linkstream2 microblog

http://medicine.yale.edu/news/article.aspx?id=16666

http://medicine.yale.edu/news/article.aspx?id=16666

http://ymm.yale.edu/autumn2017/features/feature/317720/

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Center co-director Mark B. Gerstein, Ph.D., the Albert L. Williams Professor of Biomedical Informatics, explains that succeeding with what researchers term “Big Data” requires “real thought about standards, the uniform collection of data, the distribution of samples, and the presentation and packaging of results.” After three years of planning, Gerstein and co-director Hongyu Zhao, Ph.D., a geneticist and the Ira V. Hiscock Professor of Biostatistics, have assembled a kind of central clearinghouse for research and development of these issues, particularly cloud computing and privacy, as well as for education and bridge-building collaboration on university, national, and international levels. “Our mission is really about connecting and coordinating the people and resources already here, and becoming a way to recruit the scientists we want to attract in the future for the Big Data initiatives we want to participate in,” says Gerstein. “We expect the center to have a very broad impact.” “}}

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But it’s the very specificity of genomic data that threatens privacy. Although most genomic databases strip away any information linking a name to a genome, such information is very hard to keep anonymous. “I’m not convinced you can truly de-identify the data,” says Mark Gerstein, a Yale professor who studies large genetic databases and is a fierce privacy advocate. He is concerned about whether even the most cutting-edge protections can safeguard personal data. “I am not a believer that large-scale technical solutions or ‘super-encryption’ will solely work,” he says. “There also needs to be a process for credentialing the individuals who access this data.”
…
Threats to privacy could multiply once there is an active market for genetic data. Wood speculates that it could be valuable to life insurance companies, which could use it to raise your premiums; or it could become a tool for those who want to prove or disprove paternity. White nationalist groups, who have become preoccupied with genetic testing, might find a way to weaponize the ancestry data the tests can show. It would not be the first time genetic information was used against a race or races. “Genetics has a very troubled history, from Darwin on,” says Yale’s Mark Gerstein.
…
Yet Columbia’s Yaniv Erlich and others, including Church, fear differential privacy could compromise biomedical research, with smudged data making it harder to get clear results. Mark Gerstein at Yale believes that scientists would be better off testing hypotheses on small amounts of publicly available but pure data, even if it’s not representative of the overall population, rather than using larger quantities of imperfect data.
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Is Genetic Privacy a Myth?
http://protomag.com/articles/genetic-privacy-myth
Genetic tests and genome sequencing are generating terabytes of sensitive private data. How can they be kept safe?

The absent-minded prof in the news…!

http://www.nature.com/news/cybersecurity-for-the-travelling-scientist-1.22379

Cybersecurity for the travelling scientist

Virtual private networks, tracking apps and ‘burner’ laptops: how to protect sensitive data when you take your research on the road.

Brian Owens

02 August 2017

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Mark Gerstein has had his fair share of scares when it comes to losing track of his electronic devices — and, along with them, access to his private information and research data.

“I’m very security conscious, but also a bit of an absent-minded professor,” says Gerstein, a bioinformatician at Yale University in New Haven, Connecticut.

He recalls one trip to Boston, Massachusetts, when he left his phone in a taxi, and watched it get farther and farther away on the tracking app on his iPad while he ran after the car in vain. Luckily, Gerstein was able to contact the taxi company, and eventually watched his phone make the return journey to his pocket.

Gerstein’s story had a happy ending, but all too often, hardware lost on the road is lost for good.
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http://news.yale.edu/2015/09/30/research-news-catalogue-human-genetic-variation-revealed

Sequenced genomes reveal mutations that disable single genes and can point to new drugs.

Ewen Callaway

28 October 2014 Corrected:
29 October 2014

http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239

You should also read the Corrections to this article
http://www.nature.com/news/geneticists-tap-human-knockouts-1.16239#/correction1

QT:{{”

The poster child for human-knockout efforts is a new class of drugs that block a gene known as PCSK9 (see Nature 496, 152–155; 2013). The gene was discovered in French families with extremely high cholesterol levels in the early 2000s. But researchers soon found that people with rare mutations that inactivate one copy ofPCSK9 have low cholesterol and rarely develop heart disease. The first PCSK9-blocking drugs should hit pharmacies next year, with manufacturers jostling for a share of a market that could reach US$25 billion in five years.

“I think there are hundreds more stories like PCSK9 out there, maybe even thousands,” in which a drug can mimic an advantageous
loss-of-function mutation, says Eric Topol, director of the Scripps Translational Science Institute in La Jolla, California. Mark Gerstein, a bio­informatician at Yale University in New Haven, Connecticut, predicts that human knockouts will be especially useful for identifying drugs that treat diseases of ageing. “You could imagine there’s a gene that is beneficial to you as a 25-year-old, but the thing is not doing a good job for you when you’re 75.”

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http://chronicle.com/article/Still-Hunting-Medical/143221/

Paul Basken
The Chronicle of Higher Education

BioTechniques – The Myth of the Single Genome
http://www.biotechniques.com/news/The-Myth-of-the-Single-Genome/biotechniques-347272.html

The Myth of the Single #Genome: fetal Y chr left in women + smaller microchimerism in specific tissues
http://www.biotechniques.com/news/The-Myth-of-the-Single-Genome/biotechniques-347272.html MT @xberthet

A post in Science Careers discussed type of collaborative environment in the lab.

http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2013_09_13/science.opms.r1300136