. T., Rossiello, F., Gioia, U., Aguado, J., Jones-Weinert, C., Luke, B., et al. (2018) · Chemical Reviews

RNA Research and SplicingDNA Repair Mechanisms

Cited by 85

Trehalose-Enhanced Isolation of Neuronal Sub-Types from Adult Mouse Brain

Saxena, A., Wagatsuma, A., Noro, Y., Kuji, T., Asaka-Oba, A., Watahiki, A., Gurnot, C., Fagiolini, M., Hensch, T. K., & Carninci, P. (2012) · BioTechniques

Single-cell and spatial transcriptomicsNeuroscience and Neuropharmacology Research

Cited by 84

Recombination of repeat elements generates somatic complexity in human genomes

Pascarella, G., Hon, C. C., Hashimoto, K., Busch, A., Luginbühl, J., Parr, C., Hin Yip, W., Abe, K., Kratz, A., Bonetti, A., et al. (2022) · Cell

Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

Cited by 77

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

Hashimoto, K., Suzuki, A. M., Dos Santos, A., Desterke, C., Collino, A., Ghisletti, S., Braun, E., Bonetti, A., Fort, A., Qin, X.-Y., et al. (2015) · Genome Research

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 64

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

Nepal, C., Hadzhiev, Y., Balwierz, P., Tarifeño-Saldivia, E., Cardenas, R., Wragg, J. W., Suzuki, A.-M., Carninci, P., Peers, B., Lenhard, B., et al. (2020) · Nature Communications

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 52