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Copasetic analysis: a framework for the blind analysis of microarray imagery

K. Fraser, Z. Wang, P. O'Neill, X. Liu
2004 IEE Proceedings - Systems Biology  
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

Zidong Wang, Xiachui Liu
2008 IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews)  
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

Zidong Wang, Bachar Zineddin, Jinling Liang, Nianyin Zeng, Yurong Li, Min Du, Jie Cao, Xiaohui Liu
2013 Computer Methods and Programs in Biomedicine  
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

Bachar Zineddin, Zidong Wang, Xiaohui Liu
2010 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)  
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

Bachar Zineddin, Zidong Wang, Xiaohui Liu
2011 IEEE Transactions on Image Processing  
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

Michael J. Heller
2002 Annual Review of Biomedical Engineering  
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

Adel Aloraini, Karim M ElSawy
2018 Cancer Informatics  
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  
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

Nisrine Jrad, Edith Grall-Maës, Pierre Beauseroy
2009 Journal of Biomedicine and Biotechnology  
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

PELLEGRINI , SILVIA, MELISSARI, E., DI RUSSO, M.
2013 Archives Italiennes de Biologie  
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]

Darawan Rinchai, Jessica Roelands, Wouter Hendrickx, Matthew C Altman, Davide Bedognetti, Damien Chaussabel
2020 bioRxiv   pre-print
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

Matthew P. R. Berry, Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, Romain Banchereau, Jason Skinner, Robert J. Wilkinson, Charles Quinn, Derek Blankenship (+9 others)
2010 Nature  
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

Giorgia Pallocca, Marianna Grinberg, Margit Henry, Tancred Frickey, Jan G. Hengstler, Tanja Waldmann, Agapios Sachinidis, Jörg Rahnenführer, Marcel Leist
2015 Archives of Toxicology  
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

Mark R. Segal, Kam D. Dahlquist, Bruce R. Conklin
2003 Journal of Computational Biology  
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

A. Barsky, T. Munzner, J. Gardy, R. Kincaid
2008 IEEE Transactions on Visualization and Computer Graphics  
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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