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The ENCODE project

The Encyclopedia of DNA Elements (ENCODE) Consortium's mission statement was to comprehensively annotate functional elements in the human genome. Following nearly ten years of data generation by over 400 researchers across the globe, the project's findings have now been published as a group of 30+ articles in a multi-publisher collaboration. The ENCODE articles published by BioMed Central are presented below, and the publication effort is discussed in further detail on the BMC Blog. For more information on ENCODE, please see the ENCODE web portal. The ENCODE articles from all three publishers can also be downloaded as an iPad app, or browsed in the ENCODE Explorer.

  1. Research article

    Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

    Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the...

    Jainab Khatun, Yanbao Yu, John A Wrobel, Brian A Risk, Harsha P Gunawardena, Ashley Secrest, Wendy J Spitzer, Ling Xie, Li Wang, Xian Chen and Morgan C Giddings

    BMC Genomics 2013 14:141

    Published on: 28 February 2013

  2. Research

    Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

    The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is...

    Seth Frietze, Rui Wang, Lijing Yao, Yu Gyoung Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham and Victor X Jin

    Genome Biology 2012 13:R52

    Published on: 5 September 2012

  3. Research

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

    Transcription factors function by binding different classes of regulatory elements. The Encyclopedia of DNA Elements (ENCODE) project has recently produced binding data for more than 100 transcription factors ...

    Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder and Mark Gerstein

    Genome Biology 2012 13:R48

    Published on: 5 September 2012

  4. Research

    Functional analysis of transcription factor binding sites in human promoters

    The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a...

    Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Force Aldred, Nathan D Trinklein, Richard M Myers and Zhiping Weng

    Genome Biology 2012 13:R50

    Published on: 5 September 2012

  5. Research

    Modeling gene expression using chromatin features in various cellular contexts

    Previous work has demonstrated that chromatin feature levels correlate with gene expression. The ENCODE project enables us to further explore this relationship using an unprecedented volume of data. Expression...

    Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney and Zhiping Weng

    Genome Biology 2012 13:R53

    Published on: 5 September 2012

  6. Research

    Analysis of variation at transcription factor binding sites in Drosophila and humans

    Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variabil...

    Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong and Ewan Birney

    Genome Biology 2012 13:R49

    Published on: 5 September 2012

  7. Research

    The GENCODE pseudogene resource

    Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality h...

    Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Jasmine Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow and Mark B Gerstein

    Genome Biology 2012 13:R51

    Published on: 5 September 2012