WeitzGroup@GeorgiaTech

An article by members of the Weitz group titled "Unsupervised statistical clustering of environmental shotgun sequences" has been publised in BMC Bioinformatics. The article is available at http://www.biomedcentral.com/1471-2105/10/316. The full citation is as follows:

Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff and Joshua S Weitz. Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics 2009, 10:316. doi:10.1186/1471-2105-10-316

The paper describes a new method for binning metagenomic fragments, that is, classifying shotgun sequenced fragments of environmental DNA according to their origin, with a focus on low complexity communities. The unsupervised nature of this algorithm allows it to work on mixtures of DNA without regard to how many sequenced relatives of constituent bacteria are available, complementing existing algorithms for metagenomic binning that rely on supervised and semi-supervised approaches.

The Weitz group is dispersing to present results at a range of summer conferences. Here's who's going where:

Algebraic Topology in Applied Mathematics

• Yuriy Mileyko: Tutorial on computational aspects of algebraic topology

Botany and Mycology 2009

• Chuck Price: The allometry of leaf vascular networks

Ecological Society of America 2009

• Chuck Price: The allometry of leaf vascular networks
• Olga Symonova: Tradeoffs in belowground structure of rice root systems
• Joshua Weitz: Molecular basis of phage life history traits

q-Bio Conference on Cellular Information Processing

• Richard Joh: Nonlinear effect of copy number variation on gene expression.
• Gabriel Mitchell: Characterizing bacterial lysis by phage lytic enzymes using non-parametric data collapse

Society of Mathematical Biology 2009

• Yuriy Mileyko: Nonlinear effect of copy number variation on gene expression

Empirical studies of decomposition and its relationship to food web structure have revealed a seemingly incongruous set of results, which, when viewed together, we term the ``decomposition-facilitation paradox.'' To explain this paradox quantitatively, we develop a bacteria-grazer model of organic matter decomposition that incorporates protozoa-driven nutrient recycling and stoichiometry. Read more about it online here: Wang et al., FEMS Microbiology Ecology (in press).

Dangerous nutrients: Evolution of phytoplankton resource uptake subject to virus attack which was published in the J. Theor. Biol. suggests that phytoplankton should evolve towards co-limiation of resources as a winning evolutionary strategy even when such evolution exposes them to greater susceptibility to attack by phages. This result adds to the growing body of literature suggesting that co-limitation at equilibrium is a winning strategy.

Dynamics of Indirectly Transmitted Infectious Diseases with Immunological Threshold which will appear in the Bull. Math. Biol. presents and analyzes a novel family of models that incorporate immunological thresholds and explicit reservoir dynamics to describe the spread of diseases which have a strong indirect mode to transmission. We find that the spread of a disease depends on the global destabilization of an otherwise disease-free state, suggesting that it is not only the transmission dynamics that determines disease outcomes, but the magnitude of perturbations in pathogen density.