Computational analysis of microarray data

2001 ◽  
Vol 2 (6) ◽  
pp. 418-427 ◽  
Author(s):  
John Quackenbush
Keyword(s):  
Microarray Data ◽  
Computational Analysis

scholarly journals Selective Phenome Growth Adapted NK Model: A Novel Landscape to Represent Aptamer Ligand Binding

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Andrew Brian Kinghorn ◽  
Julian Alexander Tanner
Keyword(s):  
Ligand Binding ◽  
Microarray Data ◽  
Computational Analysis ◽  
Selection Process ◽  
Theoretical Models ◽  
Fitness Landscapes ◽  
New Approach ◽  
Aptamer Selection ◽  
Interaction Map ◽  
Target Binding

Aptamers are single-stranded oligonucleotides selected by evolutionary approaches from massive libraries with significant potential for specific molecular recognition in diagnostics and therapeutics. A complete empirical characterisation of an aptamer selection experiment is not feasible due to the vast complexity of aptamer selection. Simulation of aptamer selection has been used to characterise and optimise the selection process; however, the absence of a good model for aptamer-target binding limits this field of study. Here, we generate theoretical fitness landscapes which appear to more accurately represent aptamer-target binding. The method used to generate these landscapes, selective phenome growth, is a new approach in which phenotypic contributors are added to a genotype/phenotype interaction map sequentially in such a way so as to increase the fitness of a selected fit sequence. In this way, a landscape is built around the selected fittest sequences. Comparison to empirical aptamer microarray data shows that our theoretical fitness landscapes more accurately represent aptamer ligand binding than other theoretical models. These improved fitness landscapes have potential for the computational analysis and optimisation of other complex systems.

Computational analysis of high-density peptide microarray data with application from systemic sclerosis to multiple sclerosis

2012 ◽  
Vol 11 (3) ◽  
pp. 180-190 ◽  
Author(s):  
Michael Hecker ◽  
Peter Lorenz ◽  
Felix Steinbeck ◽  
Li Hong ◽  
Gabriela Riemekasten ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Systemic Sclerosis ◽  
Microarray Data ◽  
Computational Analysis ◽  
High Density ◽  
Peptide Microarray

Expression and network analysis of Illumina microarray data

2009 ◽  
Author(s):  
Giovanni Coppola ◽  
Kellen Winden ◽  
Genevieve Konopka ◽  
Fuying Gao ◽  
Daniel Geschwind
Keyword(s):  
Network Analysis ◽  
Microarray Data

Measurement and Three-Dimensional Computational Analysis for Flow Electrification in Complex-Shaped Ducts

2016 ◽  
Vol 136 (3) ◽  
pp. 318-324
Author(s):  
Naoya Miyamoto ◽  
Makoto Koizumi ◽  
Hiroshi Miyao ◽  
Takayuki Kobayashi ◽  
Kojiro Aoki
Keyword(s):  
Computational Analysis ◽  
Three Dimensional ◽  
Flow Electrification
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