Category Archives: Genomics
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
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
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
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: http://www.indiana.edu/~hahnlab/.Yes @3rdreviewer has arrived at #UCDavis #holobiont #epigenetics #aquarius pic.twitter.com/yirR4rWdio— Jonathan Eisen (@phylogenomics) October 6, 2016
New paper: SCOTTI Efficient reconstruction of transmission within outbreaks with the structured coalescent
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.
- Real-time detection of multidrug resistant tuberculosis and transmission in England
Joint with David Wyllie, molecular microbiologist, this project is focused on developing statistical methods for recognizing transmission clusters, integrating genomics approaches with molecular typing schemes and developing future-proof taxonomy for strain identification.
- Tracking future infection threats using genomic data and electronic health records
Joint with David Clifton, biomedical engineer, this project aims to develop new machine learning and statistical methods to identify genomic markers of antibiotic resistance and susceptibility within various pathogens, to help track future infection threats.
In addition to my projects, the Modernising Medical Microbiology project has announced the following PhD projects as part of the competition:
- Antimicrobial resistance gene/vector transmission across human, animal and environmental reservoirs
Supervised by Nicole Stoesser, Nicola De Maio and Derrick Crook
- Healthcare big data and genomics for infectious disease threat detection
Supervised by David Clifton, David Eyre and Tim Peto
- Prediction of Mycobacterium tuberculosis drug resistance through genome sequencing clinical samples
Supervised by Tim Walker and Tim Peto
- Antibiotic resistance in Tuberculosis: Predicting de novo the effect of individual genetic mutations
Supervised by Phil Fowler and Sarah Walker