Abstract:
:A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/.
journal_name
Comput Methods Programs Biomedjournal_title
Computer methods and programs in biomedicineauthors
Guzzi PH,Cannataro Mdoi
10.1016/j.cmpb.2013.04.006subject
Has Abstractpub_date
2013-08-01 00:00:00pages
402-9issue
2eissn
0169-2607issn
1872-7565pii
S0169-2607(13)00114-4journal_volume
111pub_type
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2011.05.001
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abstract::A convolution program (CONV) solving responses to a collimated finite diameter photon beam perpendicularly incident on a multi-layered tissue has been coded in ANSI Standard C, hence, the program can be executed on various computers. The program, employing an extended trapezoidal rule for integration, convolves the re...
journal_title:Computer methods and programs in biomedicine
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abstract:BACKGROUND AND OBJECTIVE:Gene regulatory networks (GRNs) are essential for understanding most molecular processes. In this context, the so-called model-free approaches have an advantage modeling the complex topologies behind these dynamic molecular networks, since most GRNs are difficult to map correctly by any other m...
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2013.05.001
更新日期:2013-08-01 00:00:00
abstract::The mixture cure model is a special type of survival models and it assumes that the studied population is a mixture of susceptible individuals who may experience the event of interest, and cure/non-susceptible individuals who will never experience the event. For such data, standard survival models are usually not appr...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2012.08.013
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abstract:OBJECTIVE:To observe the efficacy of distal tibial tuberosity high tibial osteotomy in treating medial compartment osteoarthritis of the knee. In the experiment, a medical image enhancement algorithm based on shear wave domain improved Gamma correction was implemented to process medical images in order to diagnose pati...
journal_title:Computer methods and programs in biomedicine
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abstract:BACKGROUND AND OBJECTIVES:Heart rate variability (HRV) has increasingly been linked to medical phenomena and several HRV metrics have been found to be good indicators of patient health. This has enabled generalised treatment plans to be developed in order to respond to subtle personal differences that are reflected in ...
journal_title:Computer methods and programs in biomedicine
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doi:10.1016/j.cmpb.2019.105127
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abstract:BACKGROUND AND OBJECTIVES:Detection and classification of pulmonary nodules are critical tasks in medical image analysis. The Lung Image Database Consortium (LIDC) database is a widely used resource for small pulmonary nodule classification research. This dataset is comprised of nodule characteristic evaluations and CT...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2018.10.009
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abstract::Characterization of carotid atherosclerosis and classification into either symptomatic or asymptomatic is crucial in terms of diagnosis and treatment planning for a range of cardiovascular diseases. This paper presents a computer-aided diagnosis (CAD) system (Atheromatic) that analyzes ultrasound images and classifies...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2012.09.008
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2015.11.006
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abstract::NONMEM is an extremely powerful tool for nonlinear mixed-effect modelling and simulation of pharmacokinetic and pharmacodynamic data. However, it is a console-based application whose output does not lend itself to rapid interpretation or efficient management. NONMEMory has been created to be a comprehensive project ma...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2005.02.003
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2014.04.011
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abstract::This paper describes an electronic database for handling the interactions between active principles administered to various patients. The computer used is a personal computer with adequate mass memory, software, and data obtained from pharmacological sources. The main features of this work are: 'all-patient' orientati...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/0169-2607(89)90147-8
更新日期:1989-03-01 00:00:00
abstract:BACKGROUND AND OBJECTIVE:T-wave alternans (TWA) is a fluctuation of the ST-T complex occurring on an every-other-beat basis of the surface electrocardiogram (ECG). It has been shown to be an informative risk stratifier for sudden cardiac death, though the lack of gold standard to benchmark detection methods has promote...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2017.04.005
更新日期:2017-07-01 00:00:00
abstract:OBJECTIVES:Postoperative delirium is a common complication after major surgery among the elderly. Despite its potentially serious consequences, the complication often goes undetected and undiagnosed. In order to provide diagnosis support one could potentially exploit the information hidden in free text documents from e...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2017.09.014
更新日期:2017-12-01 00:00:00
abstract:BACKGROUND AND OBJECTIVE:In most countries, the higher death rates are due to cardiovascular disease and stroke. These problems often derive from irregular blood flow and the circulatory system disorder. METHODS:In this paper, the blood flow is simulated in a created aneurysm in the artery upon using Lattice Boltzmann...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2019.105312
更新日期:2020-04-01 00:00:00
abstract::Lung cancer is one of the most common forms of cancer resulting in over a million deaths per year worldwide. In this paper, the usage of support vector machine (SVM) classification for lung cancer is investigated, presenting a systematic quantitative evaluation against Boosting, Decision trees, k-nearest neighbor, LAS...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2013.04.016
更新日期:2013-08-01 00:00:00
abstract::A set of programs is described by which a consistent morphometry of bone sections can be performed. The programs are written in FORTRAN IV in a PDP 11/10 minicomputer, under the RT-11 operating system. The bone sections are run through the field of vision of the microscope using a scanning stage in one of several pres...
journal_title:Computer methods and programs in biomedicine
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/s0169-2607(97)00034-5
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abstract::Gaze is a natural input for a Human Computer Interface (HCI) for disabled people, who have of course an acute need for a communication system. An efficient eye tracking procedure is presented providing a non-invasive method for real time detection of a subject eyes in a sequence of frames captured by low cost equipmen...
journal_title:Computer methods and programs in biomedicine
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journal_title:Computer methods and programs in biomedicine
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journal_title:Computer methods and programs in biomedicine
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journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2018.04.022
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abstract::Quesenberry and Hurst (1964), Goodman (1965) and Fitzpatrick and Scott (1987) proposed simultaneous construction of confidence intervals for multinomial proportions, however. statistical computing packages do not generally give one the option of specifying the type of construction to be used. We have written a SAS mac...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
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abstract::Prognosis of B-Chronic Lymphocytic Leukemia (B-CLL) remains a challenging problem in medical research and practice. While the parameters obtained by flow cytometry analysis form the basis of the diagnosis of the disease, the question whether these parameters offer additional prognostic information still remains open. ...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2012.02.009
更新日期:2012-10-01 00:00:00
abstract::In this study, the virtual reality (VR) proprioception rehabilitation system was developed for stroke patients to use proprioception feedback in upper limb rehabilitation by blocking visual feedback. To evaluate its therapeutic effect, 10 stroke patients (onset>3 month) trained proprioception feedback rehabilitation f...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2013.09.006
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abstract::In modern molecular biology, high-throughput experiments allow the simultaneous study of expression levels of thousands of biopolymers such as mRNAs, miRNAs or proteins. A typical goal of such experiments is to find molecular signatures that can distinguish between different types of tissue or that can predict a thera...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
doi:10.1016/j.cmpb.2013.05.013
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journal_title:Computer methods and programs in biomedicine
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abstract::Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the ...
journal_title:Computer methods and programs in biomedicine
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abstract::In medical systems it is often advantageous to utilize specific problem situations (cases) in addition to or instead of a general model. Decisions are then based on relevant past cases retrieved from a case memory. The reliability of such decisions depends directly on the ability to identify cases of practical relevan...
journal_title:Computer methods and programs in biomedicine
pub_type: 杂志文章
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