Nature Publishing Group continues to deceive about #OpenAccess to genome papers

I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome

That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.

UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall

And more

UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles

August 30 NCBI Minute: NCBI Hackathons, a framework for rapid prototyping of pipelines for bioinformatics, biomedical informatics and genomics

NCBI regularly organizes hackathons throughout the United States, where participants work in teams to apply their data science experience with public datasets. In this NCBI Minute, you will hear highlights from recent hackathons, see examples of the software created in … Continue reading

Six things we learned from that massive new study of intelligence genes

0000-0002-8715-2896 Six things we learned from that massive new study of intelligence genes   Posted May 26, 2017 by Tabitha M. Powledge in Uncategorized post-info AddThis Sharing Buttons above Genes help shape intelligence, period. That’s

Genomics and the Power of Public Health

On a bad day in the lab, we sometimes joke that if we really wanted to help save lives, we’d forget about molecular biology and go help people quit smoking. Relatively simple public health efforts – clean water, washing your hands before moving from one sick patient to another, basic vaccines – generally save many more lives that the cures that come out of the high tech stuff we do in the lab. Cancer immunotherapy may turn out to be a major advance in cancer treatment, but we’d reduce cancer even more if we could get everyone to quit smoking, lose weight, and stay physically active.

Genomics, whose near-term medical benefits have been the subject of a lot of hype, may turn out to be a high-tech, scientifically complex effort that actually does to have a big impact on people’s lives. As I discuss in my Pacific Standard column this week, part of that will be the long-term medical benefits that grow out of a better understanding of biology. But a more dramatic – and more near-term – impact may be how genomics changes public health. As some sort of genome analysis becomes a routine part of normal medical care, genetics will be integrated with other public health screenings (like testing your cholesterol), which, as two recent studies show, could have a big impact on avoiding preventable consequences of common diseases. Once exome sequencing is cheap enough, there could be a possible benefit of combining genomic screenings using existing medical knowledge – we don’t need to wait for distant future discoveries.

The takeaway is that policy and the infrastructure of the healthcare system, and not science, may soon be the rate-limiting step for realizing the medical benefits of genomics in some cases. Physicians, insurers, hospitals, and the health care system in general is utterly unprepared to handle the kinds of genomic data that could, in the near future, improve routine medical care.

Filed under: This Mortal Coil Tagged: genomics, medicine

Matt Hahn @3rdreviewer talk at #UCDavis – pen and paper notes

Matt Hahn was at UC Davis giving a talk yesterday.
I did not have my laptop available so took notes with - gasp - a pen and paper.  I thought it was quite a nice talk so am posting my notes here.  More about Matt and his work can be found here:

New paper: SCOTTI Efficient reconstruction of transmission within outbreaks with the structured coalescent

New paper published today in PLoS Computational Biology: Understanding how infectious disease spreads and where it originates is essential for devising policies to prevent and limit outbreaks. Whole genome sequencing of pathogens has proved an extremely promising tool for identifying transmission, particularly when combined with classical epidemiological data. Several statistical and computational approaches are available for exploiting genomics for epidemiological investigation. These methods have seen applications to dozens of outbreak studies. However, they have a number of serious drawbacks.

In this new paper Nicola De Maio, Jessie Wu and I introduce SCOTTI, a method for quickly and accurately inferring who-infected- whom from genomic and epidemiological data. SCOTTI addresses very widespread, but generally neglected problems in joint epidemiological and genomic inference, notably the presence of non-sampled and undetected intermediate cases and within-host pathogen variation caused by microevolution. Using real examples and simulations, we show that these problems cause strong misleading effects on existing popular inference methods. SCOTTI is based on BASTA, our recent breakthrough method for phylogeographic inference, and offers new standards of accuracy, calibration, and computational efficiency. SCOTTI is distributed as an open source package within BEAST2.

Prize PhD Studentships available

I am offering two PhD projects as part of the annual Nuffield Department of Medicine Prize Studentship competition:
These are fully-funded, four-year awards open to outstanding students of any nationality. Applicants nominate three projects, in order of preference, from the available pool. For how to apply, click here. Only applications submitted through the online system will be considered, but interested applicants are welcome to contact me informally. The deadline for applications is noon, 6th January 2017.

In addition to my projects, the Modernising Medical Microbiology project has announced the following PhD projects as part of the competition:

    The Genetic Nightmare of Diabetes

    After 10 years of genomic studies, our understanding of the genetic architecture of diabetes is… still a mess. Or, if you prefer, a nightmare. That’s the message of the most extensive Type 2 Diabetes GWAS to date. Looking for rare genetic variants linked with diabetes, researchers performed whole-genome or exome sequencing on 15,000 people… and came up with nothing new.

    This is an important negative result, in that it advances our knowledge of the genetic architecture of diabetes – odds are that many common genetic variants, each with individual small effects, contribute to one’s total genetic risk for the disease. It also illustrates just how hard it will be to realize the goals of personalized medicine. So let’s avoid the hype when we talk about how genomics is going to revolutionize medicine.

    I explain the study and its implications in my piece this week at Pacific Standard.  Go read it to learn more about the challenges ahead that face personalized medicine.

    Filed under: This Mortal Coil Tagged: Genome-wide association study, genomics