This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks.
Dmitry Alexeev's insight:
Fine measure of identity) - protein interaction partners Tell me who your friends and i will tell you who you are)
"As the industrial age is drawing to a close, I think that we're witnessing the dawn of the era of biological design. DNA, as digitized information, is accumulating in computer databases. Thanks to genetic engineering, and now the field of synthetic biology, we can manipulate DNA to an unprecedented extent, just as we can edit software in a computer. We can also transmit it as an electromagnetic wave at or near the speed of light and, via a "biological teleporter", use it to recreate proteins, viruses and living cells at another location, changing forever how we view life."
"At this point in time we are limited to making protein molecules, viruses, phages and single microbial cells, but the field will move to more complex living systems. I am confident that we will be able to convert digitised information into living cells that will become complex multicellular organisms or functioning tissues."
"We could send sequence information to a digital-biological converter on Mars in as little as 4.3 minutes, that's at the closest approach of the red planet, to provide colonists with personalised drugs. Or, if Nasa's Mars Curiosity rover were equipped with a DNA-sequencing device, it could transmit the digital code of a Martian microbe back to Earth, where we could recreate the organism in the laboratory. We can rebuild the Martians in a P4 spacesuit lab -- that is, a maximum-containment lab -- instead of risking them crash-landing on the surface. I am assuming that Martian life is, like life on Earth, based on DNA. I think that because we know that Earth and Mars have continually exchanged material, in the order of 100kg a year, making it likely that Earth microbes have travelled to and populated Martian oceans long ago and that Martian microbes have survived to thrive on Earth. Simple calculations indicate that there is as much biology and biomass in the subsurface of our Earth as in the entire visible world on the planet's surface. The same could be true for Mars."
"If the life-digitalizing technology works, then we will have a new means of exploring the universe and the Earth-sized exoplanets and super Earths. To get a sequencer to them soon is out of the question with present-day rocket technology -- the planets orbiting the red dwarf Gliese 581 are "only" about 22 light-years away -- but it would take only 22 years to get the beamed data back. And that if advanced DNA-based life does exist in that system, perhaps it has already been broadcasting sequence information."
"Creating life at the speed of light is part of a new industrial revolution. Manufacturing will shift from centralised factories to a distributed, domestic manufacturing future, thanks to the rise of 3D printer technology. Since my own genome was sequenced, my software has been broadcast into space in the form of electromagnetic waves, carrying my genetic information far beyond Earth. Whether there is any creature out there capable of making sense of the instructions in my genome, well, that's another question."
Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities.
Dmitry Alexeev's insight:
getting ready to our first soil metagenome article
When it comes to determining whether lung nodules are malignant or benign, a patient typically faces surgery and a biopsy. It's an invasive and costly response, and, in 80 percent of cases, unnecessary.
We will be able to distinguish normal from diseased individuals.In most cases, we’ll be able to diagnose the disease very early.We will be able to follow the progression of disease.We will be able to follow the response to the therapy and how effective it is.We can take the disease such as lung cancer and stratify it into its different subgroups, which will be
One of the world’s most advanced data mining projects applies this same kind of analysis to cancer. Ilya Shmulevich, a lead genomicist who directs a Genome Data Analysis Center at the National Institutes of Health’s The Cancer Genome Atlas, says the project was born out of a shared frustration among cancer researchers at being forced, by a dearth of data, to study cancer one defective gene at a time, even while suspecting that the disease is actually the result of many genomic malfunctions, all happening at once.