Posts Tagged ‘scinews’

The future of DNA sequencing

November 14, 2017

The Future of DNA Seq. Apps v Tech. QT: “Platforms for…#sequencing have changed dramatically…Yet the trajectories of other technologies…Internet, digital
photography…suggest…real disrupters will be the resulting applications, not the new tech”

Killer applications –
Over the years, the platforms for DNA sequencing have changed dramatically (see ”). Yet the trajectories of other technologies for which there is a seemingly insatiable demand — smartphones, the Internet, digital photography — suggest that the real disrupters will be the resulting applications, not the new technologies.


Wikipedia shapes language in scientific papers

October 27, 2017

"Wikipedia is one of the world’s most popular websites, but scientists rarely cite it in their papers. Despite this, the online encyclopedia seems to be shaping the language that researchers use in papers, according to an experiment showing that words and phrases in recently published Wikipedia articles subsequently appeared more frequently in scientific papers"

“Thompson and co-author Douglas Hanley, an economist at the University of Pittsburgh in Pennsylvania, commissioned PhD students to write 43 chemistry articles on topics that weren’t yet on Wikipedia. In January 2015, they published a randomized set of half of the articles to the site. The other half, which served as control articles, weren’t uploaded.

Using text-mining techniques to measure the frequency of words, they found that the language in the scientific papers drifted over the study period as new terms were introduced into the field. This natural drift equated to roughly one new term for every 250 words, Thompson told Nature. On top of those natural changes in language over time, the authors found that, on average, another 1 in every 300 words in a scientific paper was influenced by language in the Wikipedia article.”


#Wikipedia shapes lang. in science Seeding it with new pages & watching them evolve (v ctrls) as a type of soc. expt

Cryo-electron microscopy wins chemistry Nobel : Nature News & Comment

October 5, 2017

Cryo-EM wins chem Nobel Key techdev work in ’80s on flash freezing + atomic res. imaging of xtal & unordered samples

Big names in statistics want to shake up much-maligned P value

August 8, 2017

Big names in #statistics want to shake up…#Pvalue Stronger significance cutoffs (.005?) but danger of FNs

“Lowering P-value thresholds may also exacerbate the “file-drawer problem”, in which studies with negative results are left unpublished, says Tom Johnstone, a cognitive neuroscientist at the University of Reading, UK. But Benjamin says all research should be published, regardless of P value.

Other scientific fields have already cracked down on P values — and in 2015, one psychology journal banned them. Particle physicists, who collect reams of data from atom-smashing experiments, have long demanded a P value below 0.0000003 (or 3 × 10−7) because of concerns that a lower threshold could lead to mistaken claims, notes Valen Johnson, a statistician at Texas A&M University in College Station and a co-lead author of the paper. More than a decade ago, geneticists took similar steps to establish a threshold of 5 × 10−8 for
genome-wide association studies, which look for differences between people with a disease and those without across hundreds of thousands of DNA-letter variants.”

The Genomics Landscape: A monthly update from the NHGRI Director – July 2017

July 9, 2017

.@Genome_Gov Extramural Grant Portfolio
https://www.Genome.Gov/27569006/july-6-2017-the-nhgri-extramural-grant-portfolio-using-different-approaches-to-fund-genomics-research Nice grid divides programs into PI-initiated/consortia & RFA-solicited v not

US cancer institute to overhaul tumour cell lines

July 9, 2017

“The NCI will continue to supply the NCI-60 cell lines to researchers, but will eventually refocus its drug screening on newer models. It is developing hundreds of ‘patient-derived xenografts’ (PDXs), which are created by implanting small chunks of human tumours into mice. There, the tumours grow in an environment that, although not human, better mimics their native environment”

Clues from the resilient

July 4, 2017

Clues from the resilient Potential 2nd site mutations that neutralize #Mendelian-disease mutations

“For 127 catastrophic Mendelian diseases (those caused by a single gene such as cystic fibrosis and ataxia-telangiectasia), there are presently 164 genes harboring 685 known recurrent variants that are highly penetrant and causal for deleterious traits, most typically manifesting in individuals before the age of 18 (). …For common diseases, the observed small effect sizes of individual gene variants limit diagnostic potential, and given that most variants identified have an unclear function, how to target the corresponding gene for therapeutic intervention is typically unclear. For rarer Mendelian disorders, although genetics directly implicate a specific gene in a disease, a majority of such cases relate to loss-of-function mutations. Designing small molecules to fix the corresponding broken protein has proven difficult….
The prominent role of second-site mutations and environmental factors that enable resistance to (or buffer against) disease traits has been well established in a multitude of model organisms from yeast to mice (–). Screening for second-site mutations in “resilient” individuals that prevent disease-causing alleles from manifesting their effects could identify targets to which drugs would be designed to disrupt their function, as opposed to targeting the disease-causing gene directly. Genetic studies examining seemingly healthy people have revealed, for example, rare mutations in chemokine (C-C motif) receptor type 5 (the co-receptor for human immunodeficiency virus) that block HIV infection (), and secondary mutations in fetal globin genes that modify the severity of sickle cell disease by buffering primary mutations in β-globin genes ()

Shedding light on the dark proteome

April 24, 2017

“The dark proteome could be an evolutionary playground for trying out new folds

Ultimately one would expect particularly useful variations to get fixed at the genetic level. But it needn’t be where that variation begins. What’s more, organisms needn’t be quite so dependent for their molecular repertoire on their evolutionary heritage. O’Donoghue thinks that all organisms probably have a significant fraction of proteins unique just to them.

‘The fact that the dark matter of the proteome has less evolutionary constraint than the other bits of proteome may suggest that it’s under less selection,’ says Gerstein. ‘This is perhaps because it’s more flexible structurally, but also in a sense more flexible in terms of accommodating various amino-acid changes compared to the structurally inflexible and fixed parts of the crystallised proteome.’ This adds momentum to the picture of genomics as a rather more fluid affair than is suggested by the old picture of identical proteins being
mass-produced from a fixed genetic template.

Gerstein feels that studying the dark proteome opens up a host of interesting questions. For example, although known bacteria have a smaller dark proteome than eukaryotes, there’s a huge ‘dark
microbiome’ of unculturable bacteria. Might that be more full of dark proteins – perhaps useful ones?

And what about us? ‘How does the human dark proteome compare to that of eukaryotes as a whole?’ Gerstein wonders. How well, really, do we know ourselves?”

Shedding light on the dark proteome

The quiet rise of the NIH’s hot new metric : Nature News & Comment

November 16, 2016

The quiet rise of the NIH’s hot new #metric [RCR] Rank a popular paper in boring field be highly? HT @Magda_Skipper

Researchers wrestle with a privacy problem

September 25, 2016

Researchers wrestle w. a #privacy problem Qt: “Public trust is…fragile – it’s difficult to build & easy to break”

“The lesson is to not underestimate public concerns,” she says. “Public trust is very fragile — it’s difficult to build and easy to break.””