Abstract：
:Linkage analysis uses information from family pedigrees to map genes and locate disease genes on particular chromosomes. A recombination fraction denoted as theta is estimated as a measure of crossing over between two loci. Genetic linkage calculations are very time-consuming particularly for large family pedigrees, a large number of theta values, and an increased number of markers. This paper reports the implementation of a dynamic master-slave scheme for the parallelization of the Linkmap program on a high-performance cluster such as the Origin 2000 (O2K) consisting of 56 R12000 processors. The Linkmap program is one of four programs in the LINKAGE/FASTLINK legacy package widely used by the medical research community. Implementations issues are addressed and results are compared with previous results on a cluster of DEC Alphas, and with the sequential execution on the O2K machine.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Kothari K,Lopez-Benitez N,Poduslo SEdoi
10.1006/jbin.2002.1031keywords:
subject
Has Abstractpub_date
2001-12-01 00:00:00pages
406-14issue
6eissn
1532-0464issn
1532-0480pii
S1532-0464(02)91031-2journal_volume
34pub_type
杂志文章abstract：:Computer-based clinical decision support (CDS) has been pursued for more than five decades. Despite notable accomplishments and successes, wide adoption and broad use of CDS in clinical practice has not been achieved. Many issues have been identified as being partially responsible for the relatively slow adoption and ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2017.12.005
更新日期：2018-02-01 00:00:00
abstract：OBJECTIVE:To examine the impact of the implementation of an electronic handoff tool (the Handoff Tool) on shared mental models (SMM) within patient care teams as measured by content overlap and discrepancies in verbal handoff presentations given by different clinicians caring for the same patient. MATERIALS AND METHOD...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.03.004
更新日期：2017-05-01 00:00:00
abstract：:In this study, we proposed a new medical diagnosis system based on principal component analysis (PCA), k-NN based weighting pre-processing, and Artificial Immune Recognition System (AIRS) for diagnosis of atherosclerosis from Carotid Artery Doppler Signals. The suggested system consists of four stages. First, in the f...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2007.04.001
更新日期：2008-02-01 00:00:00
abstract：:Large-scale mapping efforts have been done in attempts to migrate systems that use proprietary concepts to ones that use terminological standards such as SNOMED CT. As efforts move towards implementation, the target maps should retain a predictable structure including those targets requiring post-coordination of SNOME...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.03.004
更新日期：2009-06-01 00:00:00
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：: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：: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：:Game-based interventions (GBI) have been used to promote health-related outcomes, including cognitive functions. Criteria for game-elements (GE) selection are insufficiently characterized in terms of their adequacy to patients' clinical conditions or targeted cognitive outcomes. This study aimed to identify GE applied...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103287
更新日期：2019-10-01 00:00:00
abstract：:Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which iden...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.01.003
更新日期：2015-04-01 00:00:00
abstract：:Protein name recognition aims to detect each and every protein names appearing in a PubMed abstract. The task is not simple, as the graphic word boundary (space separator) assumed in conventional preprocessing does not necessarily coincide with the protein name boundary. Such boundary disagreement caused by tokenizati...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2004.08.001
更新日期：2004-12-01 00:00:00
abstract：BACKGROUND:Data collection and extraction from noisy text sources such as social media typically rely on keyword-based searching/listening. However, health-related terms are often misspelled in such noisy text sources due to their complex morphology, resulting in the exclusion of relevant data for studies. In this pape...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.11.007
更新日期：2018-12-01 00:00:00
abstract：:The term registry is widely used to refer to any database storing clinical information collected as a byproduct of patient care. Despite the use of this single characterizing term (registry), these databases exist in various forms and support functions ranging from biomedical informatics and clinical research, to publ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.01.009
更新日期：2008-12-01 00:00:00
abstract：:An open research question when leveraging ontological knowledge is when to treat different concepts separately from each other and when to aggregate them. For instance, concepts for the terms "paroxysmal cough" and "nocturnal cough" might be aggregated in a kidney disease study, but should be left separate in a pneumo...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.01.002
更新日期：2012-06-01 00:00:00
abstract：:Social media has been identified as a promising potential source of information for pharmacovigilance. The adoption of social media data has been hindered by the massive and noisy nature of the data. Initial attempts to use social media data have relied on exact text matches to drugs of interest, and therefore suffer ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103307
更新日期：2019-11-01 00:00:00
abstract：BACKGROUND:The majority of current medical CBIR systems perform retrieval based only on "imaging signatures" generated by extracting pixel-level quantitative features, and only rarely has a feedback mechanism been incorporated to improve retrieval performance. In addition, current medical CBIR approaches do not routine...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.002
更新日期：2018-08-01 00:00:00
abstract：:In oncology, the reuse of data is confronted with the heterogeneity of terminologies. It is necessary to semantically integrate these distinct terminologies. The semantic integration by using a third terminology as a support is a conventional approach for the integration of two terminologies that are not very structur...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.08.013
更新日期：2017-10-01 00:00:00
abstract：OBJECTIVE:To classify and characterize the variables commonly used to measure the impact of Information Technology (IT) adoption in health care, as well as settings and IT interventions tested, and to guide future research. MATERIALS AND METHODS:We conducted a descriptive study screening a sample of 236 studies from a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.07.018
更新日期：2016-10-01 00:00:00
abstract：:Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public da...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.02.004
更新日期：2016-04-01 00:00:00
abstract：:While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architec...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.10.015
更新日期：2016-12-01 00:00:00
abstract：:The Breast Imaging Reporting and Data System (BI-RADS) was developed to reduce variation in the descriptions of findings. Manual analysis of breast radiology report data is challenging but is necessary for clinical and healthcare quality assurance activities. The objective of this study is to develop a natural languag...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.04.011
更新日期：2017-05-01 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：:The physical spaces within which the work of health occurs - the home, the intensive care unit, the emergency room, even the bedroom - influence the manner in which behaviors unfold, and may contribute to efficacy and effectiveness of health interventions. Yet the study of such complex workspaces is difficult. Health ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.07.007
更新日期：2015-10-01 00:00:00
abstract：:The centralized and public availability of molecular sequence and clinical trial data presents an opportunity to identify potentially valuable linkages across the bench-to-bedside "T1" translational barrier. In this study, we sought to leverage keyword metadata (Medical Subject Heading [MeSH] descriptors) to infer rel...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.10.003
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：:Three-dimensional (3D) visualization of preoperative and intraoperative medical information becomes more and more important in minimally invasive surgery. We develop a 3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display for surgeons to observe surgical...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.05.014
更新日期：2017-07-01 00:00:00
abstract：:The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function....
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.01.008
更新日期：2015-04-01 00:00:00
abstract：:We introduce a distance (similarity)-based mapping for the visualization of high-dimensional patterns and their relative relationships. The mapping preserves exactly the original distances between points with respect to any two reference patterns in a special two-dimensional coordinate system, the relative distance pl...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2004.07.005
更新日期：2004-10-01 00:00:00
abstract：:The development of convenient serum bioassays for cancer screening, diagnosis, prognosis, and monitoring of treatment is one of top priorities in cancer research community. Although numerous biomarker candidates have been generated by applying high-throughput technologies such as transcriptomics, proteomics, and metab...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.08.010
更新日期：2011-12-01 00:00:00
abstract：:Causal inference often relies on the counterfactual framework, which requires that treatment assignment is independent of the outcome, known as strong ignorability. Approaches to enforcing strong ignorability in causal analyses of observational data include weighting and matching methods. Effect estimates, such as the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103515
更新日期：2020-09-01 00:00:00
abstract：OBJECTIVE:Clinicians face numerous information needs during patient care activities and most of these needs are not met. Infobuttons are information retrieval tools that help clinicians to fulfill their information needs by providing links to on-line health information resources from within an electronic medical record...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.07.001
更新日期：2009-02-01 00:00:00
