Towards a comprehensive catalogue of validated and target-linked human enhancers

M Gasperini, JM Tome, J Shendure - Nature Reviews Genetics, 2020 - nature.com
The human gene catalogue is essentially complete, but we lack an equivalently vetted
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …

Clinical epigenetics: seizing opportunities for translation

M Berdasco, M Esteller - Nature Reviews Genetics, 2019 - nature.com
Biomarker discovery and validation are necessary for improving the prediction of clinical
outcomes and patient monitoring. Despite considerable interest in biomarker discovery and …

Ensembl 2022

F Cunningham, JE Allen, J Allen… - Nucleic acids …, 2022 - academic.oup.com
Abstract Ensembl (https://www. ensembl. org) is unique in its flexible infrastructure for access
to genomic data and annotation. It has been designed to efficiently deliver annotation at …

Regulatory genomic circuitry of human disease loci by integrative epigenomics

CA Boix, BT James, YP Park, W Meuleman, M Kellis - Nature, 2021 - nature.com
Annotating the molecular basis of human disease remains an unsolved challenge, as 93%
of disease loci are non-coding and gene-regulatory annotations are highly incomplete …

Ensembl 2020

AD Yates, P Achuthan, W Akanni, J Allen… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Ensembl (https://www. ensembl. org) is a system for generating and distributing
genome annotation such as genes, variation, regulation and comparative genomics across …

A reference map of the human binary protein interactome

K Luck, DK Kim, L Lambourne, K Spirohn, BE Begg… - Nature, 2020 - nature.com
Global insights into cellular organization and genome function require comprehensive
understanding of the interactome networks that mediate genotype–phenotype relationships …

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

D Aran, AP Looney, L Liu, E Wu, V Fong, A Hsu… - Nature …, 2019 - nature.com
Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins
by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific …

GENCODE reference annotation for the human and mouse genomes

A Frankish, M Diekhans, AM Ferreira… - Nucleic acids …, 2019 - academic.oup.com
The accurate identification and description of the genes in the human and mouse genomes
is a fundamental requirement for high quality analysis of data informing both genome …

Ensembl 2019

F Cunningham, P Achuthan, W Akanni… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Ensembl project (https://www. ensembl. org) makes key genomic data sets
available to the entire scientific community without restrictions. Ensembl seeks to be a …

Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

S Battaglia, K Dong, J Wu, Z Chen, FJ Najm, Y Zhang… - Nature …, 2022 - nature.com
Epigenomic maps identify gene regulatory elements by their chromatin state. However,
prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate …