Mailund on the Internet

The morning session today started with two invited talks:

Bailin Hao: Independent verification of 16S rRNA based prokaryotic phylogeny by composition vector approach

The first one was a bit strange.  The presentation consisted of reading the slides aloud and the topic was never really completely clear to me.

They had, apparently, constructed a phylogeny for prokaryotes using a new method called CVTree — essentially neighbour-joining but with a distance measure based on K-mer statistics and thus parameter and alignment free — and compared that with the tree of life 16S RNA phylogeny and the taxonomy.

The talk was mainly bashing the taxonomy for having classes that are not monophylitic, but there wasn’t much on actual tree comparisons of the tree hierarchies/phylogenies.

Pavel Pevzner: Genome rearrangements: from biological problems to combinatorial algorithms

The second talk, on the other hand, was absolutely great.

Pevzner first warned us that he would give a more “computer science” talk than most of the talks so far, and would prove three theorems (one of which would be wrong).

He took three controversial biological problems

1. Do rodents and primates group, with carnivores as an outgroup, or do primates and carnivores group with rodents as an outgroup
2. Does the mamalian genome contain rearrangement hotspots or are rearrangements randomly distributed
3. Was there a whole genome duplication in yeast

and he reduced these questions to combinatorial problems that can be tested

1. Ancestral genome reconstruction
2. Breakpoint re-use analysis
3. The genome halving problem

The first problem is essentially a matter of constructing a parsimony tree based on rearrangement events, and he showed that that favoured the ((carnivore,primate),rodent) topology.

The second problem was a question on putting a lower bound on the number of rearrangement events between human and mouse and showing that this lower bound was greater than the observed number of breakpoints, which means that some breakpoints must have been reused.

Time ran out before he could talk about the third problem, so I don’t know what the results are there.

I would have preferred if he had been given more time, ’cause it was really interesting.

The incorrect theorem, by the way, was in a proof for the number of steps needed in transposition sorting, which complicated the results on the second problem.

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14-19 = -5

Crossing the street here in Beijing is an unsettling experience.  There doesn’t seem to be any correlation with the traffic light and the traffic. Both cars and pedestrians seem to just cross whenever they get the chance.

We’ve solved the problem by hiding in a group of chinese whenever we need to cross, and just follow the crowed.  When they walk, we walk, and when they run, we run.

Yesterday, when crossing the street, Søren commented: “I’m not completely comfortable with being in a country where human life is not a scarce resource”.

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14-18=-4

“Buyer beware”

Yesterday, after dinner — that for my case was a wok dish consisting of half chili and half meat and definitely too spicy — we went looking for a bar to get a beer.  We didn’t find one.  There isn’t even one at the hotel.

So we found a convenience store and asked — in broken Mandarin — for beer.  We got a bottle that looked a bit like the beer bottles we’ve seen.  It turned out not to be beer but on closer inspection to be 56% vol terribly tasting alcohol.

It did kill the taste of chili, but the replacement was not really any better.

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14-17 = -3

We are now half-way through day one of APBC.

So far it has been fun.

Association mapping tutorial

The day started with tutorials. Four tutorials in two tracks.  For the first tutorial, we attended Matthew Stephens’ tutorial on Bayesian and imputation methods for association mapping.

It was a very nice tutorial.  He started out with presenting the general setup in a genome wide association study — so nothing new here for us — and then talked about Bayesian approaches and the benefit of using those.

Mainly motivated by the problem that a p-value does not tell you anything about the probability of there being no association — which is what you are probably interested in knowing — and does not capture uncertainty in the data caused by sample size of minor allele frequency.  Well, in some way it does, since the power depends on sample size and MAF, but under the null model all p-values are equally likely, so the p-value in itself does not tell you about the probability of the null model being true.

In the Bayesian setup, you can calculate the probability of the null being true, the false discovery rate, fdr = P(null-model | data), from the posterior odds, PO = P(alternative-model | data) / P(null-model | data), since fdr = 1/(1+PO).

The posterior odds, of course, depends on the Bayes’ factor and the prior odds, but makes it easy to explicitly quantify the belief that the posterior or alternative model is the true model.

He spent a lot of time on ways of testing single markers for association in this framework, so very little time was left for multi-locus methods — which he skipped — and imputation methods — covered very quickly.

While I would have preferred to hear more about the last two topics, I still very much enjoyed the tutorial.

Off for coffee

In the break between tutorials Besenbacher and I talked imputation with Matthew, so we missed the beginning of the next tutorial session and decided to skip the next tutorial and instead the three of us went for coffee in a nearby Starbucks and continue our association mapping discussion.

Afternoon

The afternoon program started with a keynote talk by David Lipman on the molecular evolution of Influenza.

I’m personally very fascinated by influenza, especially because of the global pandemics it has caused, so this was a very interesting talk for me.

The last part of the afternoon is the first session with paper presentations, but the jet lag is kicking in and that — combined with the high temperature in the lecture hall — makes it hard to stay awake.

We’ve decided to skip this session and rest a bit, so we are ready for the reception in the evening.

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13-15 = -2

We’ve just arrived at the hotel now, about 24 hours after we left Aarhus.  The trip here went pretty smooth — even though the first flight was number 666 — but finding the hotel is a different story.

Naturally, neither of us had thought to print out the address of the hotel.  I am proud to say that I did print out the hotel reservation, containing the hotel name but not the address.  I have a map of the area around the hotel on my laptop, so I figured it wouldn’t be much of a problem to get the address if the name was not enough.

The name was not enough, and it was much of a problem to get the address.

See, my laptop battery decided that it was time to move on to the after life, so I can now only use the machine when it is wired to the power grid. That is not much help in an airport.

Anyway, we got into a taxi armed only with the name of the hotel.  The driver didn’t speak a word of English and couldn’t read latin letters, so needless to say there were a few communication problems, but not something that could stop us.

After all, how hard can it be to find a hotel in Beijing, if you only know the name?

What saved us was that I could look up the address on the Net using my phone.  Showing the address to the driver didn’t work, ’cause he couldn’t read the letters, but Besenbacher did his best to pronounce it and we made it here at last.

We’ve decided to take a short break now. Have a shower.  Then head out to get lunch and register for the conference.

I’ve managed to boot the laptop, now that I’ve connected it to the power plug — well, sort of, ’cause I forgot my adapter, but I’ve kludged it and I have power.  So here I am blogging.

The hotel room is similar to all hotel rooms all over the world, but two things strikes me as out of the ordinary.  First, there is an ashtray in the room.  Does this mean that smoking is allowed?  There is a sign that asks me not to smoke in bed, but what about in the room?  I haven’t seen a hotel room where smoking was allowed ever before.

The second thing is even cooler.  There are complementary condoms left in the room.

You’ve gotta love this.

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12-13 = -1