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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.

Collection published: 5 September 2012

Last updated: 28 February 2013

		Research article Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions Jainab Khatun, Yanbao Yu, John A Wrobel, Brian A Risk, Harsha P Gunawardena, Ashley Secrest, Wendy J Spitzer, Ling Xie, Li Wang, Xian Chen, Morgan C Giddings BMC Genomics 2013, 14:141 (28 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
		Research Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif
		Research The GENCODE pseudogene resource Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection
		Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
		Research Analysis of variation at transcription factor binding sites in Drosophila and humans Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon
		Research Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
		Research article Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data Yunyun Ni, Amelia Weber Hall, Anna Battenhouse, Vishwanath R Iyer BMC Genetics 2012, 13:46 (5 September 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A new approach to simultaneously discover SNPs and perform transcription factor binding bias analysis using ChIP-seq data generated in the ENCODE Project reveals widespread heritable allele-specific binding and significant enrichment for disease-associated variants.

		Research article Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions Jainab Khatun, Yanbao Yu, John A Wrobel, Brian A Risk, Harsha P Gunawardena, Ashley Secrest, Wendy J Spitzer, Ling Xie, Li Wang, Xian Chen, Morgan C Giddings BMC Genomics 2013, 14:141 (28 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
		Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
		Research Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3 Seth Frietze, Rui Wang, Lijing Yao, Yu Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham, Victor X Jin Genome Biology 2012, 13:R52 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The transcription factor TCF7L2 can be tethered to the genome by GATA3, and therefore can target sites lacking its own motif
		Research The GENCODE pseudogene resource Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng Mu, Rachel Harte, Suganthi Balasubramanian, Andrea Tanzer, Mark Diekhans, Alexandre Reymond, Tim J Hubbard, Jennifer Harrow, Mark B Gerstein Genome Biology 2012, 13:R51 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The GENCODE pseudogene resource includes evidence for dead genes undergoing resurrection
		Research Functional analysis of transcription factor binding sites in human promoters Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Shelley Aldred, Nathan D Trinklein, Richard M Myers, Zhiping Weng Genome Biology 2012, 13:R50 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary TFBSs are predicted from ENCODE data, and experiments in four cell lines find 70% to be functional
		Research Analysis of variation at transcription factor binding sites in Drosophila and humans Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon
		Research Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors Kevin Y Yip, Chao Cheng, Nitin Bhardwaj, James B Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder, Mark Gerstein Genome Biology 2012, 13:R48 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
		Research article Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data Yunyun Ni, Amelia Weber Hall, Anna Battenhouse, Vishwanath R Iyer BMC Genetics 2012, 13:46 (5 September 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary A new approach to simultaneously discover SNPs and perform transcription factor binding bias analysis using ChIP-seq data generated in the ENCODE Project reveals widespread heritable allele-specific binding and significant enrichment for disease-associated variants.