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New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

2019 Nucleic Acids Research  
The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes.  ...  Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC).  ...  , IHEC, GA4GH, 4DN, T2D AMP Consortium, UCSC Genome, ENSEMBL and Valis browsers and the many talented graduate researchers, postdocs, bioinformaticians and EN-CODE portal users for countless hours of data  ... 
doi:10.1093/nar/gkz1062 pmid:31713622 pmcid:PMC7061942 fatcat:mnobxd5yyjhv3lesviputi5qeq

ENCODE data at the ENCODE portal

Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer (+5 others)
2015 Nucleic Acids Research  
The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance.  ...  The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome.  ...  ACKNOWLEDGEMENTS We would like to thank all of the contributing labs of the ENCODE consortium for their extensive involvement in developing new data models as well as for their valuable datasets and metadata  ... 
doi:10.1093/nar/gkv1160 pmid:26527727 pmcid:PMC4702836 fatcat:lhm3ka23wjcxhb37xcxyhosp7q

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

Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan, Kathrina C Onate, Keenan Graham (+6 others)
2017 Nucleic Acids Research  
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium.  ...  Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly  ...  ACKNOWLEDGEMENTS We would like to thank past and current members of the ENCODE, modENCODE, modERN, GGR and REMC consortia in addition to the staff at the UCSC Genome and ENSEMBL Browsers and the many talented  ... 
doi:10.1093/nar/gkx1081 pmid:29126249 pmcid:PMC5753278 fatcat:hvtenqaaevfsxnppcdtgxgpxqu

The ENCODEdb portal: Simplified access to ENCODE Consortium data

L. L. Elnitski, P. Shah, R. T. Moreland, L. Umayam, T. G. Wolfsberg, A. D. Baxevanis
2007 Genome Research  
The Encyclopedia of DNA Elements (ENCODE) project aims to identify and characterize all functional elements in a representative chromosomal sample comprising 1% of the human genome.  ...  The ENCODEdb portal was developed to address this problem.  ...  Acknowledgments We thank Webb Miller, Ross Hardison, Gretchen Gibney, Elise Feingold, Peter Good, and Laura Liefer for their thoughtful insights and feedback during the development of ENCODEdb.  ... 
doi:10.1101/gr.5582207 pmid:17568011 pmcid:PMC1891354 fatcat:6wg7vxquuffzxnpvru5p3nhxq4

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown (+2 others)
2016 Nucleic Acids Research  
Although rapidly accumulating publicly available ChIPseq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation  ...  , quality control and analysis procedures have hindered extensive reuse of these data.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge Sujun Chen, Qi Liao and Sheng'en Hu for their helpful discussions about the project.  ... 
doi:10.1093/nar/gkw983 pmid:27789702 pmcid:PMC5210658 fatcat:u5pqf2gijffvnlc75jji7y5z2e

Perspectives on ENCODE

Michael P. Snyder, The ENCODE Project Consortium, Thomas R. Gingeras, Jill E. Moore, Zhiping Weng, Mark B. Gerstein, Bing Ren, Ross C. Hardison, John A. Stamatoyannopoulos, Brenton R. Graveley, Elise A. Feingold, Michael J. Pazin (+10 others)
2020 Nature  
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome.  ...  In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific  ...  This work was supported by grants from the NIH: U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999  ... 
doi:10.1038/s41586-020-2449-8 pmid:32728248 pmcid:PMC7410827 fatcat:o7smdehuj5eslnb5hi5wxnee5e

ENCODE: The human encyclopaedia

Brendan Maher
2012 Nature  
at Yale University in New Haven, Connecticut, who helped to design the data architecture for ENCODE.  ...  Even before the human genome sequence was finished 2 EXPERIMENTAL TARGETS CELL LINES Scientists in the Encyclopedia of DNA Elements Consortium have applied 24 experiment types (across) to more than  ... 
doi:10.1038/489046a pmid:22962707 fatcat:dsfdowc3ezegrn4mn4exfcebzy

The ENCODE Project at UC Santa Cruz

D. J. Thomas, K. R. Rosenbloom, H. Clawson, A. S. Hinrichs, H. Trumbower, B. J. Raney, D. Karolchik, G. P. Barber, R. A. Harte, J. Hillman-Jackson, R. M. Kuhn, B. L. Rhead (+5 others)
2007 Nucleic Acids Research  
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome.  ...  This paper describes the portal to the data, highlights the data that has been made available, and presents the tools that have been developed within the ENCODE project.  ...  ACKNOWLEDGEMENTS This work was supported by grants from the National Human Genome Research Institute (NHGRI) for browser development and for the ENCODE project, the Howard Hughes Medical Institute (HHMI  ... 
doi:10.1093/nar/gkl1017 pmid:17166863 pmcid:PMC1781110 fatcat:jqr7rfuv3zgglfwdmcuirlebwu

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

Benjamin C. Hitz, Laurence D. Rowe, Nikhil R. Podduturi, David I. Glick, Ulugbek K. Baymuradov, Venkat S. Malladi, Esther T. Chan, Jean M. Davidson, Idan Gabdank, Aditi K. Narayana, Kathrina C. Onate, Jason Hilton (+10 others)
2017 PLoS ONE  
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome  ...  genomic data in the manner of ENCODE.  ...  Acknowledgments We wish to thank all participants in the ENCODE Consortium for our collaborations that have enhanced the metadata definitions, as well as ENCODE Portal users for their useful feedback.  ... 
doi:10.1371/journal.pone.0175310 pmid:28403240 pmcid:PMC5389787 fatcat:6ejh7ky2czag3pxztylf7bxwn4

An encyclopedia of mouse DNA elements (Mouse ENCODE)

John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson (+74 others)
2012 Genome Biology  
9 Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America. 10  ...  A log of data releases is available at the Mouse ENCODE portal site [18] and through the main UCSC browser [17] .  ...  An online tutorial developed for facilitating the viewing of human ENCODE data is also directly applicable to the Mouse ENCODE data [28] .  ... 
doi:10.1186/gb-2012-13-8-418 pmid:22889292 pmcid:PMC3491367 fatcat:hwc2zpdwjfaf5ky2obd3cz2q4y

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

Benjamin Hitz, Laurence D Rowe, Nikhil Podduturi, David Glick, Ulugbek Baymuradov, Venkat Malladi, Esther Chan, Jean Davidson, Idan Gabdank, Aditi Narayanan, Kathrina Onate, Jason Hilton (+9 others)
2016 bioRxiv   pre-print
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort[1-6] to create a comprehensive catalog of functional elements initiated shortly after the completion of the Human Genome  ...  genomic data in the manner of ENCODE.  ...  Acknowledgments We wish to thank all participants in the ENCODE Consortium for our collaborations that have enhanced the metadata definitions, as well as ENCODE Portal users for their useful feedback.  ... 
doi:10.1101/044578 fatcat:wlphtxha4vcprbdmggyn5wuxci

Cracking the ENCODE: From transcription to therapeutics

Gautam Mehta, Rajiv Jalan, Rajeshwar P Mookerjee
2013 Hepatology  
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.  ...  Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.  ...  From Proteomics to Transcriptomics An international collaborative effort to determine the functional importance of noncoding DNA was developed which generated an encyclopedia of DNA elements (ENCODE).  ... 
doi:10.1002/hep.26449 pmid:23609523 fatcat:5xtx3tbjbvh5lddczddhtes554

ENCODE Data in the UCSC Genome Browser: year 5 update

Kate R. Rosenbloom, Cricket A. Sloan, Venkat S. Malladi, Timothy R. Dreszer, Katrina Learned, Vanessa M. Kirkup, Matthew C. Wong, Morgan Maddren, Ruihua Fang, Steven G. Heitner, Brian T. Lee, Galt P. Barber (+9 others)
2012 Nucleic Acids Research  
The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome  ...  Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis.  ...  They also thank members of the ENCODE Consortium for providing these valuable data sets. Special appreciation to Michael Pazin of NHGRI for extensive contributions to the ENCODE portal content.  ... 
doi:10.1093/nar/gks1172 pmid:23193274 pmcid:PMC3531152 fatcat:ubjbo4yrofb75ibsxztzj2qp4e

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

Peter B. Becker
2011 PLoS Biology  
Citation: The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046.  ...  The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and  ...  Wexler and Julia Zhang at the National Human Genome Research Institute for their support in administering the ENCODE Consortium, additional members of our laboratories and institutions who have contributed  ... 
doi:10.1371/journal.pbio.1001046 pmid:21526222 pmcid:PMC3079585 fatcat:cfshtutffzhfvdqgwnda2sxlym

Ontology application and use at the ENCODE DCC

Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart Miyasato, Gregory R. Roe, Matt Simison (+6 others)
2015 Database: The Journal of Biological Databases and Curation  
The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations.  ...  Additionally, we provide examples of how ontologies are used to annotate ENCODE metadata and how the annotations can be identified via ontology-driven searches at the ENCODE portal.  ...  Acknowledgements We thank all participants in the ENCODE Consortium for collaborations that have enhanced the metadata definitions and the ENCODE Portal users for their useful feedback.  ... 
doi:10.1093/database/bav010 pmid:25776021 pmcid:PMC4360730 fatcat:7ccxq7rgmje7nffans7edld5da
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