Abstract:
:Microarray data is a key source of experimental data for modelling gene regulatory interactions from expression levels. With the rapid increase of publicly available microarray data comes the opportunity to produce regulatory network models based on multiple datasets. Such models are potentially more robust with greater confidence, and place less reliance on a single dataset. However, combining datasets directly can be difficult as experiments are often conducted on different microarray platforms, and in different laboratories leading to inherent biases in the data that are not always removed through pre-processing such as normalisation. In this paper we compare two frameworks for combining microarray datasets to model regulatory networks: pre- and post-learning aggregation. In pre-learning approaches, such as using simple scale-normalisation prior to the concatenation of datasets, a model is learnt from a combined dataset, whilst in post-learning aggregation individual models are learnt from each dataset and the models are combined. We present two novel approaches for post-learning aggregation, each based on aggregating high-level features of Bayesian network models that have been generated from different microarray expression datasets. Meta-analysis Bayesian networks are based on combining statistical confidences attached to network edges whilst Consensus Bayesian networks identify consistent network features across all datasets. We apply both approaches to multiple datasets from synthetic and real (Escherichia coli and yeast) networks and demonstrate that both methods can improve on networks learnt from a single dataset or an aggregated dataset formed using a standard scale-normalisation.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Steele E,Tucker Adoi
10.1016/j.jbi.2008.01.011subject
Has Abstractpub_date
2008-12-01 00:00:00pages
914-26issue
6eissn
1532-0464issn
1532-0480pii
S1532-0464(08)00020-8journal_volume
41pub_type
杂志文章,meta分析abstract:OBJECTIVE:To investigate whether SNOMED CT covers the terms used in pre-operative assessment guidelines, and if necessary, how the measured content coverage can be improved. METHODS:Pre-operative assessment guidelines were retrieved from the websites of (inter)national anesthesia-related societies. The recommendations...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.07.009
更新日期:2010-12-01 00:00:00
abstract:BACKGROUND:One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virulence factors and increased resistance to antibiotic therapeutics. To tra...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.03.007
更新日期:2015-06-01 00:00:00
abstract::The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) wi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.01.009
更新日期:2012-08-01 00:00:00
abstract::Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biome...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.10.001
更新日期:2014-02-01 00:00:00
abstract::We propose a model-driven methodology aimed to shed light on complex disorders. Our approach enables exploring shared etiologies of comorbid diseases at the molecular pathway level. The method, Comparative Comorbidities Simulation (CCS), uses stochastic Petri net simulation for examining the phenotypic effects of pert...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.08.008
更新日期:2016-10-01 00:00:00
abstract::Gene selection is important for cancer classification based on gene expression data, because of high dimensionality and small sample size. In this paper, we present a new gene selection method based on clustering, in which dissimilarity measures are obtained through kernel functions. It searches for best weights of ge...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.05.007
更新日期:2016-08-01 00:00:00
abstract::Data analytics is routinely used to support biomedical research in all areas, with particular focus on the most relevant clinical conditions, such as cancer. Bioinformatics approaches, in particular, have been used to characterize the molecular aspects of diseases. In recent years, numerous studies have been performed...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章,评审
doi:10.1016/j.jbi.2020.103466
更新日期:2020-07-01 00:00:00
abstract::A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metada...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.06.017
更新日期:2017-08-01 00:00:00
abstract::Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security modu...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/s1532-0464(02)00524-5
更新日期:2002-06-01 00:00:00
abstract:OBJECTIVE:To create an analytics platform for specifying and detecting clinical phenotypes and other derived variables in electronic health record (EHR) data for quality improvement investigations. MATERIALS AND METHODS:We have developed an architecture for an Analytic Information Warehouse (AIW). It supports transfor...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.01.005
更新日期:2013-06-01 00:00:00
abstract::The aim of this study is to explore the word sense disambiguation (WSD) problem across two biomedical domains-biomedical literature and clinical notes. A supervised machine learning technique was used for the WSD task. One of the challenges addressed is the creation of a suitable clinical corpus with manual sense anno...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.02.003
更新日期:2008-12-01 00:00:00
abstract::Attention Deficit Hyperactive Disorder (ADHD) is one of the most common diseases in school aged children. In this paper, we consider using fMRI data with classification techniques to aid the diagnosis of ADHD and propose a bi-objective ADHD classification scheme based on L1-norm support vector machine (SVM). In our cl...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.07.011
更新日期:2018-08-01 00:00:00
abstract::This research aims to depict the methodological steps and tools about the combined operation of case-based reasoning (CBR) and multi-agent system (MAS) to expose the ontological application in the field of clinical decision support. The multi-agent architecture works for the consideration of the whole cycle of clinica...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.06.012
更新日期:2015-08-01 00:00:00
abstract:BACKGROUND:The realization of the potential benefits of health information exchange systems (HIEs) for emergency departments (EDs) depends on the way these systems are actually used. The attributes of volume of information and duration of information processing are important for the study of HIE use patterns in the ED,...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.05.007
更新日期:2017-07-01 00:00:00
abstract::The Research Electronic Data Capture (REDCap) data management platform was developed in 2004 to address an institutional need at Vanderbilt University, then shared with a limited number of adopting sites beginning in 2006. Given bi-directional benefit in early sharing experiments, we created a broader consortium shari...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103208
更新日期:2019-07-01 00:00:00
abstract::Quantitative gait analysis allows clinicians to assess the inherent gait variability over time which is a functional marker to aid in the diagnosis of disabilities or diseases such as frailty, the onset of cognitive decline and neurodegenerative diseases, among others. However, despite the accuracy achieved by the cur...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.07.009
更新日期:2016-08-01 00:00:00
abstract:OBJECTIVE:Our aim is to extract clinically-meaningful phenotypes from longitudinal electronic health records (EHRs) of medically-complex children. This is a fragile set of patients consuming a disproportionate amount of pediatric care resources but who often end up with sub-optimal clinical outcome. The rise in availab...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103125
更新日期:2019-05-01 00:00:00
abstract:BACKGROUND:Word embeddings have been prevalently used in biomedical Natural Language Processing (NLP) applications due to the ability of the vector representations being able to capture useful semantic properties and linguistic relationships between words. Different textual resources (e.g., Wikipedia and biomedical lit...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.09.008
更新日期:2018-11-01 00:00:00
abstract::With rapid adoption of Electronic Health Records (EHR) in China, an increasing amount of clinical data has been available to support clinical research. Clinical data secondary use usually requires de-identification of personal information to protect patient privacy. Since manually de-identification of free clinical te...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.07.017
更新日期:2017-09-01 00:00:00
abstract::Text categorization has been used extensively in recent years to classify plain-text clinical reports. This study employs text categorization techniques for the classification of open narrative forensic autopsy reports. One of the key steps in text classification is document representation. In document representation,...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.04.013
更新日期:2018-06-01 00:00:00
abstract::Rare diseases are often hard and long to be diagnosed precisely, and most of them lack approved treatment. For some complex rare diseases, precision medicine approach is further required to stratify patients into homogeneous subgroups based on the clinical, biological or molecular features. In such situation, deep phe...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103308
更新日期:2019-12-01 00:00:00
abstract::To extract biomedical information about bio-entities from the huge amount of biomedical literature, the first key step is recognizing their names in these literatures, which remains a challenging task due to the irregularities and ambiguities in bio-entities nomenclature. The recognition performances of the current po...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.01.002
更新日期:2008-08-01 00:00:00
abstract::Medication errors are common and cause serious health issues during care transitions, particularly for older adults with multiple chronic conditions. In this paper, we discuss the design and evaluation of the Colorado Care Tablet, a Personal Health Application (PHA) that helps older adults and their lay caregivers man...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.05.007
更新日期:2010-10-01 00:00:00
abstract::Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDSDM) is a Galaxy-based, open source disease-specific web portal for diabetes. It consists of three modules namely (i) data library (ii) data processing and (iii) data analysis tools. The data library (target library and literature) module provide extensive an...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.08.003
更新日期:2018-09-01 00:00:00
abstract:OBJECTIVE:Clinical pathways (CPs) are widely studied methods to standardize clinical intervention and improve medical quality. However, standard care plans defined in current CPs are too general to execute in a practical healthcare environment. The purpose of this study was to create hospital-specific personalized CPs ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2014.07.017
更新日期:2014-12-01 00:00:00
abstract::Investigators in the translational research and systems medicine domains require highly usable, efficient and integrative tools and methods that allow for the navigation of and reasoning over emerging large-scale data sets. Such resources must cover a spectrum of granularity from bio-molecules to population phenotypes...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2011.07.006
更新日期:2011-12-01 00:00:00
abstract::Sensitive biomedical data is often collected from distributed sources, involving different information systems and different organizational units. Local autonomy and legal reasons lead to the need of privacy preserving integration concepts. In this article, we focus on anonymization, which plays an important role for ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.12.002
更新日期:2014-08-01 00:00:00
abstract::Intensive care monitoring systems are typically developed from population data, but do not take into account the variability among individual patients' characteristics. This study develops patient-specific alarm algorithms in real time. Classification tree and neural network learning were carried out in batch mode on ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.03.011
更新日期:2008-06-01 00:00:00
abstract::Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies give us a 'snapshot' of this disease process over a large number of people but do not allow us to model the temporal ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.11.003
更新日期:2013-04-01 00:00:00
abstract::Computers allow describing the progress of a disease using computerized models. These models allow aggregating expert and clinical information to allow researchers and decision makers to forecast disease progression. To make this forecast reliable, good models and therefore good modeling tools are required. This paper...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.06.003
更新日期:2010-10-01 00:00:00