GENCODE: reference annotation for the human and mouse genomes in 2023

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

(2022) Joannella Morales et al.   NATURE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Standardized annotation of translated open reading frames

(2022) Jonathan M. Mudge et al.   NATURE BIOTECHNOLOGY

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

Base-resolution models of transcription-factor binding reveal soft motif syntax

(2021) Žiga Avsec et al.   NATURE GENETICS

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

(2021) Irwin Jungreis et al.   Nature Communications

The clinical importance of tandem exon duplication-derived substitutions

(2021) Laura Martinez Gomez et al.   NUCLEIC ACIDS RESEARCH

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

(2021) Irwin Jungreis et al.   VIROLOGY

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

(2021) Tamara Ouspenskaia et al.   NATURE BIOTECHNOLOGY

APPRIS: selecting functionally important isoforms

(2021) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2022 update

(2021) Brian T Lee et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

An analysis of tissue-specific alternative splicing at the protein level

(2020) Jose Manuel Rodriguez et al.   PLoS Computational Biology

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

(2018) Ian T. Fiddes et al.   GENOME RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

High-confidence coding and noncoding transcriptome maps

(2017) Bo-Hyun You et al.   GENOME RESEARCH

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

(2017) Chung-Chau Hon et al.   NATURE

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

(2015) Adam Frankish et al.   BMC GENOMICS

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The Ensembl REST API: Ensembl Data for Any Language

(2014) Andrew Yates et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS