The ENCODE
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The ENCODE
The ENCyclopedia Of DNA Elements
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ENCODE's 'junk DNA' findings renew debate about creation, evolution | Deseret News

ENCODE's 'junk DNA' findings renew debate about creation, evolution | Deseret News | The ENCODE | Scoop.it

New research findings on DNA have not only heightened interest in and enthusiasm for human genome research, but also fanned the flames of the debate between proponents of creationism or intelligent design and believers in Darwinism or evolution.

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ENCODE Goes to Court | The Daily Scan | GenomeWeb

The Electronic Frontier Foundation is asking a court considering the legality of DNA collection upon arrest to weigh the findings of the ENCODE project in its decision. In a letter to the US Court of Appeals for the Ninth Circuit, the EFF says that the court's panel opinion in Haskell v. Harris "relied heavily on the assumption that a DNA profile does nothing more than identify a person" and that the 13 CODIS markers commonly used in forensic cases comprise "junk DNA" that is "not linked to any genetic of physical trait."

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"Junk" DNA Holds Clues to Common Diseases: Scientific American

"Junk" DNA Holds Clues to Common Diseases: Scientific American | The ENCODE | Scoop.it
With the new annotation of the human genome, researchers are finding that most of the code between genes is controlling crucial functions for life and health...
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Researchers: 'Junk' DNA plays major role in disease

Researchers: 'Junk' DNA plays major role in disease | The ENCODE | Scoop.it
Regulatory genes turn on and off to control genes that produce bone and other tissues. They also play a major role in disease.
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Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome

Nature ENCODE: Explore the wealth of information about the project's key findings and numerous integrative analyses.
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Nature News Blog: Fighting about ENCODE and junk : Nature News Blog

Nature News Blog: Fighting about ENCODE and junk : Nature News Blog | The ENCODE | Scoop.it
On Wednesday, a handful of journals including this one released more than 30 papers describing results from the second phase of ENCODE: a consortium-driven project tasked with building the “ENCyclopedia Of DNA Elements,” a manual of sorts defining...
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New DNA Encyclopedia Attempts to Map Function of Entire Human Genome | Wired Science | Wired.com

New DNA Encyclopedia Attempts to Map Function of Entire Human Genome | Wired Science | Wired.com | The ENCODE | Scoop.it
A torrent of new data charts the human genome in unprecedented detail, a landmark accomplishment compared by some scientists to the genome’s sequencing in 1999.
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The ENCODE project: lessons for scientific publication « Genomes Unzipped

The ENCODE project: lessons for scientific publication « Genomes Unzipped | The ENCODE | Scoop.it


The ENCODE Project has this week released the results of its massive foray into exploring the function of the non-protein-coding regions of the human genome. This is a tremendous scientific achievement, and is receiving plenty of well-deserved press coverage; for particularly thorough summaries see Ed Yong’s excellent post at Discover and Brendan Maher at Nature.

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Now - The Rest of the Genome - NYTimes.com

Now - The Rest of the Genome - NYTimes.com | The ENCODE | Scoop.it
Only 1 percent of the genome is made up of classic genes. Scientists are exploring the other 99 percent and uncovering new secrets and new questions.
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Nature News Blog: Fighting about ENCODE and junk : Nature News Blog

Nature News Blog: Fighting about ENCODE and junk : Nature News Blog | The ENCODE | Scoop.it
On Wednesday, a handful of journals including this one released more than 30 papers describing results from the second phase of ENCODE: a consortium-driven project tasked with building the “ENCyclopedia Of DNA Elements,” a manual of sorts defining...
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An integrated encyclopedia of DNA elements in the hum... [Nature. 2012] - PubMed - NCBI

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

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Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome

Nature ENCODE: Explore the wealth of information about the project's key findings and numerous integrative analyses.
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Mysterious DNA ≠ "Junk DNA"

Mysterious DNA ≠ "Junk DNA" | The ENCODE | Scoop.it
The Junk DNA story is mostly junk, but the press has done a lousy job of telling the truth, says bioblogger Brian Krueger:...
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Detailed map of genome function

Detailed map of genome function | The ENCODE | Scoop.it
Scientists have published the most detailed analysis to date of the human genome, which could lead to better treatments for many diseases.
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Scientists Unveil 'Google Maps' For Human Genome : NPR

For decades, scientists thought that most of our genetic code was essentially useless filler between our genes.
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Thematic Minireview Series on Results from the ENCODE Project: Integrative Global Analyses of Regulatory Regions in the Human Genome

The Encyclopedia of DNA Elements (ENCODE) Project (http://www.genome.gov/10005107) is an international collaboration of research groups funded by the National Human Genome Research Institute, with the goal of delineating all functional elements encoded in the human genome (1). This project began in 2003 with a targeted analysis of a selected 1% of the human genome. The results from the pilot project were published in 2007 (2), and a second phase of funding was then provided to scale the project to the entire human genome. Genome-scale projects in ENCODE involve the identification and quantification of RNA species in whole cells and subcellular compartments, mapping of noncoding and protein-coding genes by manual review and experimental methods, delineation of chromatin and DNA accessibility, mapping of histone modifications and transcription factor-binding sites by ChIP, and measurement of DNA methylation. More recently, ENCODE has adopted additional approaches that have not yet resulted in extensive data sets, including the examination of long-range chromatin interactions, analysis of RNA-binding proteins, and validation of transcriptional enhancers and silencers. To date, >2000 data sets have been deposited for public use by the ENCODE Project at the University of California Santa Cruz (UCSC) Genome Browser (3); to encourage public use of the data sets, a “user's guide” to the ENCODE data sets has been published (4). As the second phase of the ENCODE Project nears completion, the ENCODE Consortium has prepared a large integrative manuscript that includes analyses of experiments from 147 cell types and provides a summary of their functional annotation of the human genome (5). Additionally, other more narrowly focused studies on subsets of ENCODE data have been or will soon be published; for a list of ENCODE publications, see the ENCODE tab at the UCSC Genome Bioinformatics site.

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The making of ENCODE: Lessons for big-data projects : Nature : Nature Publishing Group

The making of ENCODE: Lessons for big-data projects : Nature : Nature Publishing Group | The ENCODE | Scoop.it
To be successful, consortia need clear management, codes of conduct and participants who are committed to working for the common good, says ENCODE lead analysis coordinator Ewan Birney.
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The Genome's Dark Matter - Technology Review

The Genome's Dark Matter - Technology Review | The ENCODE | Scoop.it

Evidence is growing that your DNA sequence does not determine your entire genetic fate. Joseph Nadeau is trying to find out what accounts for the rest. (The Genome's Dark Matter - Technology Review: http://bit.ly/hr9PpA via @addthis)


Via Portable Genomics
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ENCODE Virtual Machine and Cloud Resource

The ENCODE consortium have published an integrated analysis of ENCODE genome wide data link to Nature website/paper. Every analysis presented in the paper depends upon specific software processing that has a series of source data files, that are then transformed into output files for that analysis from which the final figure(s) and statements in the paper are made. As part of the supplementary material for this paper, we have established a virtual machine instance of the software, using the code bundles from ftp.ebi.ac.uk/pub/databases/ensembl/encode/supplementary/, where each analysis program has been tested and run. Where possible the VM enables complete reproduction of the analysis as it was performed to generate the figures, tables or other information. However in some cases the analysis involved highly parallelised processing within a specialised multiprocessor environment. In these cases, a partial example has been implemented leaving it to the reader to decide whether and how to scale to a full analysis. We hope that this structure provides the opportunity to run the same analyses in the wild.

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Most of what you read was wrong: how press releases rewrote scientific history

Most of what you read was wrong: how press releases rewrote scientific history | The ENCODE | Scoop.it
Repeating myths may make good stories, but it breeds confusion. See the ENCODE news.
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ENCODE (2012) vs. Comings (1972). « Genomicron

The coining of the term “junk DNA” is credited to Susumu Ohno, who used it in two conference presentations that were later published as Ohno (1972) and Ohno (1973). However, Ohno only used the term once per paper — in the titles. The first detailed discussion of “junk DNA” was by Comings (1972), and in fact his review appeared in print slightly before Ohno’s papers (Comings cites Ohno’s work as “in press”). So, if we’re going to frame the findings of ENCODE or any other genome analysis in terms of a comparison what the “junk DNA” view argued, we should probably refer to Comings (1972) even more so than to Ohno (1972). In that regard, I thought it would be interesting to compare some of the major claims made by the ENCODE authors in 2012 with Coming’s review of ideas on similar topics from 40 years earlier.

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ENCODE: the rough guide to the human genome | Not Exactly Rocket Science | Discover Magazine

ENCODE: the rough guide to the human genome | Not Exactly Rocket Science | Discover Magazine | The ENCODE | Scoop.it

Back in 2001, the Human Genome Project gave us a nigh-complete readout of our DNA. Somehow, those As, Gs, Cs, and Ts contained the full instructions for making one of us, but they were hardly a simple blueprint or recipe book. The genome was there, but we had little idea about how it was used, controlled or organised, much less how it led to a living, breathing human.

 

That gap has just got a little smaller. A massive international project called ENCODE – the Encyclopedia Of DNA Elements – has moved us from “Here’s the genome” towards “Here’s what the genome does”. Over the last 10 years, an international team of 442 scientists have assailed 147 different types of cells with 24 types of experiments. Their goal: catalogue every letter (nucleotide) within the genome that does something. The results are published today in 30 papers across three different journals, and more.

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ENCODE and modENCODE Projects

An overview of the goals of the ENCODE project. Includes links to other ENCODE project sites and materials.
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