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Understanding the human genome: ENCODE at BioMed Central

BioMed Central

The completion of the human genome project in 2003 was an immeasurably important milestone, but (like an book written in code) left many biologists wondering what the sequence might actually mean. Consequently, the focus of human genomics that year began the transition from generating sequence - to annotating the functional elements, hidden within the human genome's 3.2 billion As, Cs, Gs and Ts. With this goal in mind the ENCODE (Encyclopedia of DNA Elements) consortium was formed.

Some combinations of these nucleotides would together constitute the exons and introns that make up genes, while some would form regulatory elements. ENCODE set out to comprehensively annotate these elements in as much functional detail as possible which can now be found in the ENCODE explorer, a novel micro-site allowing seamless navigation between articles.

Following nearly ten years of data generation, the project's findings have now been published as a series of over 30 articles in a ground-breaking, multi-publisher collaboration, between BioMed Central, Nature and Genome Research.

Genome Biology, one of BioMed Central's flagship journals has published six articles from this project. A further article is published in BMC Genetics. These articles address important questions relating to regulatory elements, specifically how they are defined and how they correlate with gene expression. In particular, The GENCODE pseudogene resource one of the Genome Biology papers, describes genes that have suffered a lethal number of mutations. but whose 'fossil' traces are still apparent in the genome. The article shows that some of these pseudogenes may still be functional, in some cases having been partially resurrected from gene death.

Professor Mark Gerstein, the lead author of two of these articles, explained, "Among the oddities turned up by the ENCODE project are pseudogenes - stretches of fossil DNA, evolutionary relics of the biological past. Moreover, the project's data has shown that a number of pseudogenes may be active, not as protein-coding genes but as ncRNAs."

BioMed Central has been publishing peer reviewed, open access journals for 12 years and now has a portfolio of 270 journals in science and medicine. All of the 30 ENCODE articles will be open access - meaning these articles will be freely accessible online for all and will be available as a collection on the micro-site ENCODE explorer, which is hosted by Nature and also through an iPad App.

Professor Ewan Birney, the head of the ENCODE consortium stated that, "The ENCODE consortium was very excited to work with Genome Biology, BMC Genetics and BioMed Central to make the details of our work widely available. By coordinating these publications and creating clear paths to the original data, and by ensuring that it is all open access, we have made these large-scale ENCODE resources truly transparent and accessible for the scientific community."


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Dr Hilary Glover
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Notes to Editors

1. 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 and Mark B Gerstein Genome Biology 2012, 13:R48 doi:10.1186/gb 2012 13 9 r48

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 and Ewan Birney
Genome Biology 2012, 13:R49 doi:10.1186/gb‐2012‐13‐9‐r49

Functional analysis of transcription factor binding sites in human promoters
Troy W Whitfield, Jie Wang, Patrick J Collins, E Christopher Partridge, Nathan D Trinklein, Shelley F Aldred, Richard M Myers and Zhiping Weng
Genome Biology 2012, 13:R50 doi:10.1186/gb2012139r50

The GENCODE pseudogene resource
Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald, Lukas Habegger, Xinmeng J 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 doi:10.1186/gb2012139r51

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 Gyoung Tak, Zhenqing Ye, Malaina Gaddis, Heather Witt, Peggy J Farnham and Victor X Jin
Genome Biology 2012, 13:R52 doi:10.1186/gb2012139r52

Modeling gene expression using chromatin features in various cellular contexts
Xianjun Dong, Melissa Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Mark Gerstein, Roderic Guigó Serra, Ewan Birney and Zhiping Weng
Genome Biology 2012, 13:R53 doi:10.1186/gb2012139r53

Simultaneous SNP identification and assessment of allele specific bias from ChIP seq data
Yunyun Ni, Amelia W Hall, Anna Battenhouse and Vishwanath R Iyer
BMC Genetics 2012, 13:46 doi:10.1186/147121561346

Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.

Article citations and URLs available on request on the day of publication.

2. Genome Biology publishes research articles, new methods and software tools, in addition to reviews and opinions, from the full spectrum of biology, including molecular, cellular, organism or population biology studied from a genomic perspective, as well as sequence analysis, bioinformatics, proteomics, comparative biology and evolution. @GenomeBiology BMC Genetics is an open access, peer-reviewed journal that considers articles on all aspects of inheritance and variation in individuals and among populations. @BMC_Series

3. BioMed Central ( is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.

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