I just got back from a fantastic ISMB 2012. The talks were very good this year, and it was fun to see many people I met last year in Vienna again.
I presented three documents at the conference:
- A talk about Topic Pages at the Bioinformatics Open Source Conference (BOSC) before the main ISMB. Why Scientists Should Contribute to Wikipedia
- A poster for BOSC about the same. Topic Pages: The Peer-reviewed Wikipedia Article
- A poster for ISMB about my research. The Evolution of Protein Folds
I went to talks at BOSC, 3DSIG, and ISMB. Here are a my favorites:
- Jonathan Eisen Science Wants to Be Open: If Only We Could Get Out of Its Way (BOSC)
Great talk about the history of PLoS and the barriers to Open Access. Eisen calls for hiring and tenure committees to actually read papers, rather than making snap judgements based on journal names.
- Titus Brown Doing Next-gen Sequencing Analysis in the Cloud (BOSC)
Titus manages to speed up, reduce memory, and improve accuracy of genome assembly by throwing away unneeded reads.
- Chris Sander Decoding genetic variation to compute 3D structures of proteins (3DSIG)
Sander talks about his new EVFold method for predicting structure from multiple alignments. It’s a very exciting method with the potential to really leverage nextgen sequencing for structure prediction.
- John-Marc Chandonian The next generation of SCOP and ASTRAL (3DSIG)
SCOP has now given up on fully manual classification and started doing automated classification of close homologues, called SCOP 1.75A. They’re also working on SCOP 2.0, which will change from a structure hierarchy to a DAG representing both evolution and structural similarity, add hyperfamilies, show evolutionary clades, and allow tagging with other info like Uniprot IDs.
- Ada Yonath What was first? The genetic code or its products (3DSIG)
Ada talked a bit about her Nobel Prize work on the ribosome. I was particularly interested to hear how symmetry is essential at the ribosomal catalytic site. However, the most thought-provoking bit of her talk was speculation about the RNA-only protoribosome, which she thinks was a small, symmetric RNA dimer.
- Sheng Wang Protein structure alignment beyond spatial proximity (3DSIG)
DeepAlign is a good-looking protein alignment algorithm that uses both sequence and structural similarity in its scoring term. It also includes orientation information, so it’s better at avoiding register errors in sheets and helices. Oh, and it’s as fast as TM-Align! Jianzhu Ma from the same lab gave good a talk at ISMB about using DeepAlign for protein threading, so it’s practically useful.
- Saliha Ece Acuner Ozbabacan Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes (ISMB)
Haiyuan Yu Understanding human disease through 3D protein interactome network (ISMB)
Yu Xia A three-dimensional map of protein networks within and between species (ISMB)
Several ISMB talks focused on using structural information about protein-protein interactions. Saliha Ece Acuner Ozbabacan introduced a pretty flexible method for modelling PPI structuctures based on structurally similar interfaces, although I wonder about the false positive rate. Haiyuan Yu showed that by localizing mutations to a particular protein interface we can much more accurately predict downstream effects and pathology, as opposed to just binning them by gene. Yu Xia compared viral-host interfaces with host-host interfaces and found significant overlap. Furthermore, the overlapping regions are rapidly evolving, suggesting a race between viruses creating inhibitors and hosts trying to avoid them. The increasing availability of protein comple structures and high-quality models seems to have stimulated some very interesting biology in the last few years.
- Karen Lasker Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach (ISMB)
Andrej Šali Integrative Structural Biology (ISMB)
Crystal structures are known for some subunits of the proteasome, but the whole complex seems to be too flexible to crystallize. So instead they took a low-resolution EM structure of the whole complex and combined it with high-resolution monomers, PPI information, and cross-linking data to get the complete structure. Karen talked about the proteasome in depth, while Andrej sold us on the integrative method as the next great thing for solving big biological structures. Phil has a planning grant relating to visualizing big hybrid structures, so we’re hoping to see more big complexes solved like this in the future.
- Carl Kingsford Uncovering Ancient Networks from Present-Day Interactions (ISMB)
Carl has an interesting method for creating plausible ancestral networks (eg the PPI network of LUCA/LUCE). Unfortunately it uses a pretty naive model of evolution, so the results can’t be taken too literally. Maybe this could be applied to structural similarity networks, given a smarter evolutionary model?
- Arun Konagurthu Minimum Message Length Inference of Secondary Structure from Protein Coordinate Data (ISMB)
The problem with secondary structure assignment is that no one can agree on exactly the same definition. Although it may be a little too complex for most biologists, Arun proposes an interesting definition based on the concept of compression, of all things. It’s a compelling mathematical definition, although I’ll have to see more examples to know if it’s really any good.
- Alex Bateman Assessing the contribution of scientists to Wikipedia for Pfam and Rfam annotation (ISMB)
Long before Topic Pages started, Alex started utilizing Wikipedia to crowd-source RNA and protein family annotation. He’s now compiled some fascinating data on how Rfam/Pfam articles grow, finding that they tend to be expanded gradually by wikipedians, punctuated by large, short increases when a scientist or annotator takes an interest. He also notes that professional curators are still essential for maintaining the quality and organization of the annotations, even if the brunt of the workload is distributed across the community.
- Michal Linial Viral-host coevolution: Playing ‘seek and hide’ (ISMB)
Viruses often steal genes from their hosts. Michal looks at such cases and finds a couple ways viruses modify the proteins. Because of the pressure viruses face for small genome sizes, they tend to shed unnecessary parts of the genes, such as domain linkers or even whole domains. This brings up some very interesting open questions about the function of those domains to the virus. Maybe they can compensate for domain loss by using symmetry and homomers? It would be interesting to look!
- Fantastic (I thought) talks by my colleagues and collaborators:
Andreas Prlić How to Use BioJava to Calculate One Billion Alignments at the RCSB PDB website (BOSC)
Andreas Prlić Internal Pseudo-symmetry in Proteins (ISMB)
Peter Rose Efficient Searching and Mining of the RCSB Protein Data Bank (ISMB)
Philip Bourne Hiring and Supervising (ISMB)
Lei Xie A structural systems biology approach to polypharmacological drug discovery (ISMB)
Andreas talked about our research on symmetry and protein alignments. He has some really intriguing examples of why protein symmetry is important in his slides. Peter highlighted changes to the PDB over the last year, and Phil drew from his “Ten simple rules” series for a professional development talk. It was really nice to see Lei again, and hear about his latest research with his new lab at Hunter college.
The conference was fun too. It was my first time in Long Beach, and I grew to like the downtown area. The colored lights that project everywhere from fountains to bus stops at night are a little kitsch, but the restaurants and nightlife are nice. The Monday-night reception at the Aquarium of the Pacific was phenomenal—I want to go back and spend some more time with the bat rays! They have a couple cool webcams set up in lieu of visiting.