ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)

(2020) Sanjida H. Rangwala et al.   GENOME RESEARCH

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

From ArrayExpress to BioStudies

(2020) Ugis Sarkans et al.   NUCLEIC ACIDS RESEARCH

GTRD: an integrated view of transcription regulation

(2020) Semyon Kolmykov et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2021 update

(2020) Jairo Navarro Gonzalez et al.   NUCLEIC ACIDS RESEARCH

FlyBase: updates to the Drosophila melanogaster knowledge base

(2020) Aoife Larkin et al.   NUCLEIC ACIDS RESEARCH

A map of direct TF–DNA interactions in the human genome

(2019) Marius Gheorghe et al.   NUCLEIC ACIDS RESEARCH

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

(2018) Shinya Oki et al.   EMBO REPORTS

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

A mouse tissue transcription factor atlas

(2017) Quan Zhou et al.   Nature Communications

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data

(2016) Ke-Ren Zhou et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

(2015) Robert Lesurf et al.   NUCLEIC ACIDS RESEARCH

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

BRENDA in 2015: exciting developments in its 25th year of existence

(2014) Antje Chang et al.   NUCLEIC ACIDS RESEARCH

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

(2014) Benoit Ballester et al.   eLife

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

The Ontology Lookup Service: bigger and better

(2010) R. Cote et al.   NUCLEIC ACIDS RESEARCH

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY