ENCODE whole-genome data in the UCSC Genome Browser

By Kate R. Rosenbloom, Timothy R. Dreszer, Michael Pheasant, Galt P. Barber, L. Meyer, A. Pohl, Brian J. Raney, Ting Wang, A. Hinrichs, Ann S. Zweig and 8 more. Nucleic Acids Res., 2009

438 citations recorded by the source corpus.

The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access.

Subfields: Molecular Biology

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Citations in the corpus

Ensembl 2011 (2010, methodology): “We also integrate data resources available in species or domain speciﬁc databases such as ZFIN (1), HGNC (2), the Single Nucleotide Polymorphism Database (dbSNP) (3), UniProt (4) and the Encyclopedia of DNA Elements (ENCODE) portal at UCSC (5).”
Next-Generation Genomics: an Integrative Approach (2010, neutral): “edu">University of California-Santa Cruz (UCSC) Genome Browser”
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data (2016, methodology): “…regions, and to do the simulation in amore realistic fashion, we used the ENCODE chromatin state segmentation of a lymphoblastoid cell line (GM12878) (Ernst and Kellis 2010; Ernst et al. 2011; Raney et al. 2011) to obtain a set of real promoter and nonpromoter regions on Chromosome 10.”
Dynamic DNA methylation across diverse human cell lines and tissues (2013, methodology): “The data are readily available for visualization and analysis using the UCSC Genome Browser (Fujita et al. 2011; Raney et al. 2011) and will provide a valuable resource for future comparisons to other cell types, disease states, and functional genomic assays.”
The 1000 Genomes Project: Data Management and Community Access (2012, background): “With nine different sequencing centers and more than two dozen major analysis groups1, the most important initial challenges are (1) collating all the sequencing data centrally for necessary quality control (QC) and standardization; (2) exchanging the data between participating institutions; (3) ens”
Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms (2014, positive): “We removed sites that had a Duke Uniqueness 20bp-mapability score 1 (downloaded from the UCSC Genome Browser, [31]), to avoid potential errors due to mismapping or miscalling in regions of the genome that are not uniquely mapable.”