genomics
awild | January 15, 2009This weekend, Arizona State University is hosting a slate of myrmecologists to brainstorm on ant genomes. I'd link to the meeting information, but apparently the gathering is so informal that they've not given the event a web page. In any case, the topic is this: in the age of (relatively) cheap genomes, which ants should we sequence? And, what should we do with the assembled data?
I originally planned to attend, but life intervenes and I'm frozen to the tundra of central Illinois. Instead, I will register here a few suggestions about which species should considered, in addition to…
sporte | January 2, 2009The New York Times had a great article a couple of days ago on the need for personalized medicine to become more than a catchy phrase.
As we're learning more about the interaction between genes and drug metabolism, we're also learning that large numbers of people are either taking the wrong drug or taking drugs that won't work.
tags: personal genomics,pharmacogenomics
Researchers have known for some time that genetic variants determine how well drugs work. Some versions of a gene cause a drug to be metabolized faster, some slower, and when combined, at an intermediate rate. In the…
mikethemadbiologist | December 22, 2008I'm loath to call Scienceblogling Josh of Thoughts from Kansas out since he was one of my earliest linkers and readers, back when I was but a wee Mad Biologist; I probably wouldn't have the readership that I have, in part, were it not for Josh. But Josh wrote something about Eric Lander that really pissed me off:
Lander's work is very important, but the development of large-scale genome sequencing is largely a technical challenge, which scientists often distinguish from the challenges in testing our broad conceptual understanding of the laws of nature. While "test tube jockeys" often…
evolgen | December 18, 2008A couple of years ago, there was talk in the bioblogosphere about getting the general public interested in bioinformatics and molecular evolution:
Amateur bioinformatics?
Lowering the Ivory Tower with Molecular Evolution
Molecular Evolution for the Masses
The idea was inspired by the findings of armchair astronomers -- people who have no professional training, but make contributions to astronomy via their stargazing hobbies. With so much data available in publicly accessible databases, there's no reason we can't motivate armchair biologists to start mining for interesting results.
But how do…
sb admin | December 17, 2008Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Why microarray study conclusions are so often wrong
Three reasons to distrust microarray results
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a proxy…
evolgen | December 17, 2008Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Why microarray study conclusions are so often wrong
Three reasons to distrust microarray results
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a proxy…
mikethemadbiologist | November 28, 2008One of things I've done in my job is write letters of recommendation for various genome sequencing projects, particularly antibiotic resistance related projects, so it's always good to see that those letters might result in published work. So onto to an incredibly resistant Escherichia coli strain.
E. coli SMS-3-5 is a strain of environmental E. coli that is incredibly resistant to a broad range of antibiotics, to the point where the antibiotic does not go into solution. Of 33 antibiotics tested, only imipenem, meropenem, amikacin, gentamicin, and nitrofurantoin were effective against this…
sporte | November 19, 2008Genome Web's Daily Scan noted an interesting blog post today from John D. Halamka, one of the people to get his genome sequenced through the personal genome project.
I was interested to see his post since Genome Web wrote that he was discussing data standards and we have been writing quite a bit, ourselves, about data measurements for Next Gen sequencing (e.g. Next Gen-Omics) on our company blog, FinchTalk.
But Halamka didn't write about standards for data.
He wrote about standards for metadata, like family histories, and the things that are done with data after it's been collected.
All of…
edyong | November 19, 2008About 18,545 years ago, give or take a few decades, a woolly mammoth died. Succumbing to causes unknown, the creature was buried in Siberian snow. Many other mammoths must have met similar fates but this one, which we now know as M4, is special. Almost 20 millennia later, its beautifully preserved remains were unearthed by scientists who have revealed both its body and its genetic code. For the first time, the genome of an extinct species has been sequenced almost to completion.
Webb Miller from Pennsylvania State University together with a large team of American and Russian scientists has…
evolgen | November 19, 2008Back in the day, you could sequence a genome and get a Nature paper out of it. Pretty soon, the sexiness of genome sequencing wore off, and it took a bit more to get into a vanity journal. You had to sequence something cute and cuddly, something extinct, or a lot of genomes at once. Any other genome sequencing projects were relegated to lower tier journals.
Now, it appears that even sequencing the genome of charismatic megafauna only gets you a press release. As TR Gregory points out, the sequencing of the Kangaroo genome was announced in such a manner (Science by press release). But check…
sb admin | November 16, 2008
Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of…
sporte | November 14, 2008Masha Gessen was faced with a terrifying choice: cut off her breasts, and possibly save herself from cancer, or use them to feed her child.
It was late at night when I walked back to my empty dorm room at the conference. Shivering, I stood on the narrow bed, quickly shut the windows, tore the blankets off the other bed, and wrapped myself up, trying to get warm. Too cold to sleep, I picked up my copy of Masha Gessen's "Blood Matters: From Inherited Illness to Designer Babies, How the World and I Found Ourselves in the Future of the Gene," expecting boredom to lull me into unconsiousness…
edyong | November 3, 2008Mammals like ourselves pass our genes 'vertically' from parent to child. But bacteria aren't quite so limited; they have mastered the art of gene-swapping and regularly transfer DNA 'horizontally' from one cell to another. This "horizontal gene transfer" has been largely viewed as a trademark of single-celled organisms, with few examples among animals and plants. That is, until now.
A group of American researchers have discovered a group of genetic sequences that have clearly jumped around the genomes of several mammals, one reptile and one amphibian. It's the most dramatic example yet that…
sporte | October 21, 2008Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it.
And now that a genome is no longer an entirely personal bit of information, you may be in for a surprise meeting someday, with the end result.
That's right.
Male adoptees are getting their DNA tested and getting information about their possible surnames.
According to the BBC news:
At least 30 men registered with US consumer genetic testing firm Family Tree DNA have found their…
sporte | October 13, 2008Last week, while attending the ISB "DNA of Innovation" symposium in honor of Lee Hood's 70th birthday, I decided to try live-blogging for the first time. Unbeknownst to others in the audience, except my husband, I quietly typed away, collecting notes and uploading impressions.
But battery power has its limits, even when I have more notes to share. And despite all the fascinating speakers, I have notes enough to describe just one more.
The personal genome days have only just begun, but George Church is already looking into the future. In a true "Lee Hood style tour de force" Church talked…
evolgen | October 5, 2008The human genome (like all mammalian genomes) is loaded with sequences that don't perform any known function. And many of these sequences are junk. And it's not just mammals -- many animal genomes are loaded with junk, as are those of other eukaryotes. That's not to say that some of the sequences of unknown function do, in fact, have a function that we have yet to identify. However, much of the junk comes from the remnants of transposable element (parasitic sequences that hop around the genome).
That's not the impression you get from the introduction to a review of transposable elements (TEs…
mikethemadbiologist | October 2, 2008This will be something of a technical post, but I've decided to pick the hivemind's brain. In some projects I'm involved with, we're generating lists of SNPs for a bunch of bacterial strains using Illumina.
For a given strain, anywhere from ten to forty percent of the SNPs are indels (actually 'SNP' is a bit of a misnomer because we can detect small multi-nucleotide insertions and deletions). Here's the question: is there any way to use maximum likelihood methods with indels? I could just use parsimony methods, and treat the indels as characters, but I don't want to lose information about…
sporte | September 26, 2008Let's play anomaly!
Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome.
During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things.
You've got a week to give it a try. Let's see what you find! The method is…
sporte | September 25, 2008Lots of bloggers in the DNA network have been busy these past few days writing about Google's co-founder Sergey Brin, his blog, his wife's company (23andme), and his mutation in the LRRK2 gene.
I was a little surprised to see that while other bloggers (here, here, here, and here) have been arguing about whether or not the mutation really increases the risk to the degree (20-80%) mentioned by Brin, no one has really looked into the structure and biochemistry of the LRRK2 protein to see if there's a biochemical explanation for Parkinson's risk. I guess that task is up to me.
Let's begin at…
sporte | September 25, 2008Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank
This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.
In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III.…