@EncodeDCC

The Data Coordinating Center for the Encyclopedia of DNA Elements. Free, accessible data at your fingertips.

 Stanford, CA
encodeproject.org
Joined December 2011
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  • Following482
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43Media
Excited to announce that "The EN-TEx resource of personal epigenomes & variant impact models" just came out: Cell.com/cell/fulltext/S0092…. The paper represents the culmination of many years of work by >100 authors & has lots of useful information about allele-specific activity.
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Does anybody know if chromatin segmentation (either ChromHMM or Segway) for NIH3T3 cells is available? I admit I’m not able to find it (mm10, possibly)
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ENCODE DCC retweeted
4DN DCIC@4dn_dcic2 May 2022
Read about the @4DNucleome data portal, now out in @NatureComms #FAIRdata nature.com/articles/s41467-0…

The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Nature Communications - This paper describes the ‘4DN Data Portal’ that hosts data generated by the 4D Nucleome network, including Hi-C and other chromatin conformation capture assays,...

nature.com
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Are you running the data or are you run over by petabytes of data? These ten simple rules will help you to tame large-scale datasets. Read more: ow.ly/BnnS50HUP3U @Chai_Arkarachai #bioinformatics #genomics #BigData

Ten simple rules for large-scale data processing

journals.plos.org
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ENCODE DCC retweeted
4DNucleome@4DNucleome8 Dec 2021
Supporting Talented Early Career Researchers in Genomics RFA-HG-22-001 grants.nih.gov/grants/guide/…
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ENCODE DCC retweeted
4DN DCIC@4dn_dcic8 Dec 2021
Looking forward to seeing everyone (virtually) and hearing about all the exciting new research at the @4DNucleome annual meeting today! DCIC demo session tomorrow (Thursday) at 11:53am PST!
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**RFA Announcement** Supporting Talented Early Career Researchers in Genomics RFA-HG-22-001 For more information: ow.ly/7kTc50H6bZq
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Model organism databases are in jeopardy | Development | The Company of Biologists journals.biologists.com/dev/…

Model organism databases are in jeopardy

Model organisms (MOs), including yeast, worm (C. elegans), fruit fly (Drosophila), zebrafish, frog (Xenopus), mouse and rat, contribute greatly to our understanding of human development and disease....

journals.biologists.com
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#TBT! ENCODE started in September 2003 and is now in its final stages in September of 2021! 18 years of science and innovation have taken place thanks to the ENCODE team and NHGRI #ENCODE #science #genomics #humangenome #NHGRI
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Interested in genome-wide profiles of chromatin accessibility? Perform quality control and signal processing to produce alignments and measures of enrichment with the ENCODE ATAC-seq Pipeline, released on the Seven Bridges Cancer Genomics Cloud platform. @ENCODE_NIH @EncodeDCC
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Interested in analyzing chromatin modifications and binding patterns of transcription factors and other proteins? Check out the ENCODE ChIP-Seq Pipeline 2 released on the Seven Bridges Cancer Genomics Cloud platform. @ENCODE_NIH @EncodeDCC
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Today we reached 130,000 #cellline entries in the #Cellosaurus. We tried to find a good image representing that number and found this picture of 130,000 spectators attending a mega concert of Madonna on August 29, 1987 at Parc de Sceaux near Paris
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I don’t think the long read community realizes how long PacBio cDNA reads can be with the right protocol & much higher quality thanks to CCS. The final @ENCODE_NIH long read dataset for human and mouse will be a treasure trove for the community!
This Post is from an account that no longer exists. Learn more
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GENCODE are excited to support international community efforts to produce reference annotation for human ORFs discovered by Ribo-seq. Preprint: bit.ly/2Ty4Mdo Website text: bit.ly/3iCFiX0
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Full details of how #LRAGSP Challenge 1 will be evaluated in thread below. See link for more info.
AnaConesa@anaconesa2 Jun 2021
#LRAGSP Twitter thread of the week is about the evaluation of Challenge 1. Challenge 1 is transcript reconstruction using long reads when a well-annotated genome is available. More information about #LRGASP can be found at gencodegenes.org/pages/LRGAS… 1/12 @GencodeGenes
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This is an infrastructure project. Join us gopetition.com/petitions/a-u… @anshulkundaje @ontowonka 16/16

A Universal Scientific Data Coordination Platform

Large genomics projects often have specific “Data Coordination Centers” which have demonstrated (at a prototype…

gopetition.com
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... full time data scientists and professionals, thousands - maybe millions of lines of code, and training. In particular, scientists will have to be re-trained to be more collaborative, more open, and more rigorous in detailing exactly how to reproduce their work. 15/x
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Preliminary findings and interesting data could be shared instantaneously with collaborators across the globe. This will never happen without top down organization. It would require equipment on the ground, computational clouds, ... 14/x
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This work needs to be extended throughout all of NIH funded research. Not just genomics experiments, not just “machine-learning ready” computable data files, but all experimental protocols need to be registered in a machine-readable format. 12/x
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We estimate that it would take 5-10% of the TOTAL NIH research budget to actually bring this to fruition across all federally funded labs in the biological arena. 11/x
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