genomics
evolgen | July 12, 2006The genome encodes all of the RNAs and contains sequences responsible for the transcription of those RNAs and the proper folding and wrapping of the cromosomes. The RNAs encoded by the genome are collectively known as the transcriptome. The transcripts that are translated into proteins represent the proteome or the ORFeome (depending on the context).
I'm fascinated by the growing list of "-omes" out there. Genomics and proteomics appear to be the most established "-omics" disciplines, but a new paper in PNAS has introduced me to an "-ome" with which I was previously not familiar: the…
sporte | July 10, 2006How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes?
In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more background, see the post on qualitative measures of DNA quality.
Later on, when the genome sequencing turned into a race, and the pace of DNA sequencing began to increase, some genome centers realized that it was too expensive and time consuming to have Ph.D. scientists, or even technicians, review all…
sporte | July 5, 2006What do genetic testing and genealogy have in common?
The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one.
Another answer is that both tests can involve DNA sequence data.
And that leads us to another question. If the sequence of my mitochondrial DNA is only two bases different from Cleopatra's, am I really a distant relative? And how do I really even know that my mitochondrial DNA is only two bases different in the first place? What does having a DNA sequence really mean?
Students sequencing mitochondrial DNA
I wrote earlier…
evolgen | June 15, 2006Andy Clark has written a review of comparative evolutionary genomics for Trends in Ecology and Evolution. His review deals with identifying functional regions of the genome and inference of both positively and negatively selected sequences.
Clark is one of the leaders in the field of evolutionary genetics (and now genomics), actively participating in the analysis of both the human and Drosophila genomes. He also brings a solid understanding of biology, as well as an appreciation of statistical rigor. You can sense his excitement about the union of molecular biology and evolution in the…
evolgen | June 14, 2006Another review of Michael Ashburner's book Won for All is available on PLoS Biology. PZ Myers also wrote a review of the book, and the two pieces complement each other nicely.
evolgen | June 3, 2006John Hawks' really needs to permit comments on his blog. I mean, without comments, is it really a blog? I bring this up because this post really belongs in the (non-existent) comments of this post from Hawks. Hawks discusses this article on human gut flora fauna microbes.
According to the article, we are superorganisms that depend on our gut microbes to assist us in digesting food, much like these guys. We get a lot of our intestinal buddies when we pass through the birth canal, and we pick up others throughout life (see here for more on intestinal microbes). The worms that are attached to…
evolgen | May 31, 2006...or how a learned to stop worrying and love evo-devo.
As my mind gets a chance to process some of the stuff I heard and talked about at the meeting I just returned from, I'll post some thoughts that will help me organize my ideas (hopefully better organized than that last sentence). This is the first (of perhaps few, perhaps many) of those (possibly incoherent) ramblings -- interrupted by as few paranthetical remarks as possible.
In this post, I'll try to tie together:
A talk by Sean Carrol on the evolution of wing pigmentation.
A talk by Peter Andolfatto on the evolution of Drosophila non-…
evolgen | May 16, 2006Michael Ashburner has written a book. No, not that book. This one's a bit smaller, less expensive, and about the sequencing of the Drosophila melanogaster genome. You can read a review of the book here and buy it from here. It's not The Genome War; Matt Ridley describes it as Ashburner's "immediate reactions, mostly committed to paper at the time -- an idiosyncratic, gonzo romp through the crazy days of 1998-99."
In his review, Ridley describes Ashburner's dislikes, joys, and vices:
Being a scientist, Ashburner hates hotels (especially Marriotts), Microsoft, bad coffee and suits -- the…
evolgen | May 16, 2006Don't expect much from me in terms of substantial posting. I'm getting prepared for the SMBE meeting, and devoting most of my time to finishing up some data analysis and putting together my talk. If you want to read about some evolutionary genetics research, here are some links:
Check out this report on genome duplications in angiosperms from Claude dePamphilis's lab (Indian Cowboy has more here).
I'm pretty interested in copy number variation, so I definitely need to read this article comparing copy number polymorphisms in humans and chimps (news release here). From the snippets I've…
evolgen | May 12, 2006I've been busy this past week (and I'll be busy in the next couple of weeks to come), so I don't have much time to post to evolgen. For this reason this week's Phylogeny Friday is a recycled post from the old site. Check out the comments on the original entry for some remarks from one of the authors of the paper I discuss. I'll try to get some original content up here, but blogging may be slow until the end of the month.
Now that we have entered the post-genomics era, with the genomes of most model organisms completely sequenced (as well as the human genome), it is up to genome centers,…
evolgen | May 2, 2006I'm trying to emerge from hibernation, and I'll hopefully have some good blogging material up in the next few days. In lieu of my own ideas, I'm going to link to what other people have written. Read them, because I ain't saying much right now. The list can be found below the fold.
Neil Saunders points us to this article from the BBC on a new function for "junk DNA". I hope Neil is right: "one day the term 'junk DNA' will fall into disuse."
John Hawks has a good discussion of a recent paper on inferring population size using mtDNA. Apparently cytoplasmic DNA is under selection, and that,…
evolgen | April 26, 2006If you know anything about bioinformatics, you know that programmers love to come up with clever names for their applications. NCBI's BLAST (Basic Local Alignment Search Tool) programs are some of the most used tools, but behind every successful program is a stupid acronym or cute name. Do the people who name these programs realize the confusion this may cause?
Many of these bioinformaticians provide list serves for updates on their software and public discussions. TIGR (The Institute for Genomic Research, another acronym) developed a genome annotation tool and named it Manatee. A…
evolgen | April 5, 2006I attended a seminar in the Math Department today. The topic was assembling genomes. Even though this is a computationally rigorous field, the speaker glazed over all the mathematically interesting details. Maybe he thought the mathematicians in the audience would be bored by the math. Because he was sponsored by the Math Department, however, he felt obligated to give a poor summary of genetics for all of the non-biologists in the audience. The mathematicians then proceeded to ask the speaker some interesting questions about biology, which was ironic considering there were at least 20…
evolgen | March 30, 2006
The Coalition Against Biopiracy has announced their winners for the 2006 Captain Hook Awards for Biopiracy, and they're a hoot. We already knew that Darwin was a pirate, but now we learn that so are Craig Venter and Google. What are their crimes? Venter is accused of being the "Greediest Biopirate", and Google is accused of being the "Biggest Threat to Genetic Privacy". I have some more details on these charges below the fold, in addition to showing why the Coalition Against Biopiracy needs to walk the plank.
Venter is accused of:
"undertaking, with flagrant disregard for national…
evolgen | March 27, 2006My little screed on junk DNA elicited some good feedback, including a comment from Dan Graur. In a somewhat ill-thought out rant, I implied that anyone who uses the term 'junk DNA' should be ostracized from the scientific community (or something along those lines). I restated my opinion in a far more diplomatic manner in the discussion that followed in the comments: junk DNA is an appropriate term for DNA that serves no function (non-transcribed, non-regulatory, and non-structural), but we should refrain from using that term for all non-coding DNA. I elaborate my opinion and reference a…
evolgen | March 24, 2006The title is, obviously, an overstatement, exaggeration, and blatant misrepresentation. But it gets your attention, don't it? Anyway, Hawks has been questioning whether genomics is really any different from genetics. In this post, he says something that I've been thinking for a while:
"Actually, the thing that bothers me about genomics is not the renaming -- I'm totally fine with coming up with clever new names, even if they carry little information content . . . What bothers me is that so many people are being trained in genomics without learning any genetics!"
I agree. Entirely. I know…
evolgen | March 19, 2006The human Y, that is. The Science Creative Quarterly has a very thorough (ie, make sure you have some time to spare) review of the mammalian Y chromosome (focusing on the human Y). The article covers the origin and evolution of the mammalian Y and what the degeneration of the Y means for the future of human male fertility and sex determination. I should point out that the mammalian Y chromosome is an anomaly in origin and sex determination. In fact, every single sex determination system and sex chromosome system that I know of differs from all of the others in some manner. It looks like…
evolgen | March 17, 2006PLoS Computational Biology has an article in the pipeline on detecting natural selection in humans in chimps. The authors looked for genes evolving at unequal rates between the two species and genes with signals of positive selection. I have not read the entire article, but it looks like a good attempt to distinguish actual positive selection from changes in selective constraint.
evolgen | March 14, 2006PLoS Biology (the people that brought you the recent paper from Jonathan Pritchard on detecting selection in the human genome and George Zhang's paper on selection on human pseudogenes) has published an editorial on detecting natural selection. It is a good follow up to my series on detecting natural selection using molecular data.
evolgen | March 10, 2006I commented a couple of days ago on a news item about a journal article on the evolution of gene expression in primates that had yet to be published. Well, the article has been published, and I've read it (Nature has also published a news and views piece on the study by Rasmus Nielsen). I have a few comments on why this research is unique, what the researchers found, and the implications of this research below the fold.
WHY THIS STUDY IS UNIQUE: This is the first large scale study to examine gene expression in primates using species specific probes. Gene expression can be measured by…