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Copasetic analysis: a framework for the blind analysis of microarray imagery
2004
IEE Proceedings - Systems Biology
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This paper presents a dynamic framework that aims to automate the process of microarray image analysis using a variety of techniques. ...
As far as the authors are aware, this is the first time such a comprehensive framework concept has been directly applied to the area of microarray image analysis. ...
Copasetic analysis overview Copasetic analysis (CA) is a framework in which automated blind microarray image analysis can be conducted. ...
doi:10.1049/sb:20045002
pmid:17052129
fatcat:mvaxwywq3ncmzkcvarc2fp3sbi
Guest Editorial Foreword to the Special Issue on Intelligent Computation for Bioinformatics
2008
IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews)
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In the paper "Blind Microarray Gridding: A New Framework" by Morris, the author demonstrates that the parameter-free gridding of a microarray image is possible, and implements a subgrid detection algorithm ...
The approach toward gridding differs significantly from most of the other gridding frameworks in the literature as it does not make use of 1-D projections at any stage. ...
doi:10.1109/tsmcc.2007.906053
fatcat:kiiumuayvnbpnggrarkln63lxm
A novel neural network approach to cDNA microarray image segmentation
2013
Computer Methods and Programs in Biomedicine
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In this paper, a new method utilizing a series of artificial neural networks, which are based on multi-layer perceptron (MLP) and Kohonen networks, is proposed. ...
Microarray images typically contain several thousands of small spots, each of which represents a different gene in the experiment. ...
A Complete blind microarray image gridding framework developed in [39] is used to accomplish the spotting task. ...
doi:10.1016/j.cmpb.2013.03.013
pmid:23669179
fatcat:o2yw2juwu5f23gbukazvn3up2a
Cellular Neural Networks, Navier-Stokes equation and microarray image reconstruction
2010
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
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Our aim in this paper is to present a new image-reconstruction algorithm using the cellular neural network that solves the Navier-Stokes equation. ...
Although the last decade has witnessed a great deal of improvements achieved for the microarray technology, many major developments in all the main stages of this technology, including image processing ...
In this paper, a new methodology for cDNA microarray image reconstruction is proposed. ...
doi:10.1109/bibmw.2010.5703805
fatcat:hoyaienuivgunk7v3eyqgkh3iy
Cellular Neural Networks, the Navier–Stokes Equation, and Microarray Image Reconstruction
2011
IEEE Transactions on Image Processing
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Our aim in this paper is to present a new image-reconstruction algorithm using the cellular neural network that solves the Navier-Stokes equation. ...
Although the last decade has witnessed a great deal of improvements achieved for the microarray technology, many major developments in all the main stages of this technology, including image processing ...
In this paper, a new methodology for cDNA microarray image reconstruction is proposed. ...
doi:10.1109/tip.2011.2159231
pmid:21659025
fatcat:xi2x2l45ljgqzpwv2sxoexzgbu
DNA Microarray Technology: Devices, Systems, and Applications
2002
Annual Review of Biomedical Engineering
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Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed. ...
This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. ...
Q Array is a dedicated microarrayer with 16-pin (Christchurch, UK) microarraying head for spotting slides. (Continued ) HELLER lab-on-a-chip technologies. ...
doi:10.1146/annurev.bioeng.4.020702.153438
pmid:12117754
fatcat:7n62vwyqbfaurll42k6l2bah5i
Potential Breast Anticancer Drug Targets Revealed by Differential Gene Regulatory Network Analysis and Molecular Docking: Neoadjuvant Docetaxel Drug as a Case Study
2018
Cancer Informatics
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The work, therefore, provides a new route for understanding the effect of the drug mode of action from the viewpoint of the change in the topology of gene-gene regulatory networks and provides a new avenue ...
On the contrary, the sensitive network is highly disrupted with a lower degree of connectivity. ...
A grid cell extent of 64 Å was used throughout. For each grid cell, the grid potentials were computed at 0.5-Å resolution for the docking calculations. ...
doi:10.1177/1176935118755354
pmid:29449773
pmcid:PMC5808968
fatcat:4oyyphg2bnepxflhl2tbk75vgm
Systems and Applications
[chapter]
2009
Intelligent Video Surveillance
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Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed. ...
This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. ...
Q Array is a dedicated microarrayer with 16-pin (Christchurch, UK) microarraying head for spotting slides. (Continued ) HELLER lab-on-a-chip technologies. ...
doi:10.1201/9781439813300-p5
fatcat:i6py3lyzmre5xnvvrpurahvmai
Gene-Based Multiclass Cancer Diagnosis with Class-Selective Rejections
2009
Journal of Biomedicine and Biotechnology
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Supervised learning of microarray data is receiving much attention in recent years. Multiclass cancer diagnosis, based on selected gene profiles, are used as adjunct of clinical diagnosis. ...
Two experiments are carried out in the Bayesian and the class selective rejection frameworks. Five genes selected datasets are used to assess the performance of the proposed method. ...
set of 1 blinded patient. ...
doi:10.1155/2009/608701
pmid:19584932
pmcid:PMC2703706
fatcat:mlkgtxm7mjdrldnllgnf4sjrb4
Interpreting the gene expression microarray results: a user-based evaluation of 10 bioinformatics tools
2013
Archives Italiennes de Biologie
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Strengths and weaknesses of each tool are highlighted: a. to provide useful tips to users dealing with the biological interpretation of microarray results; b. to draw the attention of software developers ...
In this paper, ten tools for the interpretation of gene expression microarray results have been tested on eleven microarray datasets and evaluated according to eight assessment criteria: 1. interface design ...
CI was supported by IRIs Foundation (Castagneto Carducci, Livorno, Italy), a nonprofit organization for the rehabilitation of individuals with psychiatric disturbances. ...
doi:10.12871/00039829201324
fatcat:f5leigbfrfgppbezxnzbiw6pwa
Blood transcriptional module repertoire analysis and visualization using R
[article]
2020
bioRxiv
pre-print
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Third, the results are expressed at the module level as percent of genes increased or decreased and plotted in a fingerprint grid format. ...
A parallel workflow has been developed for computing module repertoire changes for individual samples rather than groups of samples. Such results are plotted in a heatmap format. ...
Importantly, the framework and 2 scripts provided here have been found to be suitable for the analysis of various microarray 3 platforms but also RNAseq data [e.g. ...
doi:10.1101/2020.07.16.205963
fatcat:rd2hzw5f2rhanlfdhuhzgtryxu
An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis
2010
Nature
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The immune response to M. tuberculosis is complex and incompletely characterized, hindering development of new diagnostics, therapies and vaccines 4,5 . ...
A subset of patients with latent TB had signatures similar to those in patients with active TB. ...
-A. Nguyen (BIIR) and colleagues for providing technical assistance with microarray processing, and S. Caidan (NIMR), J. Wills (NIMR) and S. ...
doi:10.1038/nature09247
pmid:20725040
pmcid:PMC3492754
fatcat:cpnhkxri3jbshpjmtxs22bqy5i
Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration
2015
Archives of Toxicology
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Transcript profiling allowed clear separation of different toxicants and the identification of toxicant types in a blinded test study. ...
We also developed a diagrammatic system to visualize and compare toxicity patterns of a group of chemicals by giving a quantitative overview of altered superordinate biological processes (e.g. activation ...
creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a ...
doi:10.1007/s00204-015-1658-7
pmid:26705709
pmcid:PMC4710658
fatcat:fwqlomqghjfhjozaqzqh6kqmay
Regression Approaches for Microarray Data Analysis
2003
Journal of Computational Biology
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A variety of new procedures have been devised to handle the two-sample comparison (e.g., tumor versus normal tissue) of gene expression values as measured with microarrays. ...
The methods are evaluated using a microarray-based study of cardiomyopathy in transgenic mice. ...
West et al. (2001) develop a Bayesian regression framework customized to phenotype-gene expression association studies in the microarray context. ...
doi:10.1089/106652703322756177
pmid:14980020
fatcat:ieai3cq5p5hibc6jdvd2nd2cpy
Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context
2008
IEEE Transactions on Visualization and Computer Graphics
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Our graph layout algorithm uses simulated annealing with constraints, optimized with a uniform grid to have an expected runtime of Small multiple views of different experimental conditions and a measurement-driven ...
These graphs represent dynamic knowledge of the biological system being studied and evolve as new insight is gained from the experimental data. ...
Acknowledgements I thank my supervisor Tamara Munzner, for finding a project that matched my passions and kept me enthused for years, for suggesting fruitful avenues of exploration, and quickly quashing ...
doi:10.1109/tvcg.2008.117
pmid:18988971
fatcat:qrvntizd7vdczbse2ejfrnkz7q
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