PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. - Alistair R. R. Forrest; Darrin F. Taylor; J. Lynn Fink; M. Milena Gongora; Cameron Flegg; Rohan D. Teasdale; Harukazu Suzuki; Mutsumi Kanamori; Chikatoshi Kai; Yoshihide Hayashizaki; Sean M. Grimmond (BMC Bioinform., 2006)

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. - Hideya Kawaji; Jessica Severin; Marina Lizio; Alistair R. R. Forrest; Erik van Nimwegen; Michael Rehli; Kate Schroder; Katharine M. Irvine; Harukazu Suzuki; Piero Carninci; Yoshihide Hayashizaki; Carsten O. Daub (Nucleic Acids Res., 2011)

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. - Emmanuel Dimont; Oliver Hofmann 001; Shannan J. Ho Sui; Alistair R. R. Forrest; Hideya Kawaji; Winston Hide (Bioinform., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. - Stuart Aitken; Shigeyuki Magi; Ahmad M. N. Alhendi; Masayoshi Itoh; Hideya Kawaji; Timo Lassmann; Carsten O. Daub; Erik Arner; Piero Carninci; Alistair R. R. Forrest; Yoshihide Hayashizaki; Levon M. Khachigian; et al. (PLoS Comput. Biol., 2015)

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. - Imad Abugessaisa; Hisashi Shimoji; Serkan Sahin; Atsushi Kondo; Jayson Harshbarger; Marina Lizio; Yoshihide Hayashizaki; Piero Carninci; Alistair R. R. Forrest; Takeya Kasukawa; Hideya Kawaji (Database J. Biol. Databases Curation, 2016)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. - Hans Ienasescu; Kang Li; Robin Andersson; Morana Vitezic; Sarah Rennie; Yun Chen; Kristoffer Vitting-Seerup; Emil Lagoni; Mette Boyd; Jette Bornholdt; Michiel J. L. de Hoon; Hideya Kawaji; et al. (Database J. Biol. Databases Curation, 2016)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (Bioinform., 2016)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - Marina Lizio; Jayson Harshbarger; Imad Abugessaisa; Shuei Noguchi; Atsushi Kondo; Jessica Severin; Chris Mungall; David J. Arenillas; Anthony Mathelier; Yulia A. Medvedeva; Andreas Lennartsson; Finn Drabløs; et al. (Nucleic Acids Res., 2017)

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. - J. Kenneth Baillie; Andrew Bretherick; Christopher S. Haley; Sara Clohisey; Alan Gray; Lucile P. A. Neyton; Jeffrey Barrett; Eli A. Stahl; Albert Tenesa; Robin Andersson; J. Ben Brown; Geoffrey J. Faulkner; et al. (PLoS Comput. Biol., 2018)

scMatch: a single-cell gene expression profile annotation tool using reference datasets. - Rui Hou 006; Elena Denisenko; Alistair R. R. Forrest (Bioinform., 2019)

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments. - Hamid Alinejad-Rokny; Rassa Ghavami Modegh; Hamid R. Rabiee; Ehsan Ramezani Sarbandi; Narges Rezaie; Kin Tung Tam; Alistair R. R. Forrest (PLoS Comput. Biol., 2022)

Correction: MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments. - Hamid Alinejad-Rokny; Rassa Ghavami Modegh; Hamid R. Rabiee; Ehsan Ramezani Sarbandi; Narges Rezaie; Kin Tung Tam; Alistair R. R. Forrest (PLoS Comput. Biol., 2022)