Abstract：
:The ultimate goal of genomics research is to describe the network of molecules and interactions that govern all biological functions and disease processes in cells. Nonlinear interactions among genes in terms of their logic relationships play a key role for deciphering the networks of molecules that underlie cellular function. We present a method based on a graph coloring scheme and information theory to identify the gene expression network with lower and higher order logic interactions of genes. The analysis of oncogenes and suppressor genes from a colon cancer mRNA microarray dataset identifies a gene expression network with directionality and weights that reflects intracellular communication pathways. The success of the proposed method in mining hidden, complicated gene interactions and reliably interpreting experimental results suggests that the proposed method is a useful tool for understanding cancer systems. Extension of this method holds the potential to be fruitful for understanding other complex, nonsymmetric systems.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Ruan X,Wang J,Li H,Perozzi RE,Perozzi EFdoi
10.1016/j.jbi.2007.11.006subject
Has Abstractpub_date
2008-08-01 00:00:00pages
530-43issue
4eissn
1532-0464issn
1532-0480pii
S1532-0464(07)00143-8journal_volume
41pub_type
杂志文章abstract：:As a result of recent advances in cancer research and "precision medicine" approaches, i.e. the idea of treating each patient with the right drug at the right time, more and more cancer patients are being cured, or might have to cope with a life with cancer. For many people, cancer survival today means living with a c...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103342
更新日期：2020-01-01 00:00:00
abstract：:Identification of co-referent entity mentions inside text has significant importance for other natural language processing (NLP) tasks (e.g. event linking). However, this task, known as co-reference resolution, remains a complex problem, partly because of the confusion over different evaluation metrics and partly beca...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.03.007
更新日期：2013-06-01 00:00:00
abstract：:Methods for surveillance of adverse events (AEs) in clinical settings are limited by cost, technology, and appropriate data availability. In this study, two methods for semi-automated review of text records within the Veterans Administration database are utilized to identify AEs related to the placement of central ven...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.06.003
更新日期：2007-04-01 00:00:00
abstract：OBJECTIVE:The timely acknowledgement of critical patient clinical reports is vital for the delivery of safe patient care. With current EHR systems, critical reports reside on different screens. This leads to treatment delays and inefficient work flows. As a remedy, the R.A.P.I.D. (Root Aggregated Prioritized Informatio...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,随机对照试验
doi：10.1016/j.jbi.2016.04.001
更新日期：2016-06-01 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：: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：:Chronic patients must carry out a rigorous control of diverse factors in their lives. Diet, sport activity, medical analysis or blood glucose levels are some of them. This is a hard task, because some of these controls are performed very often, for instance some diabetics measure their glucose levels several times eve...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.12.015
更新日期：2014-04-01 00:00:00
abstract：:CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.03.010
更新日期：2015-06-01 00:00:00
abstract：:This study examines the ability of nonclinical adverse event observations to predict human clinical adverse events observed in drug development programs. In addition it examines the relationship between nonclinical and clinical adverse event observations to drug withdrawal and proposes a model to predict drug withdraw...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.02.008
更新日期：2015-04-01 00:00:00
abstract：:Hypotheses of homology are the basis of phylogenetic analysis. All character data are considered to be equivalent regardless of the source of those characters. Putative homology statements are designated based on observations of similarity. Pairwise sequence alignment using the Needleman-Wunsch algorithm is the basis ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2005.11.005
更新日期：2006-02-01 00:00:00
abstract：:Epidemiological time series forecasting plays an important role in health public systems, due to its ability to allow managers to develop strategic planning to avoid possible epidemics. In this paper, a hybrid learning framework is developed to forecast multi-step-ahead (one, two, and three-month-ahead) meningitis cas...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103575
更新日期：2020-11-01 00:00:00
abstract：:Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.06.005
更新日期：2011-12-01 00:00:00
abstract：:Drug therapeutic indications and side-effects are both measurable patient phenotype changes in response to the treatment. Inferring potential drug therapeutic indications and identifying clinically interesting drug side-effects are both important and challenging tasks. Previous studies have utilized either chemical st...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.03.014
更新日期：2014-10-01 00:00:00
abstract：:Big data technologies are critical to the medical field which requires new frameworks to leverage them. Such frameworks would benefit medical experts to test hypotheses by querying huge volumes of unstructured medical data to provide better patient care. The objective of this work is to implement and examine the feasi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.12.005
更新日期：2016-02-01 00:00:00
abstract：:We describe the process of introducing RFID technology in the trauma bay of a trauma center to support fast-paced and complex teamwork during resuscitation. We analyzed trauma resuscitation tasks, photographs of medical tools, and videos of simulated resuscitations to gain insight into resuscitation tasks, work practi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.04.003
更新日期：2012-10-01 00:00:00
abstract：:In Electronic Health Records (EHRs), much of valuable information regarding patients' conditions is embedded in free text format. Natural language processing (NLP) techniques have been developed to extract clinical information from free text. One challenge faced in clinical NLP is that the meaning of clinical entities...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.02.010
更新日期：2015-04-01 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：: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：: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：:Real-time Obstructive Sleep Apnea (OSA) episode detection and monitoring are important for society in terms of an improvement in the health of the general population and of a reduction in mortality and healthcare costs. Currently, to diagnose OSA patients undergo PolySomnoGraphy (PSG), a complicated and invasive test ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.02.015
更新日期：2014-06-01 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：:We address the assignment of ICD-10 codes for causes of death by analyzing free-text descriptions in death certificates, together with the associated autopsy reports and clinical bulletins, from the Portuguese Ministry of Health. We leverage a deep neural network that combines word embeddings, recurrent units, and neu...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.02.011
更新日期：2018-04-01 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：RATIONALE:Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. METHODS:The tw...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.07.019
更新日期：2017-07-01 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：OBJECTIVE:Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evidence used for synthesizing systematic reviews or practicing Evidence Based Medicine (EBM). Finding all relevant published evidence for a particular medical case is a time and labour intensiv...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103321
更新日期：2019-12-01 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：:Automated software for cancer registration, called Open Registry and developed by ourselves was adopted by the Varese (population-based) Cancer Registry starting from 1997. Since the use of automated cancer registration is increasing, it is important to assess the quality and completeness of the automated data being p...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2007.03.003
更新日期：2008-02-01 00:00:00
abstract：:Evaluating automated indexing applications requires comparing automatically indexed terms against manual reference standard annotations. However, there are no standard guidelines for determining which words from a textual document to include in manual annotations, and the vague task can result in substantial variation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2005.06.004
更新日期：2006-04-01 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
