Abstract：
:Computer simulations have been used to model infectious diseases to examine the outcomes of alternative strategies for managing their spread. Methicillin resistant Staphylococcus aureus (MRSA) skin and soft tissue infections have become prominent in many communities and efforts are underway to reduce the spread of this organism both in hospitals and communities. Currently, there are few tools for policy makers to use to examine the outcome of various choices when making decisions about MRSA. Using the example of MRSA, we describe, in this paper, a rigorous approach for development and validation of a tool that simulates the spread of MRSA infections. We used sensitivity analyses in a novel way and validated the simulation results against local data over time. Our approach for simulation development and validation is generalizeable to simulations of other diseases.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Panchanathan SS,Petitti DB,Fridsma DBdoi
10.1016/j.jbi.2010.03.013subject
Has Abstractpub_date
2010-08-01 00:00:00pages
602-7issue
4eissn
1532-0464issn
1532-0480pii
S1532-0464(10)00046-8journal_volume
43pub_type
杂志文章abstract：:Named entity recognition is an extremely important and fundamental task of biomedical text mining. Biomedical named entities include mentions of proteins, genes, DNA, RNA, etc which often have complex structures, but it is challenging to identify and classify such entities. Machine learning methods like CRF, MEMM and ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.12.012
更新日期：2009-10-01 00:00:00
abstract：:With recent advances in fluorescence microscopy imaging techniques and methods of gene knock down by RNA interference (RNAi), genome-scale high-content screening (HCS) has emerged as a powerful approach to systematically identify all parts of complex biological processes. However, a critical barrier preventing fulfill...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.04.007
更新日期：2009-02-01 00:00:00
abstract：:In this paper we propose a novel approach to the design and implementation of knowledge-based decision support systems for translational research, specifically tailored to the analysis and interpretation of data from high-throughput experiments. Our approach is based on a general epistemological model of the scientifi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.11.005
更新日期：2010-06-01 00:00:00
abstract：:Building classification models from clinical data using machine learning methods often relies on labeling of patient examples by human experts. Standard machine learning framework assumes the labels are assigned by a homogeneous process. However, in reality the labels may come from multiple experts and it may be diffi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.08.007
更新日期：2013-12-01 00:00:00
abstract：BACKGROUND:The association of genotyping information with common traits is not satisfactorily solved. One of the most complex traits is pain and association studies have failed so far to provide reproducible predictions of pain phenotypes from genotypes in the general population despite a well-established genetic basis...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.07.010
更新日期：2013-10-01 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 management of chronic and out-patients is a complex process which requires the cooperation of different agents belonging to several organizational units. Patients have to move to different locations to access the necessary services and to communicate their health status data. From their point of view there should ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.12.002
更新日期：2007-10-01 00:00:00
abstract：:Patient discharge summaries provide detailed medical information about individuals who have been hospitalized. To make a precise and legitimate assessment of the abundant data, a proper time layout of the sequence of relevant events should be compiled and used to drive a patient-specific timeline, which could further ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.09.007
更新日期：2013-12-01 00:00:00
abstract：:The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular bio-ontologies used for describing gene product characteristics. GO annotation data containing terms from multiple sub-ontologies and at different levels in the ontologies is an important source of implicit relationships between terms fr...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.06.012
更新日期：2013-10-01 00:00:00
abstract：:Patient monitoring algorithms that analyze multiple features from physiological signals can produce an index that serves as a predictive or prognostic measure for a specific critical health event or physiological instability. Classical detection metrics such as sensitivity and positive predictive value are often used ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.09.008
更新日期：2017-11-01 00:00:00
abstract：:Cloud computing is emerging as the next-generation IT architecture. However, cloud computing also raises security and privacy concerns since the users have no physical control over the outsourced data. This paper focuses on fairly retrieving encrypted private medical records outsourced to remote untrusted cloud server...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.02.008
更新日期：2014-08-01 00:00:00
abstract：:Previous research on standardization of eligibility criteria and its feasibility has traditionally been conducted on clinical trial protocols from ClinicalTrials.gov (CT). The portability and use of such standardization for full-text industry-standard protocols has not been studied in-depth. Towards this end, in this ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.06.001
更新日期：2013-10-01 00:00:00
abstract：:Modern biomedical data mining requires feature selection methods that can (1) be applied to large scale feature spaces (e.g. 'omics' data), (2) function in noisy problems, (3) detect complex patterns of association (e.g. gene-gene interactions), (4) be flexibly adapted to various problem domains and data types (e.g. g...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.015
更新日期：2018-09-01 00:00:00
abstract：:In the past, algorithms exploiting varying semantics in interactions between biological objects such as genes and diseases have been used in bioinformatics to uncover latent relationships within biological datasets. In this paper, we consider the algorithm Medusa in parallel with binary classification in order to find...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.005
更新日期：2018-08-01 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：:A software framework can reduce costs related to the development of an application because it allows developers to reuse both design and code. Recently, companies and research groups have announced that they have been employing health software frameworks. This paper presents the design, proof-of-concept implementation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.06.002
更新日期：2016-08-01 00:00:00
abstract：:We describe a novel experiment that we conducted with the Drug Interaction Knowledge-base (DIKB) to determine which combinations of evidence enable a rule-based theory of metabolic drug-drug interactions to make the most optimal set of predictions. The focus of the experiment was a group of 16 drugs including six memb...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.05.010
更新日期：2009-12-01 00:00:00
abstract：:The explosive growth of biomedical literature has created a rich source of knowledge, such as that on protein-protein interactions (PPIs) and drug-drug interactions (DDIs), locked in unstructured free text. Biomedical relation classification aims to automatically detect and classify biomedical relations, which has gre...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103294
更新日期：2019-11-01 00:00:00
abstract：:The potential of plant-based remedies has been documented in both traditional and contemporary biomedical literature. Such types of text sources may thus be sources from which one might identify potential plant-based therapies ("phyto-therapies"). Concept-based analytic approaches have been shown to uncover knowledge ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.04.008
更新日期：2013-08-01 00:00:00
abstract：UNLABELLED:Responding to public health emergencies requires rapid and accurate assessment of workforce availability under adverse and changing circumstances. However, public health information systems to support resource management during both routine and emergency operations are currently lacking. We applied scenario-...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.07.004
更新日期：2011-12-01 00:00:00
abstract：:A graphical representation of DNA sequences in which the distribution of a particular base B=A,C,G,T is represented by a set of discrete lines has been formulated. The methodology of this approach has been borrowed from two areas of physics: spectroscopy and dynamics. Consequently, the set of discrete lines is referre...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.06.001
更新日期：2017-08-01 00:00:00
abstract：BACKGROUND:Control systems engineering methods, particularly, system identification (system ID), offer an idiographic (i.e., person-specific) approach to develop dynamic models of physical activity (PA) that can be used to personalize interventions in a systematic, scalable way. The purpose of this work is to: (1) appl...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.01.010
更新日期：2018-03-01 00:00:00
abstract：:Genomics has contributed to a growing collection of gene-function and gene-disease annotations that can be exploited by informatics to study similarity between diseases. This can yield insight into disease etiology, reveal common pathophysiology and/or suggest treatment that can be appropriated from one disease to ano...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.11.017
更新日期：2012-04-01 00:00:00
abstract：:The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of acti...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.07.013
更新日期：2017-09-01 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：OBJECTIVES:RxNorm is a standardized nomenclature for clinical drug entities developed by the National Library of Medicine. In this paper, we audit relations in RxNorm for consistency and completeness through the systematic analysis of the graph of its concepts and relationships. METHODS:The representation of multi-ing...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.04.004
更新日期：2009-06-01 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：:Proper understanding of textual data requires the exploitation and integration of unstructured and heterogeneous clinical sources, healthcare records or scientific literature, which are fundamental aspects in clinical and translational research. The determination of semantic similarity between word pairs is an importa...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2010.09.002
更新日期：2011-02-01 00:00:00
abstract：BACKGROUND:Knowledge Organization Systems (KOS) and their associated mappings play a central role in several decision support systems. However, by virtue of knowledge evolution, KOS entities are modified over time, impacting mappings and potentially turning them invalid. This requires semi-automatic methods to maintain...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.04.001
更新日期：2015-06-01 00:00:00
abstract：:The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, mak...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1006/jbin.2001.1024
更新日期：2001-08-01 00:00:00
