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

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

(2020) Alessandro Bonetti et al.   Nature Communications

The Secret Life of lncRNAs: Conserved, yet Not Conserved

(2020) Harshita Sharma et al.   CELL

Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells

(2020) Chun-Jie Guo et al.   CELL

Comparative transcriptomics of primary cells in vertebrates

(2020) Tanvir Alam et al.   GENOME RESEARCH

Functional annotation of human long noncoding RNAs via molecular phenotyping

(2020) Jordan A. Ramilowski et al.   GENOME RESEARCH

RIKEN MetaDatabase

(2018) Norio Kobayashi et al.   International Journal on Semantic Web and Information Systems

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Chung-Chau Hon et al.   NATURE

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

(2017) Derek de Rie et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

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

(2017) Imad Abugessaisa et al.   Scientific Data

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

(2017) Hiromasa Ono et al.   Scientific Data

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

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

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

(2016) Imad Abugessaisa et al.   Database-The Journal of Biological Databases and Curation

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

(2016) Alexander D. Diehl et al.   Journal of Biomedical Semantics

Paradigm shifts in genomics through the FANTOM projects

(2015) Michiel de Hoon et al.   MAMMALIAN GENOME

Towards a molecular understanding of microRNA-mediated gene silencing

(2015) Stefanie Jonas et al.   NATURE REVIEWS GENETICS

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

(2014) Jessica Severin et al.   NATURE BIOTECHNOLOGY

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

(2012) Phil Arnold et al.   BIOINFORMATICS

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS