Person:

Weitz, Joshua S.

Permanent Link

https://hdl.handle.net/1853/71830

Associated Organization(s)

Organizational Unit

School of Biological Sciences

Full item page

Publication Search Results

Now showing 1 - 9 of 9

Predictive biology: adaptability, robustness, and the fundamental laws of ...

(Georgia Institute of Technology, 2010-10-05) Weitz, Joshua S. ; Dushoff, Jonathan
Unsupervised statistical clustering of environmental shotgun sequences

(Georgia Institute of Technology, 2009-10-02) Kislyuk, Andrey ; Bhatnagar, Srijak ; Dushoff, Jonathan ; Weitz, Joshua S.

Background: The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed. Results: We derive an unsupervised, maximum-likelihood formalism for clustering short sequences by their taxonomic origin on the basis of their k-mer distributions. The formalism is implemented using a Markov Chain Monte Carlo approach in a k-mer feature space. We introduce a space transformation that reduces the dimensionality of the feature space and a genomic fragment divergence measure that strongly correlates with the method's performance. Pairwise analysis of over 1000 completely sequenced genomes reveals that the vast majority of genomes have sufficient genomic fragment divergence to be amenable for binning using the present formalism. Using a highperformance implementation, the binner is able to classify fragments as short as 400 nt with accuracy over 90% in simulations of low-complexity communities of 2 to 10 species, given sufficient genomic fragment divergence. The method is available as an open source package called LikelyBin. Conclusion: An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples. For medium and high complexity samples, we discuss the possibility of combining the current method with other methods as part of an iterative process to enhance the resolving power of sorting reads into taxonomic and/or functional bins.
Collective decision making in bacterial viruses

(Georgia Institute of Technology, 2008-09) Weitz, Joshua S. ; Mileyko, Yuriy ; Joh, Richard I. ; Voit, Eberhard O.

For many bacterial viruses, the choice of whether to kill host cells or enter a latent state depends on the multiplicity of coinfection. Here, we present a mathematical theory of how bacterial viruses can make collective decisions concerning the fate of infected cells. We base our theory on mechanistic models of gene regulatory dynamics. Unlike most previous work, we treat the copy number of viral genes as variable. Increasing the viral copy number increases the rate of transcription of viral mRNAs. When viral regulation of cell fate includes nonlinear feedback loops, very small changes in transcriptional rates can lead to dramatic changes in steady-state gene expression. Hence, we prove that deterministic decisions can be reached, e.g., lysis or latency, depending on the cellular multiplicity of infection within a broad class of gene regulatory models of viral decision-making. Comparisons of a parameterized version of the model with molecular studies of the decision structure in the temperate bacteriophage l are consistent with our conclusions. Because the model is general, it suggests that bacterial viruses can respond adaptively to changes in population dynamics, and that features of collective decision-making in viruses are evolvable life history traits.
The Evolution of Dispersal in Reserve Networks

(Georgia Institute of Technology, 2007-07) Baskett, Marissa L. ; Weitz, Joshua S. ; Levin, Simon A.

The fragmentation of an environment into developed and protected areas may influence selection pressure on dispersal by increasing the chance of moving from a favorable to an unfavorable habitat. We theoretically explore this possibility through two cases: (1) marine systems in which reduced predation and/or increased feeding drive the evolution of planktonic larval duration and (2) more generally, where stochasticity in reproductive yield drives the evolution of the proportion of offspring dispersing. Model results indicate that habitat fragmentation generally shifts selection pressure toward reduced dispersal, particularly when areas outside reserves are uninhabitable. However, shifts to increased dispersal may occur when temporal heterogeneity is the primary selective force and constant‐quota harvest occurs outside reserves. In addition, model results suggest the potential for changes in the genetic variability in dispersal after habitat fragmentation. The predicted evolutionary changes in dispersal will depend on factors such as the relative genetic and environmental contributions to dispersal‐related traits and the extent of anthropogenic impacts outside reserves. If the predicted evolutionary changes are biologically attainable, they may suggest altering current guidelines for the appropriate size and spacing of marine reserves necessary to achieve conservation and fisheries goals.
Evolution, Interactions, and Biological Networks

(Georgia Institute of Technology, 2007-01-16) Weitz, Joshua S. ; Benfey, Philip N. ; Wingreen, Ned S.

This essay is part of the Challenges Series: highlighting fundamental, unifying challenges in biology.
A Null Model of Morphospace Occupation

(Georgia Institute of Technology, 2005-07) Pie, Marcio R. ; Weitz, Joshua S.

Progress in understanding the relationship between lineage diversity, morphological diversity, and morphospace dynamics has been hampered by the lack of an appropriate null model of morphospace occupation. In this article, we introduce a simple class of models based on branching random walks (BRWs) for continuous traits. We show that many of the observed patterns of morphospace occupation might be simply a consequence of the dynamics of BRWs and therefore might not require special explanations.We also provide expected patterns of morphospace occupation according to a number of different conditions. In particular, we model BRWs on neutral landscapes and demonstrate that clumping in morphospace is possible even in the absence of adaptive landscapes with well-defined peaks and valleys. The quantitative definition of the BRW provides a means to analyze, both computationally and analytically, patterns of morphospace occupation according to different hypotheses.
Dynamics of a contact process with ontogeny

(Georgia Institute of Technology, 2004-08) Weitz, Joshua S. ; Rothman, Daniel H.

We propose a simple model of how sessile organisms grow, disperse, and die. Our model extends the contact process to include a spatially explicit representation of organismal growth in addition to the familiar terms denoting reproduction and mortality. We develop a size-structured mean field theory which predicts an oscillatory phase as a consequence of excess reproduction. Monte Carlo simulations of a spatial implementation show instead a transition from a dilute to a ring-like phase. The ring-like phase arises as a consequence of the competition for limited space among juvenile and mature organisms, i.e., the ecological cost of reproduction. We also calculate the phase transition between life and death in the spatial model and find that it is in the same universality class as directed percolation. Finally, we analyze the onset of the ring-like phase via a spatial autocorrelation and comment on the model’s applicability to problems in the study of ecosystem structure and dynamics
Packing-limited growth of irregular objects

(Georgia Institute of Technology, 2003-01) Dodds, Peter Sheridan ; Weitz, Joshua S.

We study growth limited by packing for irregular objects in two dimensions. We generate packings by seeding objects randomly in time and space and allowing each object to grow until it collides with another object. The objects we consider allow us to investigate the separate effects of anisotropy and nonunit aspect ratio. By means of a connection to the decay of pore-space volume, we measure power law exponents for the object size distribution. We carry out a scaling analysis, showing that it provides an upper bound for the size distribution exponent. We find that while the details of the growth mechanism are irrelevant, the exponent is strongly shape dependent. Potential applications lie in ecological and biological environments where sessile organisms compete for limited space as they grow.
Packing-limited growth

(Georgia Institute of Technology, 2002-05-06) Dodds, Peter Sheridan ; Weitz, Joshua S.

We consider growing spheres seeded by random injection in time and space. Growth stops when two spheres meet leading eventually to a jammed state. We study the statistics of growth limited by packing theoretically in d dimensions and via simulation in d52, 3, and 4. We show how a broad class of such models exhibit distributions of sphere radii with a universal exponent. We construct a scaling theory that relates the fractal structure of these models to the decay of their pore space, a theory that we confirm via numerical simulations. The scaling theory also predicts an upper bound for the universal exponent and is in exact agreement with numerical results for d54.