- 标题
- 摘要
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- 实验方案
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The Impact of Photobleaching on Microarray Analysis
摘要： DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner’s laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube’s voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results.
关键词： photobleaching,microarray,cyanine dye,bioanalytics,fluorophore,bioinformatics,DNA
更新于2025-09-23 15:22:29
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[IEEE 2019 IEEE International Conference on Telecommunications and Photonics (ICTP) - Dhaka, Bangladesh (2019.12.28-2019.12.30)] 2019 IEEE International Conference on Telecommunications and Photonics (ICTP) - Absorption Enhancement of GaAs Slab with Geometrically Varying Periodic Array of SiO <sub/>2</sub> Nanostructures
摘要： Infectious diseases are a major cause of death and economic impact worldwide. A more robust, adaptable, and scalable infrastructure would improve the capability to respond to epidemics. Because engineers contribute to the design and implementation of infrastructure, there are opportunities for innovative solutions to infectious disease response within existing systems that have utility, and therefore resources, before a public health emergency. Examples of innovative leveraging of infrastructure, technologies to enhance existing disease management strategies, engineering approaches to accelerate the rate of discovery and application of scientific, clinical, and public health information, and ethical issues that need to be addressed for implementation are presented.
关键词： disease,pathogen,infectious,epidemic,genomics,Bioinformatics
更新于2025-09-23 15:21:01
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[Institution of Engineering and Technology Fifth Asia International Symposium on Mechatronics (AISM 2015) - Guilin, China (7-10 Oct. 2015)] Fifth Asia International Symposium on Mechatronics (AISM 2015) - Enhanced plasmonic effects in Ag decorated amorphous TiO2 nanotube arrays
摘要： The process of converting raw RNA sequencing (RNA-seq) data to interpretable results can be circuitous and time-consuming, requiring multiple steps. We present an RNA-seq mapping algorithm that streamlines this process. Our algorithm utilizes a hash table approach to leverage the availability and the power of high memory machines. SNAPR, which can be run on a single library or thousands of libraries, can take compressed or uncompressed FASTQ and BAM ?les, and output a sorted BAM ?le, individual read counts, and gene fusions, and can identify exogenous RNA species in a single step. SNAPR also does native Phred score ?ltering of reads. SNAPR is also well suited for future sequencing platforms that generate longer reads. We show how we can analyze data from hundreds of TCGA samples in a matter of hours while identifying gene fusions and viral events at the same time. With the reference genome and transcriptome undergoing periodic updates and the need for uniform parameters when integrating multiple data sets, there is great need for a streamlined process for RNA-seq analysis. We demonstrate how SNAPR does this ef?ciently and accurately.
关键词： computational biology,biology,biology computing,RNA.,genetic expression,Bioinformatics
更新于2025-09-23 15:21:01
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[IEEE 2018 25th IEEE International Conference on Image Processing (ICIP) - Athens, Greece (2018.10.7-2018.10.10)] 2018 25th IEEE International Conference on Image Processing (ICIP) - HESCNET: A Synthetically Pre-Trained Convolutional Neural Network for Human Embryonic Stem Cell Colony Classification
摘要： This paper proposes a method for improving the results of deep convolutional neural network classification using synthetic image samples. Generative adversarial networks are used to generate synthetic images from a dataset of phase-contrast, human embryonic stem cell (hESC) microscopy images. hESCnet, a deep convolutional neural network is trained, and the results are shown on various combinations of synthetic and real images in order to improve the classification results with minimal data.
关键词： Image Processing,Generative Adversarial Networks,Deep Learning,Computer Vision,Video Bioinformatics
更新于2025-09-23 15:21:01
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Bioinformatics and enzymatics investigation of Trametes laccase for optical biosensing application
摘要： Laccase has recently drawn a considerable attention as a promising tool for optical biosensing application, mainly due to its attractive intrinsic optical properties. The discovery of a laccase with great enzyme stability is the principal step for enzyme-based optical biosensing application in in vitro environments. In this paper, we found that Trametes sp. SQ1 laccase retained more than 150% activity after storage in different conditions for 96 h, and the laccase activity was not affected by freeze–thaw. The reduced form of enzyme showed a new maximal increase in absorbance peak at 400 nm, while the fluorescence intensity of the oxidized form of enzyme was much stronger than that of the reduced enzyme. Therefore, Trametes sp. SQ1 laccase with good stability and optical properties will be a competitive candidate for optical biosensing application. Moreover, bioinformatics analysis on Trametes laccases revealed that the enzymes may be modified by N-glycosylation and have intermolecular disulfide bond for forming functional oligomer, which plays a role in stabilizing enzyme function. The results indicate that Trametes laccases are able to be with good stability. It will provide a guide in searching stable laccases for optical biosensing application.
关键词： Enzyme stability,Bioinformatics analysis,Trametes sp. SQ1,Optical biosensing,Laccase
更新于2025-09-23 15:19:57
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[IEEE 2020 IEEE 33rd International Conference on Micro Electro Mechanical Systems (MEMS) - Vancouver, BC, Canada (2020.1.18-2020.1.22)] 2020 IEEE 33rd International Conference on Micro Electro Mechanical Systems (MEMS) - Direct Laser Writing of Titanium Dioxide-Laden Retinal Cone Phantoms
摘要： The process of converting raw RNA sequencing (RNA-seq) data to interpretable results can be circuitous and time-consuming, requiring multiple steps. We present an RNA-seq mapping algorithm that streamlines this process. Our algorithm utilizes a hash table approach to leverage the availability and the power of high memory machines. SNAPR, which can be run on a single library or thousands of libraries, can take compressed or uncompressed FASTQ and BAM ?les, and output a sorted BAM ?le, individual read counts, and gene fusions, and can identify exogenous RNA species in a single step. SNAPR also does native Phred score ?ltering of reads. SNAPR is also well suited for future sequencing platforms that generate longer reads. We show how we can analyze data from hundreds of TCGA samples in a matter of hours while identifying gene fusions and viral events at the same time. With the reference genome and transcriptome undergoing periodic updates and the need for uniform parameters when integrating multiple data sets, there is great need for a streamlined process for RNA-seq analysis. We demonstrate how SNAPR does this ef?ciently and accurately.
关键词： Bioinformatics,biology,genetic expression,computational biology,biology computing,RNA.
更新于2025-09-19 17:13:59
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[IEEE 2019 IEEE Asia-Pacific Microwave Conference (APMC) - Singapore, Singapore (2019.12.10-2019.12.13)] 2019 IEEE Asia-Pacific Microwave Conference (APMC) - A Kind of Slot Antenna Array Fed With Substrate Integrated Waveguide
摘要： Infectious diseases are a major cause of death and economic impact worldwide. A more robust, adaptable, and scalable infrastructure would improve the capability to respond to epidemics. Because engineers contribute to the design and implementation of infrastructure, there are opportunities for innovative solutions to infectious disease response within existing systems that have utility, and therefore resources, before a public health emergency. Examples of innovative leveraging of infrastructure, technologies to enhance existing disease management strategies, engineering approaches to accelerate the rate of discovery and application of scientific, clinical, and public health information, and ethical issues that need to be addressed for implementation are presented.
关键词： genomics,Bioinformatics,infectious,disease,pathogen,epidemic
更新于2025-09-19 17:13:59
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[Advances in Intelligent Systems and Computing] First International Conference on Artificial Intelligence and Cognitive Computing Volume 815 (AICC 2018) || Bioinformatics and Image Processing—Detection of Plant Diseases
摘要： This paper gives an idea of how a combination of image processing along with bioinformatics detects deadly diseases in plants and agricultural crops. These kinds of diseases are not recognizable by bare human eyesight. First occurrence of these diseases is microscopic in nature. If plants are affected with such kind of diseases, there is deterioration in the quality of production of the plants. We need to correctly identify the symptoms, treat the diseases, and improve the production quality. Computers can help to make correct decision as well as can support industrialization of the detection work. We present in this paper a technique for image segmentation using HSI algorithm to classify various categories of diseases. This technique can also classify different types of plant diseases as well. GA has always proven itself to be very useful in image segmentation.
关键词： Image processing,Classification,Plant diseases,Image segmentation,Bioinformatics
更新于2025-09-09 09:28:46