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Biomedical informatics

Stuart Maudsley, Viswanath Devanarayan, Bronwen Martin, Hugo Geerts
Biomedical data sets are becoming increasingly larger and a plethora of high-dimensionality data sets ("Big Data") are now freely accessible for neurodegenerative diseases, such as Alzheimer's disease. It is thus important that new informatic analysis platforms are developed that allow the organization and interrogation of Big Data resources into a rational and actionable mechanism for advanced therapeutic development. This will entail the generation of systems and tools that allow the cross-platform correlation between data sets of distinct types, for example, transcriptomic, proteomic, and metabolomic...
March 15, 2018: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
Akanksha Juneja, Bharti Rana, R K Agrawal
BACKGROUND AND OBJECTIVES: Schizophrenia is a severe brain disorder primarily diagnosed through externally observed behavioural symptoms due to the dearth of established clinical tests. Functional magnetic resonance imaging (fMRI) can capture the distortions caused by schizophrenia in the brain activation. Hence, it can be useful for developing a decision model that performs computer-aided diagnosis of schizophrenia. But, fMRI data is huge in dimension. Therefore dimension reduction is indispensable...
March 2018: Computer Methods and Programs in Biomedicine
Igor F Tsigelny
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations...
February 9, 2018: Briefings in Bioinformatics
Anna Okula Basile, Marylyn DeRiggi Ritchie
For the past decade, the focus of complex disease research has been the genotype. From technological advancements to the development of analysis methods, great progress has been made. However, advances in our definition of the phenotype have remained stagnant. Phenotype characterization has recently emerged as an exciting area of informatics and machine learning. The copious amounts of diverse biomedical data that have been collected may be leveraged with data-driven approaches to elucidate trait-related features and patterns...
February 12, 2018: Expert Review of Molecular Diagnostics
Leslie Mertz
When Leonard D'Avolio (Figure 1) was working on his Ph.D. degree in biomedical informatics, he saw the power of machine learning in transforming multiple industries; health care, however, was not among them. "The reason that Amazon, Netflix, and Google have transformed their industries is because they have embedded learning throughout every aspect of what they do. If we could prove that is possible in health care too, I thought we would have the potential to have a huge impact," he says.
January 2018: IEEE Pulse
Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang
Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many drug knowledge bases have been constructed. They range from simple ones with specific focuses to comprehensive ones that contain information on almost every aspect of a drug. These curated drug knowledge bases have made significant contributions to the development of efficient and effective health information technologies for better health-care service delivery...
January 3, 2018: Briefings in Bioinformatics
Allen Flynn, Brent I Fox, Kevin A Clauson, Terry L Seaton, Elizabeth Breeden
Computerization is transforming health care while the quantity and complexity of biomedical knowledge rapidly grows. Today, all clinicians use health information technology (HIT), but only some pharmacists need to be cross-trained in "all" that advanced informatics entails so they can devise new and better information systems to support the pharmacy practice of the future. We propose a dual approach to informatics education in pharmacy: incorporate fundamental informatics education into pharmacy curricula for all students; and train some students interested in becoming informatics experts to design, develop, implement, and evaluate novel HIT for pharmacy...
November 2017: American Journal of Pharmaceutical Education
Izet Masic
Introduction: The International Academy of Health Sciences Informatics (IAHSI) is established by International Medical Informatics Association (IMIA) which is the world body for health and biomedical informatics. The Academy will serve as an honor society that recognizes expertise in biomedical and health informatics internationally. Academy membership will be one of the highest honors in the international field of biomedical and health informatics. Aim: To present scientometric analysis of founding members of the International Academy of Health Sciences Informatics, to evaluate members and their scientific rating...
December 2017: Acta Informatica Medica: AIM
Davide Chicco
Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects...
2017: BioData Mining
William M Southerland, S Joshua Swamidass, Philip R O Payne, Laura Wiley, ClarLynda Williams-DeVane
The Diversity and Disparity in Biomedical Informatics (DDBI) workshop will be focused on complementary and critical issues concerned with enhancing diversity in the informatics workforce as well as diversity in patient cohorts. According to the National Institute of Minority Health and Health Disparities (NIMHD) at the NIH, diversity refers to the inclusion of the following traditionally underrepresented groups: African Americans/Blacks, Asians (>30 countries), American Indian or Alaska Native, Native Hawaiian or Other Pacific Islander, Latino or Hispanic (20 countries)...
2018: Pacific Symposium on Biocomputing
Shefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta-Byrska Bishop, Christian Darabos
The analysis of large biomedical data often presents with various challenges related to not just the size of the data, but also to data quality issues such as heterogeneity, multidimensionality, noisiness, and incompleteness of the data. The data-intensive nature of computational genomics problems in biomedical informatics warrants the development and use of massive computer infrastructure and advanced software tools and platforms, including but not limited to the use of cloud computing. Our session aims to address these challenges in handling big data for designing a study, performing analysis, and interpreting outcomes of these analyses...
2018: Pacific Symposium on Biocomputing
Pengyue Zhang, Heng-Yi Wu, Chien-Wei Chiang, Lei Wang, Samar Binkheder, Xueying Wang, Donglin Zeng, Sara K Quinney, Lang Li
Drug interaction is a leading cause of adverse drug events and a major obstacle for current clinical practice. Pharmacovigilance data mining, pharmacokinetic modeling, and text mining are computation and informatic tools on integrating drug interaction knowledge and generating drug interaction hypothesis. We provide a comprehensive overview of these translational biomedical informatics methodologies with related databases. We hope this review illustrates the complementary nature of these informatic approaches and facilitates the translational drug interaction research...
February 2018: CPT: Pharmacometrics & Systems Pharmacology
Dong Xu, Alexandrea G Ham, Rickey D Tivis, Matthew L Caylor, Aoxiang Tao, Steve T Flynn, Peter J Economen, Hung K Dang, Royal W Johnson, Vaughn L Culbertson
In 2009 the U.S. Food and Drug Administration (FDA) placed a black box warning on metoclopramide (MCP) due to the increased risks and prevalence of tardive dyskinesia (TD). In this study, we developed a multi-step biomedical informatics screening (MSBIS) approach leveraging publicly available bioactivity and drug safety data to identify concomitant drugs that mitigate the risks of MCP-induced TD. MSBIS includes (1) TargetSearch ( bioinformatics scoring for drug anticholinergic activity using CHEMBL bioactivity data; (2) unadjusted odds ratio (UOR) scoring for indications of TD-mitigating effects using the FDA Adverse Event Reporting System (FAERS); (3) adjusted odds ratio (AOR) re-scoring by removing the effect of cofounding factors (age, gender, reporting year); (4) logistic regression (LR) coefficient scoring for confirming the best TD-mitigating drug candidates...
December 2017: EBioMedicine
Robin J Jacobs, Hassan Iqbal, Arif M Rana, Zaid Rana, Michael N Kane
Context: The advent of health information technology (HIT) tools can affect the practice of modern medicine in many ways, ideally by improving quality of care and efficiency and reducing medical errors. Future physicians will play a key role in the successful implementation of HIT. However, osteopathic medical students' willingness to learn, adopt, and use technology in a health care setting is not well understood. Objective: To understand osteopathic medical students' knowledge, attitudes, and behaviors regarding HIT and to identify factors that may be related to their readiness to use HIT...
December 1, 2017: Journal of the American Osteopathic Association
Joshua C Denny, Sara L Van Driest, Wei-Qi Wei, Dan M Roden
Drug development continues to be costly and slow, with medications failing due to lack of efficacy or presence of toxicity. The promise of pharmacogenomic discovery includes tailoring therapeutics based on an individual's genetic makeup, rational drug development, and repurposing medications. Rapid growth of large research cohorts, linked to electronic health record (EHR) data, fuels discovery of new genetic variants predicting drug action, supports Mendelian randomization experiments to show drug efficacy, and suggests new indications for existing medications...
March 2018: Clinical Pharmacology and Therapeutics
Devika Nadkarni, Imad Elhajj, Zaher Dawy, Hala Ghattas, Muhammad H Zaman
Conflict and the subsequent displacement of populations creates unique challenges in the delivery of quality health care to the affected population. Equitable access to quality care demands a multi-pronged strategy with a growing need, and role, for technological innovation to address these challenges. While there have been significant contributions towards alleviating the burden of conflict via data informatics and analytics, communication technology, and geographic information systems, little has been done within biomedical engineering...
2017: Conflict and Health
Rodolfo A Fiorini, Izet Masic
Only once we agree upon our understanding of what words really mean can we debate whether a concept, represented by those words, is or not well represented significantly in specific application. Conceptual clarity and predicative/impredicative competence are the fundamental components for managing information more effectively in Health Informatics, Healthcare and Medicine applications, while promoting innovation and creativity. Medicine was always the art and science of healing. The science became more and more a mechanistic technology in Healthcare; the art was dropped altogether...
September 2017: Acta Informatica Medica: AIM
Shane Wilson, Michael Fitzsimons, Martin Ferguson, Allison Heath, Mark Jensen, Josh Miller, Mark W Murphy, James Porter, Himanso Sahni, Louis Staudt, Yajing Tang, Zhining Wang, Christine Yu, Junjun Zhang, Vincent Ferretti, Robert L Grossman
The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers...
November 1, 2017: Cancer Research
Matthew K Breitenstein, Hongfang Liu, Kara N Maxwell, Jyotishman Pathak, Rui Zhang
Precision medicine is at the forefront of biomedical research. Cancer registries provide rich perspectives and electronic health record(EHR)s are commonly utilized to gather additional clinical data elements needed for translational research. However, manual annotation is resource-intense and not readily scalable. Informatics-based phenotyping presents an ideal solution, but perspectives obtained can be impacted by both data source and algorithm selection. We derived breast cancer(BC) receptor status phenotypes from structured and unstructured EHR data using rule-based algorithms, including natural language processing(NLP)...
October 30, 2017: Clinical and Translational Science
Fran├žois Fenaille, Pierre Barbier Saint-Hilaire, Kathleen Rousseau, Christophe Junot
Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions...
December 1, 2017: Journal of Chromatography. A
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