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Biomedical informatics

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https://www.readbyqxmd.com/read/27919732/learning-from-heterogeneous-temporal-data-in-electronic-health-records
#1
Jing Zhao, Panagiotis Papapetrou, Lars Asker, Henrik Boström
Electronic health records contain large amounts of longitudinal data that are valuable for biomedical informatics research. The application of machine learning is a promising alternative to manual analysis of such data. However, the complex structure of the data, which includes clinical events that are unevenly distributed over time, poses a challenge for standard learning algorithms. Some approaches to modeling temporal data rely on extracting single values from time series; however, this leads to the loss of potentially valuable sequential information...
December 2, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27913029/pharmacovigilance-and-biomedical-informatics-a-model-for-future-development
#2
Paul Beninger, Michael A Ibara
PURPOSE: The discipline of pharmacovigilance is rooted in the aftermath of the thalidomide tragedy of 1961. It has evolved as a result of collaborative efforts by many individuals and organizations, including physicians, patients, Health Authorities, universities, industry, the World Health Organization, the Council for International Organizations of Medical Sciences, and the International Conference on Harmonisation. Biomedical informatics is rooted in technologically based methodologies and has evolved at the speed of computer technology...
November 29, 2016: Clinical Therapeutics
https://www.readbyqxmd.com/read/27896988/precision-medicine-data-and-discovery-for-improved-health-and-therapy
#3
Alexander A Morgan, Dana C Crawford, Josh C Denny, Sean D Mooney, Bruce J Aronow, Steven E Brenner
The major goal of precision medicine is to improve human health. A feature that unites much research in the field is the use of large datasets such as genomic data and electronic health records. Research in this field includes examination of variation in the core bases of DNA and their methylation status, through variations in metabolic and signaling molecules, all the way up to broader systems level changes in physiology and disease presentation. Intermediate goals include understanding the individual drivers of disease that differentiate the cause of disease in each individual...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27881428/genome-transcriptome-and-proteome-the-rise-of-omics-data-and-their-integration-in-biomedical-sciences
#4
Claudia Manzoni, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, Raffaele Ferrari
Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine...
November 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27830261/nursing-informatics-certification-worldwide-history-pathway-roles-and-motivation
#5
Mollie R Cummins, Adi V Gundlapalli, Aditya V Gundlapalli, Peter Murray, Hyeoun-Ae Park, Christoph U Lehmann
INTRODUCTION: Official recognition and certification for informatics professionals are essential aspects of workforce development. OBJECTIVE: To describe the history, pathways, and nuances of certification in nursing informatics across the globe; compare and contrast those with board certification in clinical informatics for physicians. METHODS: (1) A review of the representative literature on informatics certification and related competencies for nurses and physicians, and relevant websites for nursing informatics associations and societies worldwide; (2) similarities and differences between certification processes for nurses and physicians, and (3) perspectives on roles for nursing informatics professionals in healthcare Results: The literature search for 'nursing informatics certification' yielded few results in PubMed; Google Scholar yielded a large number of citations that extended to magazines and other non-peer reviewed sources...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27810480/evaluation-of-relational-and-nosql-database-architectures-to-manage-genomic-annotations
#6
Wade L Schulz, Brent G Nelson, Donn K Felker, Thomas J S Durant, Richard Torres
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 architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized...
December 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27807753/network-based-biomedical-data-analysis
#7
Yuxin Lin, Xuye Yuan, Bairong Shen
Complex diseases are caused by disorders of both internal and external factors, and they account for a large proportion of human diseases. They are multigenetic and rarely a consequence of the dysfunction of single molecules. Systems biology views the living organism as an organic network. Compared with reductionism-based viewpoints, systems biology pays more attention to the interactions among molecules located at different omics levels. Based on this theory, the concepts of network biomarkers and network medicine have been proposed sequentially, which integrate clinical data with knowledge of network sciences, thereby promoting the investigation of disease pathogenesis in the era of biomedical informatics...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27807750/biobanks-and-their-clinical-application-and-informatics-challenges
#8
Lan Yang, Yalan Chen, Chunjiang Yu, Bairong Shen
Biobanks are one of the most important biomedical research resources and contribute to the development of biomarker detection, molecular diagnosis, translational medicine, and multidisciplinary disease research, as well as studies of interactions between genetic and environmental or lifestyle factors. Aiming for the wide clinical application of biobanks, biobanking efforts have recently switched from a focus on accumulating samples to both formalizing and sustaining collections in light of the rapid progress in the fields of personalized medicine and bioinformatics analysis...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27807745/informatics-for-metabolomics
#9
Kanthida Kusonmano, Wanwipa Vongsangnak, Pramote Chumnanpuen
Metabolome profiling of biological systems has the powerful ability to provide the biological understanding of their metabolic functional states responding to the environmental factors or other perturbations. Tons of accumulative metabolomics data have thus been established since pre-metabolomics era. This is directly influenced by the high-throughput analytical techniques, especially mass spectrometry (MS)- and nuclear magnetic resonance (NMR)-based techniques. Continuously, the significant numbers of informatics techniques for data processing, statistical analysis, and data mining have been developed...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27782291/person-generated-data-in-self-quantification-a-health-informatics-research-program
#10
Kathleen Gray, Fernando J Martin-Sanchez, Guillermo H Lopez-Campos, Manal Almalki, Mark Merolli
OBJECTIVES: The availability of internet-connected mobile, wearable and ambient consumer technologies, direct-to-consumer e-services and peer-to-peer social media sites far outstrips evidence about the efficiency, effectiveness and efficacy of using them in healthcare applications. The aim of this paper is to describe one approach to build a program of health informatics research, so as to generate rich and robust evidence about health data and information processing in self-quantification and associated healthcare and health outcomes...
October 26, 2016: Methods of Information in Medicine
https://www.readbyqxmd.com/read/27742664/a-bioimage-informatics-platform-for-high-throughput-embryo-phenotyping
#11
James M Brown, Neil R Horner, Thomas N Lawson, Tanja Fiegel, Simon Greenaway, Hugh Morgan, Natalie Ring, Luis Santos, Duncan Sneddon, Lydia Teboul, Jennifer Vibert, Gagarine Yaikhom, Henrik Westerberg, Ann-Marie Mallon
High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene-phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata...
October 14, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27697070/computational-approaches-for-translational-oncology-concepts-and-patents
#12
Marco Scianna, Luca Munaron
BACKGROUND: Cancer is a heterogeneous disease, which is based on an intricate network of processes at different spatiotemporal scales, from the genome to the tissue level. Hence the necessity for the biomedical and pharmaceutical research to work in a multiscale fashion. In this respect, a significant help derives from the collaboration with theoretical sciences. Indeed, mathematical models can provide insights into tumor-related processes and support clinical oncologists in the design of treatment regime, dosage, schedule and toxicity...
October 3, 2016: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/27696690/new-york-university-school-of-medicine-drug-development-educational-program-2-year-benchmark
#13
J Plaksin, R M Cymerman, R Caso Caso, C Galeano, R Ramasamy, G Gold-von Simson
Drug development (DD) is a multidisciplinary process that spans the translational continuum, yet remains an understudied entity in medical schools and biomedical science institutes. In response to a growing interest and unmet need, we implemented a DD course series that details identification of viable molecular targets, clinical trial design, intellectual property, and marketing. Enrollment is open to faculty, postdoctoral trainees, and MD, PhD, and MS students. After 2 years, 37 students and 23 students completed the fall and spring courses, respectively...
October 1, 2016: Clinical and Translational Science
https://www.readbyqxmd.com/read/27636203/latent-patient-cluster-discovery-for-robust-future-forecasting-and-new-patient-generalization
#14
Ting Qian, Aaron J Masino
Commonly referred to as predictive modeling, the use of machine learning and statistical methods to improve healthcare outcomes has recently gained traction in biomedical informatics research. Given the vast opportunities enabled by large Electronic Health Records (EHR) data and powerful resources for conducting predictive modeling, we argue that it is yet crucial to first carefully examine the prediction task and then choose predictive methods accordingly. Specifically, we argue that there are at least three distinct prediction tasks that are often conflated in biomedical research: 1) data imputation, where a model fills in the missing values in a dataset, 2) future forecasting, where a model projects the development of a medical condition for a known patient based on existing observations, and 3) new-patient generalization, where a model transfers the knowledge learned from previously observed patients to newly encountered ones...
2016: PloS One
https://www.readbyqxmd.com/read/27629872/an-information-model-for-computable-cancer-phenotypes
#15
Harry Hochheiser, Melissa Castine, David Harris, Guergana Savova, Rebecca S Jacobson
BACKGROUND: Standards, methods, and tools supporting the integration of clinical data and genomic information are an area of significant need and rapid growth in biomedical informatics. Integration of cancer clinical data and cancer genomic information poses unique challenges, because of the high volume and complexity of clinical data, as well as the heterogeneity and instability of cancer genome data when compared with germline data. Current information models of clinical and genomic data are not sufficiently expressive to represent individual observations and to aggregate those observations into longitudinal summaries over the course of cancer care...
2016: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/27612635/a-robust-data-scaling-algorithm-to-improve-classification-accuracies-in-biomedical-data
#16
Xi Hang Cao, Ivan Stojkovic, Zoran Obradovic
BACKGROUND: Machine learning models have been adapted in biomedical research and practice for knowledge discovery and decision support. While mainstream biomedical informatics research focuses on developing more accurate models, the importance of data preprocessing draws less attention. We propose the Generalized Logistic (GL) algorithm that scales data uniformly to an appropriate interval by learning a generalized logistic function to fit the empirical cumulative distribution function of the data...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27606313/neural-correlates-of-schizophrenia-negative-symptoms-distinct-subtypes-impact-dissociable-brain-circuits
#17
Joseph J Shaffer, Michael J Peterson, Mary Agnes McMahon, Joshua Bizzell, Vince Calhoun, Theo G M van Erp, Judith M Ford, John Lauriello, Kelvin O Lim, Dara S Manoach, Sarah C McEwen, Daniel H Mathalon, Daniel O'Leary, Steven G Potkin, Adrian Preda, Jessica Turner, Jim Voyvodic, Cynthia G Wible, Aysenil Belger
BACKGROUND: The negative symptoms of schizophrenia include deficits in emotional expression and motivation. These deficits are stable over the course of illness and respond poorly to current medications. Previous studies have focused on negative symptoms as a single category; however, individual symptoms might be related to separate neurological disturbances. We analyzed data from the Functional Biomedical Informatics Research Network dataset to explore the relationship between individual negative symptoms and functional brain activity during an auditory oddball task...
December 2015: Molecular Neuropsychiatry
https://www.readbyqxmd.com/read/27595045/identifying-plant-human-disease-associations-in-biomedical-literature-a-case-study
#18
Vivekanand Sharma, Wayne Law, Michael J Balick, Indra Neil Sarkar
The impact of ethnobotanical data from surveys of traditional medicinal uses ofplants can be enhanced through the validation of biomedical knowledge that may be embedded in literature. This study aimed to explore the use of informatics approaches, including natural language processing and terminology resources, for extracting and comparing ethnobotanical leads from biomedical literature indexed in MEDLINE. Using ethnobotanical data for plant species described in Primary Health Care Manuals of the Micronesian islands of Palau and Pohnpei, the results of this study were done relative to disease concepts from the "Mental, Behavioral And Neurodevelopmental Disorders " ICD-9-CM category...
2016: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/27587087/advancing-systems-biology-in-the-international-conference-on-intelligent-biology-and-medicine-icibm-2015
#19
Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology...
August 26, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27580922/automated-detection-of-discourse-segment-and-experimental-types-from-the-text-of-cancer-pathway-results-sections
#20
Gully A P C Burns, Pradeep Dasigi, Anita de Waard, Eduard H Hovy
Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data...
2016: Database: the Journal of Biological Databases and Curation
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