The Hyphal Tip: Fungal Genomes and Comparative Genomics

Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing ... including a quick entry about what was interesting at the conference. I heard many good talks and only a few bad ones - maybe I guessed properly in darting between the multiple sessions. The meeting itsself was much better than past ones I had attended. The combination of Special Interest Groups meeting (BOSC, AFP, and Microbial Comparative Genomics being the ones I spent my time in). I got to give my talks and tutorial during the first few days and was able to just try and soak up the rest of the meeting (when my brain wasn't melting from the heat). Particularly good was Carole Goble's presentation on 7-deadly sins of bioinformatics software development. Some general evolutionary talks that I found really interesting (some of these are probably biased since I count many of the presenters as friends):

• Mike Eisen's keynote on evolution of regulatory sequences in Drosophila and other flies. Was a wild ride with a couple of different points he has made in the past, but was great to see it all come together.
• Alan Moses presented his work on predicting CDK targets through similar methodology that he pioneered in Eisen lab on cis-regulatory binding site clustering.
• Alex Hartemink gave two incredibly lucid presentations in that I really understood what he was trying to accomplish and how they did it. I wasn't lost in the algorithm complexities but still understood the approach they were taking. One on Neuronal Information Flow using songbird brain profiling data and a second talk on their work in the epigenetics session on predicting imprinted genes.
• Pilpel Yitzhak presented a summary of published work on selection on translational efficiency and found some very interesting patterns in codon biases in aerobic and anaerobic fungi.
• Ilan Wapinski talked about his approach to building orthologous groups of genes that seems to be quite robust among the ascomycete fungi he used as benchmarked against the YGOB. I'm excited to work with him to apply it to larger sample of fungi as well as other particular clades of fungi.
• Ines Hellmann from Rasmus Nielsen's group talked about some very cool work to look at population genetic analyses based on whole genome tiling data.

I'll write a quick post on the BoF session on open source and data sharing as well. Todd and I took some pictures as well.

Tags: gene regulation, ismb, mushroom, news, phylogeny, systematics