Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination

2004 ◽  
Vol 89 (1) ◽  
pp. 53-77 ◽  
Author(s):  
Hairong Wei ◽  
Yiannis Kaznessis
Keyword(s):  
Pattern Recognition ◽  
Target Pattern ◽  
Gene Regulatory

scholarly journals Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map

2019 ◽  
Author(s):  
Pablo Catalán ◽  
Susanna Manrubia ◽  
José A. Cuesta
Keyword(s):  
Regulatory Networks ◽  
Expression Patterns ◽  
Genetic Circuits ◽  
Target Pattern ◽  
Selective Pressures ◽  
Spatiotemporal Expression ◽  
Genotype Space ◽  
Great Relevance ◽  
Gene Regulatory ◽  
The Relationship

AbstractThe evolution of gene regulatory networks (GRNs) is of great relevance for both evolutionary and synthetic biology. Understanding the relationship between GRN structure and its function can allow us to understand the selective pressures that have shaped a given circuit. This is especially relevant when considering spatiotemporal expression patterns, where GRN models have been shown to be extremely robust and evolvable. However, previous models that studied GRN evolution did not include the evolution of protein and genetic elements that underlie GRN architecture. Here we use toyLIFE, a multilevel genotype-phenotype map, to show that not all GRNs are equally likely in genotype space and that evolution is biased to find the most common GRNs. toyLIFE rules create Boolean GRNs that, embedded in a one-dimensional tissue, develop a variety of spatiotemporal gene expression patterns. Populations of toyLIFE organisms choose the most common GRN out of a set of equally fit alternatives and, most importantly, fail to find a target pattern when it is very rare in genotype space. Indeed, we show that the probability of finding the fittest phenotype increases dramatically with its abundance in genotype space. This phenotypic bias represents a mechanism that can prevent the fixation in the population of the fittest phenotype, one that is inherent to the structure of genotype space and the genotype-phenotype map.

Software pattern recognition applied to nanodiffraction patterns from a STEM instrument

1986 ◽  
Vol 44 ◽  
pp. 694-695
Author(s):  
G.Y. Fan ◽  
J.M. Cowley
Keyword(s):  
Image Processing ◽  
Pattern Recognition ◽  
Computer Software ◽  
Processing System ◽  
Light Level ◽  
Host Computer ◽  
Low Light ◽  
Image Processing System ◽  
Recent Developments ◽  
On Line

In recent developments, the ASU HB5 has been modified so that the timing, positioning, and scanning of the finely focused electron probe can be entirely controlled by a host computer. This made the asynchronized handshake possible between the HB5 STEM and the image processing system which consists of host computer (PDP 11/34), DeAnza image processor (IP 5000) which is interfaced with a low-light level TV camera, array processor (AP 400) and various peripheral devices. This greatly facilitates the pattern recognition technique initiated by Monosmith and Cowley. Software called NANHB5 is under development which, instead of employing a set of photo-diodes to detect strong spots on a TV screen, uses various software techniques including on-line fast Fourier transform (FFT) to recognize patterns of greater complexity, taking advantage of the sophistication of our image processing system and the flexibility of computer software.

Bayesian removal of noise for increased sensitivity in vector pattern recognition lattice imaging of interfaces

1993 ◽  
Vol 51 ◽  
pp. 994-995
Author(s):  
L. Fei ◽  
P. Fraundorf
Keyword(s):  
Pattern Recognition ◽  
Perfect Crystal ◽  
Unit Cell ◽  
Ion Milling ◽  
Beam Radiation ◽  
Major Interest ◽  
Unit Cells ◽  
Mapping Process ◽  
Increased Sensitivity ◽  
Electron Microscopes

Interface structure is of major interest in microscopy. With high resolution transmission electron microscopes (TEMs) and scanning probe microscopes, it is possible to reveal structure of interfaces in unit cells, in some cases with atomic resolution. A. Ourmazd et al. proposed quantifying such observations by using vector pattern recognition to map chemical composition changes across the interface in TEM images with unit cell resolution. The sensitivity of the mapping process, however, is limited by the repeatability of unit cell images of perfect crystal, and hence by the amount of delocalized noise, e.g. due to ion milling or beam radiation damage. Bayesian removal of noise, based on statistical inference, can be used to reduce the amount of non-periodic noise in images after acquisition. The basic principle of Bayesian phase-model background subtraction, according to our previous study, is that the optimum (rms error minimizing strategy) Fourier phases of the noise can be obtained provided the amplitudes of the noise is given, while the noise amplitude can often be estimated from the image itself.

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