NDLI: A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

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IEEE Journal of Biomedical and Health Informatics publication information

Table of contents

Guest Editorial: Computational Solutions to Large-Scale Data Management and Analysis in Translational and Personalized Medicine

Predictive Monitoring of Mobile Patients by Combining Clinical Observations With Data From Wearable Sensors

Identification of COPD Patients’ Health Status Using an Intelligent System in the CHRONIOUS Wearable Platform

Enabling Smart Personalized Healthcare: A Hybrid Mobile-Cloud Approach for ECG Telemonitoring

Augmenting Breath Regulation Using a Mobile Driven Virtual Reality Therapy Framework

A Joint FED Watermarking System Using Spatial Fusion for Verifying the Security Issues of Teleradiology

Removing Batch Effects From Histopathological Images for Enhanced Cancer Diagnosis

On the Identification of Circulating Tumor Cells in Breast Cancer

Impact of Head Rotation on the Individualized Common Carotid Flow and Carotid Bifurcation Hemodynamics

Robust and Sensitive Video Motion Detection for Sleep Analysis

Temporal and Spatial Patterns of Gene Profiles during Chondrogenic Differentiation

Using Evolutional Properties of Gene Networks in Understanding Survival Prognosis of Glioblastoma

A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

Web-Based Workflow Planning Platform Supporting the Design and Execution of Complex Multiscale Cancer Models

Modeling Biological Pathway Dynamics With Timed Automata

The Technologically Integrated Oncosimulator: Combining Multiscale Cancer Modeling With Information Technology in the In Silico Oncology Context

An Automated Screening System for Tuberculosis

A Bicluster-Based Bayesian Principal Component Analysis Method for Microarray Missing Value Estimation

On the Seamless, Harmonized Use of ISO/IEEE11073 and OpenEHR

Design of a RESTful Web Information System for Drug Prescription and Administration

Designing an Architecture for Monitoring Patients at Home: Ontologies and Web Services for Clinical and Technical Management Integration

A Computational Tool for Preoperative Breast Augmentation Planning in Aesthetic Plastic Surgery

Treatment Planning and Image Guidance for Radiofrequency Ablation of Large Tumors

Local Mesh Patterns Versus Local Binary Patterns: Biomedical Image Indexing and Retrieval

Non-Calcified Coronary Atherosclerotic Plaque Characterization by Dual Energy Computed Tomography

Computer-Aided Staging of Lymphoma Patients With FDG PET/CT Imaging Based on Textural Information

Efficient Acceleration of Mutual Information Computation for Nonrigid Registration Using CUDA

A Spatiotemporal-Based Scheme for Efficient Registration-Based Segmentation of Thoracic 4-D MRI

A Novel MRI Tracer-Based Method for Measuring Water Diffusion in the Extracellular Space of the Rat Brain (December2013)

Multiple Kernel Learning in the Primal for Multimodal Alzheimer’s Disease Classification

Red Blood Cell Tracking Using Optical Flow Methods

Automatic Handling of Tissue Microarray Cores in High-Dimensional Microscopy Images

Exploring Early Glaucoma and the Visual Field Test: Classification and Clustering Using Bayesian Networks

Context-driven, Prescription-Based Personal Activity Classification: Methodology, Architecture, and End-to-End Implementation

Accelerometry-Based Home Monitoring for Detection of Nocturnal Hypermotor Seizures Based on Novelty Detection

Walking-Age Analyzer for Healthcare Applications

sEMG-Based Joint Force Control for an Upper-Limb Power-Assist Exoskeleton Robot

Automated Detection of Perturbed Cardiac Physiology During Oral Food Allergen Challenge in Children

Quality of the Wireless Electrocardiogram Signal During Physical Exercise in Different Age Groups

Detection of Respiratory Arousals Using Photoplethysmography (PPG) Signal in Sleep Apnea Patients

Single-Trial EEG Classification Using Logistic Regression Based on Ensemble Synchronization

Compressed Sensing Technology-Based Spectral Estimation of Heart Rate Variability Using the Integral Pulse Frequency Modulation Model

Design and Evaluation of RFID Deployments in a Trauma Resuscitation Bay

Erratum to “An Effective Approach for Detection and Segmentation of Protein Spots on 2-D Gel Images” [Jan 14 67-76]

2014 IEEE membership form

IEEE Journal of Biomedical and Health Informatics (J-BHI) information for authors

Issue 2

Issue 1

Year : 2013 Volume : 17

A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

Content Provider	IEEE Xplore Digital Library
Author	Valavanis, I. Sifakis, E.G. Georgiadis, P. Kyrtopoulos, S. Chatziioannou, A.A.
Copyright Year	2013
Abstract	High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic, and analytical pipelines for an efficient systems level analysis and interpretation. In this study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the-established in transcriptomic microarrays-logarithmic ratio of the methylated versus the unmethylated signal intensities, quoted as M -value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures exploiting the coefficient variation of DNA methylation measurements between control and case samples alleviate the impact of technical variation. The results presented here are juxtaposed to those derived by applying classical preprocessing and statistical selection methodologies. Overall, in comparison to traditional approaches, the superior performance of the proposed framework in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies.
Page Count	7
File Size	1049771
Starting Page	817
Ending Page	823
File Format	PDF
ISSN	21682194
Volume Number	18
Issue Number	3
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Probes DNA Biomedical measurement Semiconductor device measurement Measurement uncertainty Informatics Breast cancer statistical selection Bootstrap correction DNA methylation profiling epigenomic analysis intensity-based normalization microarrays
Content Type	Text
Resource Type	Article
Subject	Health Information Management Health Informatics Electrical and Electronic Engineering Computer Science Applications Biotechnology

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

Between-array normalization for 450K data

Epigenome-Wide DNA Methylation Profiling in Colorectal Cancer and Normal Adjacent Colon Using Infinium Human Methylation 450K

Characteristics of DNA methylation and gene expression in regulatory features on the Infinium 450k Beadchip

Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes

A data-driven approach to preprocessing Illumina 450K methylation array data

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data.

DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array

A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

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