Introduction: The genome of the most well studied eukaryotic model organism, Saccharomyces cerevisiae strain S288c, was sequenced and released in 1996; it was the first complete, high quality genome sequence of an eukaryal organism (1). Since then, the development ofDNAsequencing technologies has yielded scientific breakthroughs that enable us to obtain and analyze genomic DNA sequences […]
Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)
http://onlinelibrary.wiley.com/doi/10.1002/ece3.3638/full Ecology and Evolution, (2018), 8:185-196. DOI: 10.1002/ece3.3638 Michael S. Robeson II, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio Abstract Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to […]
13: The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge
Stud Health Technol Inform. 2018;249:38-49 Brochhausen M, Bona J, Blobel B Abstract In the biomedical domain, there exist a number of common data models (CDM) that have experienced wide uptake. However, none of these has emerged as the common model. Recently, the demand for integrating and analyzing increasingly large data sets in clinical and translational research […]
dBBQs: dataBase of Bacterial Quality scores
Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David Ussery From The 14th Annual MCBIOS Conference Little Rock, AR, USA. 23-25 March 2017 Abstract Background: It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore […]
Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?
Se-Ran Jun, Trudy M. Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David W. Ussery. © The Author(s). 2017 Published: 28 December 2017 Abstract Background Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological […]
Need an app for research?
The Department of Biomedical Informatics, the UAMS TRI and BioVentures, LLC is hosting an event next week to introduce clinicians and researchers to the resources we have on campus that are available to develop mobile and wearable technologies/apps. Come to the event, hear some quick presentations and talk to developers and potential collaborators about your […]
Department of Biomedical Informatics at AMIA 2017 Annual Symposium
The Department of Biomedical Informatics (DBMI) at University of Arkansas for Medical Sciences (UAMS) presented its expanded graduate educational offerings in Biomedical Informatics. The expanded program includes a graduate certificate, as well as Master of Science, and Doctor of Philosophy degrees across four tracks: Translational Bioinformatics Imaging Informatics Clinical Informatics Clinical Research Informatics Drs. Meredith […]
Arkansas Clinical Data Repository (AR-CDR)
The Arkansas Clinical Data Repository (AR-CDR) is a research data warehouse that provides a single and secure source of data for use in clinical and translational research. Since its launch in 2011, the AR-CDR has enabled UAMS researchers and faculty to conduct high quality, timely and efficient clinical and translational research. The AR-CDR houses data […]
Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics
https://doi.org/10.1016/j.ygeno.2017.03.001 Subazini Thankaswamy-Kosalai, Partho Sen, Intawat Nookaew Abstract Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, […]
Arkansas Center for Genomic & Ecological Medicine (ArC-GEM)
Under Dr. David Ussery’s leadership, the Arkansas Center for Genomic & Ecological Medicine’s (ArC-GEM) work in third-generation sequencing has exciting potential applications for a range of emerging infections, including current collaboration with the Arkansas Department of Health on a project that could lead to rapid diagnosis of the Zika virus. Biomedical informatics extracts knowledge from […]