Forrest, Alistair R.R.

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

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 1,035

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

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Denisenko, E., Guo, B. B., Jones, M., Hou, R., de Kock, L., Lassmann, T., Poppe, D., Clément, O., Simmons, R. K., Lister, R., et al. (2020) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 686

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

Denisenko, E., Guo, B. B., Jones, M., Hou, R., de Kock, L., Lassmann, T., Poppe, D., Clement, O., Simmons, R. K., Lister, R., et al. (2019) · Genome biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 686

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

The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition

Cloonan, N., Brown, M. K., Steptoe, A. L., Wani, S., Chan, W. L., Forrest, A. R., Kolle, G., Gabrielli, B., & Grimmond, S. M. (2008) · Genome Biology

MicroRNA in disease regulationCancer-related Molecular Pathways

Cited by 304

Predicting cell-to-cell communication networks using NATMI

Hou, R., Denisenko, E., Ong, H. T., Ramilowski, J. A., & Forrest, A. R. R. (2020) · Nature Communications

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 285

scMatch: a single-cell gene expression profile annotation tool using reference datasets

Hou, R., Denisenko, E., & Forrest, A. R. R. (2019) · Bioinformatics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 130

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

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

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, C., the FANTOM Consortium, Forrest, A. R. R., & Wagner, G. P. (2015) · Nature Communications

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 59

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

Therapeutic blockade of ER stress and inflammation prevents NASH and progression to HCC

Boslem, E., Reibe, S., Carlessi, R., Smeuninx, B., Tegegne, S., Egan, C. L., McLennan, E., Terry, L. V., Nobis, M., Mu, A., et al. (2023) · Science Advances

Liver Disease Diagnosis and TreatmentLiver physiology and pathology

Cited by 39

The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells

Kubosaki, A., Lindgren, G., Tagami, M., Simon, C., Tomaru, Y., Miura, H., Suzuki, T., Arner, E., Forrest, A. R. R., Irvine, K. M., et al. (2010) · Molecular Immunology

interferon and immune responsesGenomics and Chromatin Dynamics

Cited by 29

Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

Tomaru, Y., Simon, C., Forrest, A. R., Miura, H., Kubosaki, A., Hayashizaki, Y., & Suzuki, M. (2009) · Genome biology

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 21