Kawaji, Hideya

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

The systems biology graphical notation.

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 903

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

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

Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., & Meno, C. (2018) · The EMBO Reports

Genomics and Chromatin DynamicsBioinformatics and Genomic Networks

Cited by 763

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

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., et al. (2015) · Nucleic Acids Research

Bioinformatics and Genomic NetworksScientific Computing and Data Management

Cited by 755

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

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

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

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

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

Tomaru, Y., Hasegawa, R., Suzuki, T., Sato, T., Kubosaki, A., Suzuki, M., Kawaji, H., Forrest, A. R. R., Hayashizaki, Y., FANTOM Consortium, et al. (2014) · Nucleic Acids Research

Pluripotent Stem Cells ResearchGene Regulatory Network Analysis

Cited by 39