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Biomedical informatics

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
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
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
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
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
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
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
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
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...
2016: BMC Systems Biology
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
Matthias Löbe, Thomas Ganslandt, Lydia Lotzmann, Sebastian Mate, Jan Christoph, Benjamin Baum, Murat Sariyar, Jie Wu, Sebastian Stäubert
Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious...
2016: Studies in Health Technology and Informatics
Christian R Bauer, Nadine Umbach, Benjamin Baum, Karoline Buckow, Thomas Franke, Romanus Grütz, Linda Gusky, Sara Yasemin Nussbeck, Matthias Quade, Sabine Rey, Thorsten Rottmann, Otto Rienhoff, Ulrich Sax
In University Medical Centers, heterogeneous data are generated that cannot always be clearly attributed to patient care or biomedical research. Each data set has to adhere to distinct intrinsic and operational quality standards. However, only if high-quality data, tools to work with the data, and most importantly guidelines and rules of how to work with the data are addressed adequately, an infrastructure can be sustainable. Here, we present the IT Research Architecture of the University Medical Center Göttingen and describe our ten years' experience and lessons learned with infrastructures in networked medical research...
2016: Studies in Health Technology and Informatics
Joseph D Romano, Nicholas P Tatonetti
Venoms and venom-derived compounds constitute a rich and largely unexplored source of potentially therapeutic compounds. To facilitate biomedical research, it is necessary to design a robust informatics infrastructure that will allow semantic computation of venom concepts in a standardized, consistent manner. We have designed an ontology of venom-related concepts - named Venom Ontology - that reuses an existing public data source: UniProt's Tox-Prot database. In addition to describing the ontology and its construction, we have performed three separate case studies demonstrating its utility: (1) An exploration of venom peptide similarity networks within specific genera; (2) A broad overview of the distribution of available data among common taxonomic groups spanning the known tree of life; and (3) An analysis of the distribution of venom complexity across those same taxonomic groups...
2016: AMIA Summits on Translational Science Proceedings
Mark L Homer, Nathan P Palmer, Olivier Bodenreider, Aurel Cami, Laura Chadwick, Kenneth D Mandl
In biomedical informatics, assigning drug codes to categories is a common step in the analysis pipeline. Unfortunately, incomplete mappings are the norm rather than the exception with coverage values less than 85% not uncommon. Here, we perform this linking task on a nationwide insurance claims database with over 13 million members who were dispensed, according to National Drug Codes (NDCs), over 50,000 unique product forms of medication. The chosen approach employs Cerner Multum's VantageRx and the U.S. National Library of Medicine's RxMix...
2016: AMIA Summits on Translational Science Proceedings
Hossein Estiri, Terri Lovins, Nader Afzalan, Kari A Stephens
We applied a participatory design approach to define the objectives, characteristics, and features of a "data profiling" tool for primary care Electronic Health Data (EHD). Through three participatory design workshops, we collected input from potential tool users who had experience working with EHD. We present 15 recommended features and characteristics for the data profiling tool. From these recommendations we derived three overarching objectives and five properties for the tool. A data profiling tool, in Biomedical Informatics, is a visual, clear, usable, interactive, and smart tool that is designed to inform clinical and biomedical researchers of data utility and let them explore the data, while conveniently orienting the users to the tool's functionalities...
2016: AMIA Summits on Translational Science Proceedings
Sonal Kothari, Hang Wu, Li Tong, Kevin E Woods, May D Wang
Biomedical in vivo imaging has been playing an essential role in diagnoses and treatment in modern medicine. However, compared with the fast development of medical imaging systems, the medical imaging informatics, especially automated prediction, has not been fully explored. In our paper, we compared different feature extraction and classification methods for prediction pipeline to analyze in vivo endomicroscopic images, obtained from patients who are at risks for the development of gastric disease, esophageal adenocarcionoma...
February 2016: ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics
Edward H Shortliffe
No abstract text is available yet for this article.
October 17, 2016: Methods of Information in Medicine
Najeeb Al-Shorbaji, Riccardo Bellazzi, Fernan Gonzalez Bernaldo de Quiros, Sabine Koch, Casimir A Kulikowski, Nigel H Lovell, Victor Maojo, Hyeoun-Ae Park, Ferran Sanz, Indra N Sarkar, Hiroshi Tanaka
This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "The New Role of Biomedical Informatics in the Age of Digital Medicine" written by Fernando J. Martin-Sanchez and Guillermo H. Lopez-Campos [1]. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the paper of Martin-Sanchez and Lopez-Campos. In subsequent issues the discussion can continue through letters to the editor.
October 17, 2016: Methods of Information in Medicine
Fernando J Martin-Sanchez, Guillermo H Lopez-Campos
OBJECTIVES: To reflect on the recent rise of Digital Medicine, as well as to analyse main research opportunities in this area. Through the use of several examples, this article aims to highlight the new role that Biomedical Informatics (BMI) can play to facilitate progress in research fields such as participatory and precision medicine. This paper also examines the potential impact and associated risks for BMI due to the development of digital medicine and other recent trends. Lastly, possible strategies to place BMI in a better position to face these challenges are suggested...
October 17, 2016: Methods of Information in Medicine
Kirk Roberts, Mary Regina Boland, Lisiane Pruinelli, Jina Dcruz, Andrew Berry, Mattias Georgsson, Rebecca Hazen, Raymond F Sarmiento, Uba Backonja, Kun-Hsing Yu, Yun Jiang, Patricia Flatley Brennan
The field of biomedical informatics experienced a productive 2015 in terms of research. In order to highlight the accomplishments of that research, elicit trends, and identify shortcomings at a macro level, a 19-person team conducted an extensive review of the literature in clinical and consumer informatics. The result of this process included a year-in-review presentation at the American Medical Informatics Association Annual Symposium and a written report (see supplemental data). Key findings are detailed in the report and summarized here...
August 7, 2016: Journal of the American Medical Informatics Association: JAMIA
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