Posts Tagged ‘quote’

NAR Breakthrough Article: denovo-db: a compendium of human de novo variants

April 3, 2017

.@denovodb: a compendium of [initially ~33K] human de novo variants w. phenotype, freely downloadable as a TSV table
https://academic.OUP.com/nar/article-lookup/doi/10.1093/nar/gkw865

QT:{{”
As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant.
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denovo-db.gs.washington.edu/denovo-db/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210614/

Network analytics in the age of big data | Science

April 2, 2017

#Network analytics in the age of #BigData
http://science.ScienceMag.org/content/353/6295/123.full Emphasizes analyzing connectivity of graph structures (eg motifs) v nodes

QT:{{”
To mine the wiring patterns of networked data and uncover the functional organization, it is not enough to consider only simple descriptors, such as the number of interactions that each entity (node) has with other entities (called node degree), because two networks can be identical in such simple descriptors, but have a very different connectivity structure (see the figure). Instead, Benson et al. use higher-order descriptors called graphlets (e.g., a triangle) that are based on small subnetworks obtained on a subset of nodes in the data that contain all interactions that appear in the data (3). They identify network regions rich in instances of a particular graphlet type, with few of the instances of the particular graphlet crossing the boundaries of the regions. If the graphlet type is specified in advance, the method can uncover the nodes interconnected by it, which enabled Benson et al. to group together 20 neurons in the nematode worm neuronal network that are known to control a particular type of movement. In this way, the method unifies the local wiring patterning with higher-order structural modularity imposed by it, uncovering higher-order functional regions in networked data. “}}

Here, there and everywhere | The Economist

April 2, 2017

Here, there & everywhere
http://www.Economist.com/technology-quarterly/2017-03-09/quantum-devices Overview of #quantum computing mentions using it to #encrypt transmission of genomic data

QT:{{”
Thanks to the development of ever more secure links, quantum cryptography has recently been deployed more widely. ID Quantique has installed quantum links between data centres of KPN, a Dutch telecoms firm; of Battelle, an American non-profit research firm; and of Hyposwiss and Notenstein, two Swiss private banks. It offers links between financial institutions in Geneva and a disaster-recovery centre 50km away. In 2015 researchers at Toshiba in Japan began sending quantum-encrypted genomic data from a research facility in Sendai to Tohoku University, 7km away.
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How the Bitcoin protocol actually works | DDI

April 2, 2017

How…#Bitcoin…works, by @michael_nielsen
http://www.michaelnielsen.org/ddi/how-the-bitcoin-protocol-actually-works Overview focusing on why in addition to how; highlights #privacy issues

QT:{{”
How anonymous is Bitcoin? Many people claim that Bitcoin can be used anonymously. This claim has led to the formation of marketplaces such as Silk Road (and various successors), which specialize in illegal goods. However, the claim that Bitcoin is anonymous is a myth. The block chain is public, meaning that it’s possible for anyone to see every Bitcoin transaction ever. Although Bitcoin addresses aren’t immediately associated to real-world identities, computer scientists have done a great deal of work figuring out how to de-anonymize “anonymous” social networks. The block chain is a marvellous target for these techniques. I will be extremely surprised if the great majority of Bitcoin users are not identified with relatively high confidence and ease in the near future. The confidence won’t be high enough to achieve convictions, but will be high enough to identify likely targets. Furthermore, identification will be retrospective, meaning that someone who bought drugs on Silk Road in 2011 will still be identifiable on the basis of the block chain in, say, 2020. These de-anonymization techniques are well known to computer scientists, and, one presumes, therefore to the NSA. I would not be at all surprised if the NSA and other agencies have already de-anonymized many users. It is, in fact, ironic that Bitcoin is often touted as anonymous. It’s not. Bitcoin is, instead, perhaps the most open and transparent financial instrument the world has ever seen.
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The Snowbot: how Edward Snowden gets around his exile

March 30, 2017

The Snowbot: how Edward @Snowden gets around his exile
http://www.theGuardian.com/us-news/shortcuts/2016/jun/27/snowbot-edward-snowden-telepresence-robot An iPad stuck to a lawnmower (w/o the blades)

QT:{{”
“Right. So it really is an iPad stuck to a lawnmower, then? A remote-controlled, battery-powered lawnmower without the blades, yes.” “}}

WikiLeaks Shows How the CIA Can Hack a Mac’s Hidden Code

March 25, 2017

WikiLeaks Shows How the CIA Can Hack a Mac
https://www.wired.com/2017/03/wikileaks-shows-cia-can-hack-macs-hidden-code/ Modifying the firmware of Thunderbolt adapters to make spyware implanters

QT:{{”
“The CIA’s documents describe a series of tools that agents can use to install “implants” on target machines, capable of silently monitoring everything that occurs within its operating system and transmitting it to a remote operator. One manual explains how to modify the firmware of a standard Apple Thunderbolt-to-ethernet adapter, turniing it into an spyware-planting tool the CIA calls “Sonic Screwdriver.” When plugged in, the altered adapter can trick a Mac into thinking it’s booting its operating from a spoofed network source that the adapter impersonates, allowing tweaks to its firmware even in the rare cases when the user has set a password for any changes to that deep-seated code.”
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Education in Computational Biology Today and Tomorrow

March 25, 2017

Education in #CompBio, by @bffo & @joannealisonfox
http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003391 Keeping up in a rapidly changing field. Will implement some @Yale

QT:{{”
“These initiatives help to extend computational biology beyond the domain of specialized laboratories. Researchers, at all levels, need to keep themselves up-to-date with the quickly changing world of computational biology, and trainees need programs where bioinformatics skills are embedded so they can have comprehensive training. New bioinformatics workflows can be adopted more widely if education efforts keep pace. As previously pointed out , starting early is also very important. There is still room for programs that capture the excitement and enthusiasm of secondary school students and convey the potential of computational biology to the public. We welcome additions to the PLOS Computational Biology “Bioinformatics: Starting Early” collection (www.ploscollections.org/cbstartingearly).

We would like to involve the community in this endeavor. With this editorial, we are calling out to educators and researchers who have experience in teaching, specifically, those keen to raise the expectations and the inquisitiveness of the next generation of biologists. The Education collection will continue to publish leading edge education materials in the form of tutorials that can be used in a “classroom” setting (whatever that may mean nowadays: stated more generically, “the places where people learn”). We will continue to encourage articles set in the context of addressing a particular biological question and, as mentioned above, we welcome new “primers” and “quick guides.” We will also be inviting tutorials from the various computational meetings. A new category of papers that is in the pipeline for the Education collection is the “Quick Tips” format, the first of which was just published . The “Quick Tips” articles address specific tools or databases that are in wide use in the community.
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See how old Amazon’s AI thinks you are

March 23, 2017

See how old $AMZN’s AI thinks you are
http://www.theVerge.com/2017/2/10/14582192/amazon-ai-rekognition-age-guess-software Free via image Rekognition platform, in the dev toolkit part of @AWScloud

QT:{{”
“Amazon’s latest artificial intelligence tool is a piece of image recognition software that can learn to guess a human’s age. The feature is powered by Amazon’s Rekognition platform, which is a developer toolkit that exists as part of the company’s AWS cloud computing service. So long as you’re willing to go through the process of signing up for a basic AWS account — that entails putting in credit card info but Amazon won’t charge you — you can try the age-guessing software for yourself.”
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Are You My Cousin?

March 20, 2017

Are You My Cousin?
http://www.NYTimes.com/2014/02/01/opinion/sunday/are-you-my-cousin.html Combination of noisy crowd-sourced #ancestry & @23andMe linkages may connect everyone in a tree

QT:{{”
“The farther you go back, the more quantum it gets. According to Geni, my 97th great-grandfather is King David from the Bible. So what are the chances that I’m actually a direct descendant of the Goliath slayer? Count me a highly doubting Thomas. But it’s still fun to dive into the research and try to verify it.

In addition to using crowd-sourced trees, I’m trying to build my family list with genetic testing. I recently sent my saliva off to 23andMe (the F.D.A. has suspended the health-related part of 23andMe, but the ancestry service remains open). The result? I found more than a thousand fellow spitters who share enough genetic material that 23andMe says we are probable cousins. One such distant cousin: my wife. This was a tad jarring. Not to mention that it set off an avalanche of bad inbreeding and hillbilly jokes from friends. But the truth is, my wife and I aren’t unusual.
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pseudogenes that might have saved us !

March 20, 2017

#Pseudogenes that might have saved us!
http://www.sciencedaily.com/releases/2012/06/120604155554.htm?fb_ref=.T829TjfxGmI.like&fb_source=home_oneline Interesting link to infectious disease for pseudo-siglecs 13 & 17

QT:{{”
“”In a small, restricted population, a single mutation can have a big effect, a rare allele can get to high frequency,” said senior author Ajit Varki, MD, professor of medicine and cellular and molecular medicine and co-director of the Center for Academic Research and Training in Anthropogeny at UC San Diego. “We’ve found two genes that are non-functional in humans, but not in related primates, which could have been targets for bacterial pathogens particularly lethal to newborns and infants. Killing the very young can have a major impact upon reproductive fitness. Species survival can then depend upon either resisting the pathogen or on eliminating the target proteins it uses to gain the upper hand.”

In this case, Varki, who is also director of the UC San Diego Glycobiology Research and Training Center, and colleagues in the United States, Japan and Italy, propose that the latter occurred. Specifically, they point to inactivation of two sialic acid-recognized signaling receptors (siglecs) that modulate immune responses and are part of a larger family of genes believed to have been very active in human evolution.

Working with Victor Nizet, MD, professor of pediatrics and pharmacy, Varki’s group had previously shown that some pathogens can exploit siglecs to alter the host immune responses in favor of the microbe. In the latest study, the scientists found that the gene for Siglec-13 was no longer part of the modern human genome, though it remains intact and functional in chimpanzees, our closest evolutionary cousins. The other siglec gene — for Siglec-17 — was still expressed in humans, but it had been slightly tweaked to make a short, inactive protein of no use to invasive pathogens.”
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