See our guest blog post on "Adaptation and Convergence in Regulatory Systems" at phylogenomics blog "This Tree of Life"
We invite you to attend our second (now SMBE Satellite) meeting/workshop on Mechanisms of Protein Evolution (Thermodynamics, Phylogenetics, and Structure) in Denver, February 7-9 2013 (Thurs 12:00 - Saturday 5:00 pm). Early registration and abstract submission deadline is December 15, 2012. Organizers: David Pollock, David Liberles, and James McInerney ("MPEII: this time it's personal").
We are starting up a new NIH grant on comparative genomics of vertebrates, and need replacements on our existing NIH grant on protein evolutionary dynamics. We are looking for multiple talented evolutionary biologists with a mixture of training in mathematical, computational, and molecular laboratory techniques. We are especially interested in candidates at the postdoctoral level. Contact David Pollock.
Postdocs Todd Castoe and Jason de Koning are both starting new assistant professor positions this Fall, and Jill Castoe has a new genomics core job. Todd and Jill are going to the University of Texas Arlington, and Jason is going to the University of Calgary. Vijetha Vemulapalli got her PhD and has started a new job at Berg Biosystems in Boston, and Ken Daigaro Yokoyama is doing a second postdoc in Illinois.
New lab members are Corey Cox and Jaime Merlano, Robert Ruggiero; students rotating this year are Jonathan Shortt (HMGGP), Aaron Wacholder, Stephen Pollard, and Dior Hall (HS). Veronica Searles (MSTP) and Bryan Melonis (HS) completed rotations this summer.
A new version of PLEX (0.95) is up, along with a new extended user manual.
I uploaded Saturate code, but use at your own risk. Please let me know if you get it to work.
We've aborted the laboratory blog. May try again when we move to a better web service.
SP transcription factor paralogs and DNA binding sites coevolve and adaptively converge in mammals and birds, Yokoyama and Pollock, Genome Biology and Evolution (in press; abstract). 2012
Phylogenetics, Likelihood, Evolution and Complexity (PLEX), de Koning et al, Bioinformatics (Advance Access). 2012
Amino acid coevolution induces an evolutionary Stokes shift, Pollock et al, PNAS. 2012
Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake, Castoe et al, PLoS One. 2012
Modeling Protein Evolution, Pollock and Goldstein, in Dokholyan, Computational Modeling of Biological Systems. 2012
Germline TRAV5D-4 T Cell Receptor Sequence Targets a Primary Insulin Peptide of NOD Mice, Nakayama et al, Diabetes 2012
Repetitive elements may comprise over two-thirds of the human genome, de Koning et al, PLoS Genet. 2011
Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions, Pollock, et al. PLoS One. 2011
The genome of the green anole lizard and a comparative analysis with birds and mammals, Alföldi, et al. Nature. 2011
Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes, Castoe, et al, Genome Biol. 2011
Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing, Castoe, et al, Genome Biol Evol. 2011
The Genomics course for Spring 2012 is done
Updating programs: PLEX, PCLOUDS, CodeMLAncestral, TFCoEvolve, SULDEX
"I would describe...how passionately, how incandescently, how incestuously...art and science meet in an insect" Nabokov (now vindicated)
The Genome 10K project is moving forward, a project to assemble a collection of DNA sequences representing the genomes of 10,000 vertebrate species. Working towards integrating our work on snake and mammalian genomics.
web site 
NLM Training Grant postdoctoral fellowships are available yearly on a competitive basis. See Computational Bioscience Program for more information.
