Please note that this is a draft version, but one on which I would particularly appreciate feedback ([email protected]). Almost all sections are as complete as time will allow, however the document is still subject to revision. The one section remaining to be written is the conclusion, which will summarize major themes, general principles and current research directions. A PDF version of this ...

Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond ...

Systems biology of plants offers myriad opportunities and many challenges in modeling. A number of technical challenges stem from paucity of computational methods for discovery of the most fundamental properties of complex dynamical systems. In systems engineering, eigen-mode analysis have proved to be a powerful approach. Following this philosophy, we introduce a new theory that has the benefi...

The sulfur regulatory circuit of the filamentous fungus, Neurospora crassa, consists of a set of unlinked structural genes which encode sulfur catabolic and two major regulatory genes which govern their expression. The cys-3 regulatory gene encode a transacting regulatory protein which activates the expression of cys-14 and ars, whereas the other regulatory genes Scon-l and Scon-2 appear to...

Simultaneously reverse engineering a collection of condition-specific gene networks from gene expression microarray data to uncover dynamic mechanisms is a key challenge in systems biology. However, existing methods for this task are very sensitive to variations in the size of the microarray samples across different biological conditions (which we term sample size heterogeneity in network recon...

Robust performance, the attainment of a specified response under uncertainty, is a well studied problem in control engineering. In the field of systems biology, related problems are emerging from the quantitative analysis of complex biophysical networks. In this paper, connections are made between the robust performance questions in biology and engineering. Two examples are used to illustrate t...

In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to kee...

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon...

the effect of motivational self-regulatory strategies on l2 learners’ achievement has scarcely been examined within the context of our country, iran. this study is concerned with examining the relationship between motivational self-regulatory strategies and their l2 reading and l2 writing achievement. it also explores the relationship of motivational self-regulatory strategies and use of langua...