I’m packing now, getting ready for the Biology of Genomes conference in CSH. I’ve never attended this conference before, but I am quite excited to be going this year.
I probably wont have much time for blogging while there, so it might be quiet here for the next week.
I’ll go and finish my packing now. I need to check in at two but the bus connection to the airport is pretty crappy on a Sunday so I need to leave relatively early.
We came back from Beijing yesterday evening — our luggage this afternoon — and I am still pretty tired after the trip. I had to leave the office early afternoon, when my brain just shut down. So don’t expect any quality posts from me for a day or two.
In the mean time, I’ll just refer you to this list of predictions for 2009.
Most I agree with, with the possible exception of this one:
We will not see a retail complete genome sequence offered for less than $1000. I’d be happy to be proven wrong here, mind you, but I just can’t see prices tumbling this far over the next twelve months – even with the huge competition and rapid technological advances in the DNA sequencing sector. Of course, it depends what you mean by “complete” – it will no doubt be possible to offer a fragmentary, low-coverage genome at this price by the end of the year, but such a product would be almost worse than no information at all. Alternatively, cut-price genome sequences may be offered by companies at a loss, to attract attention and create a more sustainable long-term market.
It sounds very reasonable, but I’ve been pretty pessimistic in my predictions about genotyping and sequencing technology in the past, so I will choose to be optimistic for 2009 and predict that we will see a $1000 genome.
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19-31=-12
Today started with two invited talks, both on transcript factors
Martin Vingron: Transcriptional regulation: computation methods, statistcs and coregulation
Michael Eisen: Understanding and exploiting the evolution of Drosphila regulation sequences
with the latter being more biological oriented — but in my opinion more interesting — than the former.
In the morning paper session, we followed the sequence alignment and evolution track with four interesting talks. This track was more “computer science-ish” than those we followed yesterday and I am definitely going to read the papers when I have the time.
In the afternoon there were two paper sessions. In the first we followed the association study and genomic variation track. We really had to, ’cause our paper was in this track, but we would have chosen that anyway.
The first paper was on population structure, then Besenbacher presented our paper, and then there were two presentations on searching for gene-gene interaction (epistasis) mapping.
The second session in the afternoon we skipped. The topics didn’t look that interesting, and we could use a break.
Now we are getting ready for the conference dinner.
Over lunch we talked with one of the other danes here, and he told us where he’d found a bar, so we might go there for a beer after the dinner, if we are not too tired by then. We still have not completely adjusted to the time zone and we get up pretty early in the morning.
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15-23 = -8
We skipped the first half of the afternoon session. None of the two tracks seemed particularly interesting to us, so Søren took the time to prepare slides for his presentation tomorrow, and I spent the time reading some of the papers from the morning session.
In the second half of the session there was a track on association mapping and genomic variation that we went to.
Unfortunately, it was held in the main conference hall that they, for some reason, keep insainly hot, so if you are still running on GMT+1 time (and wake up at 5am local time) it is almost guaranteed to put you to sleep.
We managed to hear the first two presentations, but then we left. Too bad, I would really have liked to hear the other two as well, but I just cannot keep awake in there.
The two presentations we did manage to hear were
Copy-number-variation and copy-number-alteration region detection by cumulative plots W Li, A Lee and PK Gregersen
on a new type of plots that should make it easier to identify copy-number-variation from SNP genotyped data from a single diploid individual, and
Identifying disease associations via genome-wide association studies W Huang, P Wang, Z Liu and L Zhang
on looking for genetic commonalities between diseases by clustering regions of SNPs with (marginally) significant association with the diseases.
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14-21=-7
For the morning paper presentation session, I attended the sequence assembly track.
The papers here all concerned the new algorithmical problems you need to tackle to handle next generation sequencing technologies, with vastly more data and much smaller reads.
Parallel short sequence assembly of transcriptomes BG Jackson, PS Schnable and S Aluru
The first presentation was about a distributed graph algorithm for de novo assembly.
Graph algorithms are a nice approach to sequence assembly, but they are potentially very time and memory expensive. The method here distributes both the memory usage and the computations on multiple CPUs, thus alleviating this problem.
Finding optimal threshold for correction error reads in DNA assembling FYL Cin, HCM Leung, W-L Li and S-M Y
The second presentation was on error correction.
With NGS you get a very high number of reads, but a few percentage of the nucleotides in the reads are called incorrectly. This is corrected for by requiring that each K-mer (for a given K) should occur at least M times (where M is some threshold) before it is belived to be a correct read.
The problem addressed here was how to choose M given a data set. The approach was to model the sequences as generated by a stochastic process and the estimate the expected number of false positives and false negatives for each M and then picking the M that minimises the sum of FP and FN.
Crystallizing short-read assembly around seeds MS Hossain, N Azimi and S Skiena
The third presentation was on a new de novo assembly algorithm taylored to the paired end reads you get from the SOLiD platform.
The first half of the presentation, though, was an overview of various platforms, so I’ll need to read the paper before I have any idea about the specifics of the algorithm.
Short read DNA fragment anchoring algorithm W Wang, P Zhang and X Liu
The last presentation was not on de novo assembly but on reference genome assembly, and concerned finding anchors (sub-strings of a larger string that approximately matches a query string).
This time around I didn’t get any of the details. Perhaps because it was getting close to lunch and I was fading out…
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14-20=-6