ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data

Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses

(2022) Zhaonan Zou et al.   BMC BIOINFORMATICS

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

(2021) Fayrouz Hammal et al.   NUCLEIC ACIDS RESEARCH

The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence‐associated epigenomic remodeling

(2020) Hiroshi Tanaka et al.   AGING CELL

Landscape of G-quadruplex DNA structural regions in breast cancer

(2020) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development

(2020) Juliette Roels et al.   NATURE IMMUNOLOGY

Transient IGF-1R inhibition combined with osimertinib eradicates AXL-low expressing EGFR mutated lung cancer

(2020) Rong Wang et al.   Nature Communications

Pathophysiology of Inflammatory Bowel Diseases

(2020) John T. Chang   NEW ENGLAND JOURNAL OF MEDICINE

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

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

(2019) Scott A. Ochsner et al.   Scientific Data

Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance

(2018) Elliott Ferris et al.   Cell Reports

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

(2018) Shinya Oki et al.   EMBO REPORTS

A chromatin integration labelling method enables epigenomic profiling with lower input

(2018) Akihito Harada et al.   NATURE CELL BIOLOGY

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

(2018) Rongbin Zheng 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

RegulatorTrail: a web service for the identification of key transcriptional regulators

(2017) Tim Kehl et al.   NUCLEIC ACIDS RESEARCH

MethBank 3.0: a database of DNA methylomes across a variety of species

(2017) Rujiao Li et al.   NUCLEIC ACIDS RESEARCH

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets

(2016) Felipe Albrecht et al.   NUCLEIC ACIDS RESEARCH

jPOSTrepo: an international standard data repository for proteomes

(2016) Shujiro Okuda et al.   NUCLEIC ACIDS RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Making sense of transcribing chromatin

(2012) Tom Owen-Hughes et al.   CURRENT OPINION IN CELL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY