SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

Genomic footprinting

(2016) Jeff Vierstra et al.   NATURE METHODS

Lessons from modENCODE

(2015) James B. Brown et al.   Annual Review of Genomics and Human Genetics

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

(2015) Kerstin Haase et al.   BMC Medical Genomics

Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected

(2015) Yang Fan et al.   JOURNAL OF PROTEOME RESEARCH

The effects of omega-3 polyunsaturated fatty acids and genetic variants on methylation levels of the interleukin-6 gene promoter

(2015) Yiyi Ma et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Ontology application and use at the ENCODE DCC

(2015) Venkat S. Malladi et al.   Database-The Journal of Biological Databases and Curation

The EBI RDF platform: linked open data for the life sciences

(2014) S. Jupp et al.   BIOINFORMATICS

Epigenetics, chromatin and genome organization: recent advances from the ENCODE project

(2014) L. Siggens et al.   JOURNAL OF INTERNAL MEDICINE

Navigating and mining modENCODE data

(2014) Nathan Boley et al.   METHODS

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

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

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

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

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