Thursday, February 09, 2017

NIH and UCSF ENCODE researchers are on Reddit right now!

Check out Science AMA Series: We’re Drs. Michael Keefer and James Kobie, infectious .... (Thanks to Paul Nelson for alerting me to the discussion.)

Here's part of the introduction ...
Yesterday NIH announced its latest round of ENCODE funding, which includes support for five new collaborative centers focused on using cutting edge techniques to characterize the candidate functional elements in healthy and diseased human cells. For example, when and where does an element function, and what exactly does it do.

UCSF is host to two of these five new centers, where researchers are using CRISPR gene editing, embryonic stem cells, and other new tools that let us rapidly screen hundreds of thousands of genome sequences in many different cell types at a time to learn which sequences are biologically relevant — and in what contexts they matter.

Today’s AMA brings together the leaders of NIH’s ENCODE project and the leaders of UCSF’s partner research centers.

Your hosts today are:

Nadav Ahituv, UCSF professor in the department of bioengineering and therapeutic sciences. Interested in gene regulation and how its alteration leads to morphological differences between organisms and human disease. Loves science and juggling.
Elise Feingold: Lead Program Director, Functional Genomics Program, NHGRI. I’ve been part of the ENCODE Project Management team since its start in 2003. I came up with the project’s name, ENCODE!
Dan Gilchrist, Program Director, Computational Genomics and Data Science, NHGRI. I joined the ENCODE Project Management team in 2014. Interests include mechanisms of gene regulation, using informatics to address biological questions, surf fishing.
Mike Pazin, Program Director, Functional Genomics Program, NHGRI. I’ve been part of the ENCODE Project Management team since 2011. My background is in chromatin structure and gene regulation. I love science, learning about how things work, and playing music.
Yin Shen: Assistant Professor in Neurology and Institute for Human Genetics, UCSF. I am interested in how genetics and epigenetics contribute to human health and diseases, especial for the human brain and complex neurological diseases. If I am not doing science, I like experimenting in the kitchen.

5 comments :

  1. There are two major NIH initiatives that are sisters, ENCODE and RoadmapEpigenomics.

    If ENCODE keeps getting more money, then the combined expenditures of ENCODE and RoadmapEpigenomics is probably over 600 million and counting.

    It's hard to discern where the differences between ENCODE and RoadmapEpigenomics since they carry out many similar experiments.

    Roadmap is supposedly larger, but they aren't in the limelight.

    I asked an NIH insider where I could get more numbers on expenditures, and she said she didn't know! The data has to be somewhere.

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  2. There is a good chance that NIH project funding will be under a little more scrutiny, at least for a while. We have to start setting some priorities.

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  3. Well! It is a good idea that they will use CRISPR gene editing to rapidly alter junk DNA sequences! This way they can quickly discover why an onion needs 5X more ncDNA than I do.

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  4. Well! It is a good idea that they will use CRISPR gene editing to rapidly alter junk DNA sequences! This way they can quickly discover why an onion needs 5X more ncDNA than I do.

    Do you really believe it would matter to those who blindly worship the so called "junk DNA" that is now at %90 or so?

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  5. I think this might be a link to an official NIH ENCODE planners in 2015 to learn about the ENCODE project and future directions of the ENCODE project.

    https://www.genome.gov/27560819/from-genome-function-to-biomedical-insight--encode-and-beyond/

    A sample slide of ENCODE work from that workshop is here:

    https://www.genome.gov/multimedia/slides/encode2015/16_greenleaf.pdf

    You can contrast what you find in the official NIH planning workshop with the claim by Dan Graur that the ENCODE consortium is composed of "ignoramuses", "crooks" who are "generating piles of excrement" in the promotion of the "evolution-free Gospel of ENCODE".

    Judge for yourself if the ENCODE vanguard are as bad as Dan Graur makes them out to be.

    There is a presentation by Ewan Birney whom Dan Graur called "the scientific equivalent of Saddam Hussein" for his pioneering work with ENCODE. You can hear Ewan speaking for himself.

    Ewan's video:
    https://www.youtube.com/watch?v=-x3o4ErBNDA

    Ewan's slide:
    https://www.genome.gov/Multimedia/Slides/ENCODE015/03_Birney.pdf

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