New manuscripts from the lab

A burst of new work from the lab is available over on our publications page. Summaries and backstories for three of these manuscripts, below the fold:

  • Steve Johnson and Elon Portugaly have submitted a paper on their collaboration to accelerate HMMER2 and implement the first prototype of jackhmmer. Don’t be confused by the weird timeline here, caused by us releasing code early before we’ve published it. This is HMMER2 work, not HMMER3 work; and it happens to be the prototyping that led to the HMMER3 project. The HMMER3 speed heuristics and the HMMER3 jackhmmer implementation are different and independent, but depended on Steve and Elon’s pioneering work. Steve did a remarkable job of finishing this paper despite having moved on to his postdoc with Skip Virgin.
  • Lee Henry has submitted a paper describing a new method for fast immunopurification of genetically tagged nuclei. We want to be able to study gene regulation in specific neural cell types in vivo, using various genome-wide assays such as ChIP-seq, so we need to devise ways of isolating chromatin from specific cells. There are ways to do this with FACS (flow sorting) or by epitope-tagging of chromatin associated proteins such as histones, but we think it would be advantageous to have an alternative that’s faster and easier than flow-sorting, and with less risk of perturbing chromatin than directly epitope-tagging the stuff you’re trying to assay. Using his impressive knowledge of the old-school literature, Lee has realized that nuclei are remarkably robust and easy to isolate from whole tissues, and he’s figured out how to genetically tag the nuclear membrane with both epitopes and fluorescent markers, allowing him to purify nuclear populations by a quick magnetic bead pulldown protocol.
  • Finally, a belated link to a February PLoS Comp Bio paper from Fred Davis in collaboration with Andrej Sali at UCSF, describing a comprehensive database of ligand-binding sites on proteins that also overlap with known protein-protein interaction surfaces, suggesting places where a ligand might be expected to disrupt or modulate protein-protein interaction. The work is hosted here at Janelia in Fred’s PIBASE database. I’m not a coauthor on the paper – an example of the Janelian way of doing business, where postdocs have as much autonomy as they want, to chase ideas and collaborations of their own.

One thought on “New manuscripts from the lab

  1. Congratulation for the interesting work on the HMMERHEAD method. The only thing I am a bit surprised about is that a recently published work on accelerating HMMER2 (“Significant speedup of database searches with HMMs by search space reduction with PSSM family models”; Bioinformatics 2009) that obtained significantly higher speedups, is neither discussed nor cited in the preprint.


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