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2024 CCTS Spring Conference | Register by March 31
Apr 9, 2024 |8 a.m. - 5 p.m. |Central Bank Center in Lexington, Ky
The 19th Annual Center for Clinical and Translational Science (CCTS) Spring Conference theme is "Dissemination and Implementation across the Translational Spectrum".
Hundreds of researchers, clinicians, research staff, students, and community members will gather to share findings and foster collaborations.
Learn more → Informatics Research Day
Help Me Perfect My Research: Training for the Advanced REDCap User
Apr 2, 2024 | 11:00 AM
Presenter: Brent Seeders, REDCap Liaison, CCTS Biomedical Informatics Core (via Zoom)
VPR Lunch and Learn Series
Mar 20, 2024 | 12:00PM
Dynamic and transdisciplinary research ideas from UK’s Research Scholars Program faculty. All Lunch and Learn workshops are on zoom on Wednesdays.
Presenters: Kevin Pearson and Nancy Schoenberg (RSP Co-directors) and participants in the Research Scholars Program:
- Deirdre Dlugonski (Assistant Professor, Sports Medicine Research Institute)
- Yasminka Jakubek (Assistant Professor, Internal Medicine)
- Anel Jaramillo (Assistant Professor, Pharmaceutical Sciences)
- Jayani Jayawardhana (Associate Professor, Health Management and Policy)
- Courtney Perry (Assistant Professor, Internal Medicine)
- Rosana Zenil-Ferguson (Assistant Professor, Biology)
UK IBI team to be published in Prestigious Journal
Mar 18, 2024
The UK IBI team working with the Office of Data Analytics (ODA) has had an article accepted for publication in the journal of Medical Care. The article entitled, “Delivering the Right Care, at the Right Time, in the Right Place, from the Right Pocket: How the Wrong Pocket Problem Stymies Medical Respite Care for the Homeless, and What Can Be Done About It” was written by Dr. Matthew Walton, Darby Todd, Jake Mackie, and Ben Duncan. The article discusses Medical respite care (MRC) and how the creation of two new operational MRC units came to be - one in Louisville at a site called Hotel Louisville and the other in Covington at a homeless shelter called Welcome House of Northern Kentucky. This began with an analytical request to ODA from the Homeless and Housing Coalition of Kentucky (HHCK) and University of Louisville School of Public Health and Information Sciences (ULSPHIS) to determine the scope of the problem at hand, and later evolved into advocacy for the MRCs’ creation.
Harris, Delcher, Anthony win $50k DataWorks! Challenge Prize
Feb 26, 2024
A team consisting of Dr. Daniel Harris, Dr. Chris Delcher, and Nick Anthony has won a $50,000 prize as part of the 2023 DataWorks! Challenge sponsored by the Federation of American Societies for Experimental Biology (FASEB) and the National Institutes of Health. The 2023 DataWorks! Challenge judged data science submissions focused on tools and projects dedicated to data sharing and data reuse. Harris’s team submitted their open-source tool, geoPIPE, which acts as a pipeline for enriching open data streams with geospatial analyses and natural language processing. The team was the top-ranking entry in the data reuse category.
New Faculty Daniel Harris Joins IBI
Feb 16, 2024
Dr. Daniel Harris is a computer scientist with an interest in biomedical informatics. His research focuses on expanding the role of informatics in clinical data warehouses; in particular, he is interested in helping foster a more productive and useful data warehouse by leveraging the latest research and tools in natural language processing, visualization, and geospatial analysis. He has research interests in using these platforms to explore and understand social determinants of health. Dr. Harris contributes this expertise to research projects responding to the opioid crisis that disproportionately impacts Kentucky.
Markey study paves way for solutions to boost pediatric clinical trial enrollment
Feb 9, 2024
Every year in the U.S., about 15,000 children and teens under 20 are diagnosed with cancer. Yet, most don't get a chance to participate in clinical trials, which offer the newest, most promising treatments and improve patient outcomes.
A new University of Kentucky Markey Cancer Center study published in JCO Oncology Practice sheds light on this disparity and paves the way for solutions to increase clinical trial participation among young patients with cancer.
Co-led by Eric Durbin, Dr.P.H., director of the Kentucky Cancer Registry and Cancer Research Informatics Shared Resource Facility at the UK Markey Cancer Center, the research demonstrates the feasibility of linking central cancer registry and pediatric cancer clinical trial consortium data to track patients and describe gaps in clinical trial enrollment. The research is being used to guide a nationwide linkage study between the National Childhood Cancer Registry and the Children’s Oncology Group (COG).
Eric Durbin Selected to Collaborate on Interoperability between NCI US and NCI France
Nov. 2023
BMI faculty member, Eric Durbin, was selected by the National Cancer Institute (NCI) to help facilitate strategic planning for interoperability at the Paris Conference for an International Childhood Cancer Data Partnership in November, 2023. This represents a new and burgeoning collaboration between the U.S. NCI and the National Cancer Institute of France with the overarching goal of integrating and pooling of international data needed to advance the breadth and depth of childhood cancer research on these rare and ultra-rare tumors. Durbin co-led workshop discussions to identify barriers, potential solutions, and next steps to advance international data interoperability.
https://iccdp-parisconference.com
Paper on Diffusion CT wins distinguished 2023 AMIA Homer Warner Award
Nov 17, 2023
The Homer R. Warner Award is named for Homer R. Warner, MD, PhD, a pioneer in the field of informatics and the founder of the Department of Medical Informatics at the University of Utah. A cash prize is awarded for the AMIA Annual Symposium paper chosen that best describes approaches to improving computerized information acquisition, knowledge data acquisition and management, and experimental results documenting the value of these approaches. The candidate papers are drawn from the distinguished paper nominees and the selection of the recipient is made by the University of Utah Department of Biomedical Informatics.
DiffusionCT: Latent Diffusion Model for CT Image Standardization; M.D. Selim, Jie Zhang, Michael A. Brooks, G.E. Wang, Jin Chen (University of Kentucky and Rensselar Polytechnic Institute.
Telehealth Supports Retention in Treatment for Opioid Use Disorder
Oct 23, 2023
Federally funded study provides additional evidence supporting expanded use of telehealth services for opioid use disorder-related care.
“Our study suggests that people who have access to telehealth treatment for addiction seem to do better than those who do not. Our hope is that these findings can help inform future policy,” said Lindsey Hammerslag, Ph.D., assistant professor at the University of Kentucky and lead author on the study. “In addition, the findings also emphasize that the benefits of telehealth are not reaching all populations equitably. As we continue to integrate telehealth into standard care, we must also investigate and address the barriers that are preventing people from accessing this helpful and effective form of treatment for opioid use disorder.”
Become a CCTS Research Data Navigator for your Department
Oct 16, 2023
The Center for Clinical & Translational Science and the Institute for Biomedical Informatics is launching a new Research Data Navigator program. The program will have extensive hands-on instruction (estimated 94 hours over 3 months) in HIPAA Privacy, Data Governance, Research Design, How to work with Statisticians, Review of the data structure, work flow and regulatory compliance procedures, hands on consultations with researchers, shadowing experiences with existing honest brokers, writing data specifications and SQL code for data extractions, as well as, performing secondary reviews of code. Demonstrations and training on EPIC Slicer Dicer and COSMOS tools will also be available.
If becoming a Research Data Navigator for your College and/or Department sounds interesting, please discuss the commitment with your supervisor. The first cohort will begin November 1st and will end February 9th.
To apply to the program, please complete the Application and SQL coding test. Apply here
7th Annual Commonwealth Computational Summit
Oct 3, 2023
The University of Kentucky’s Center for Computational Science (CCS) and ITS/Research Computing Infrastructure is hosting the 7th Annual Commonwealth Computational Summit (CCS) on October 16-17, 2023, focused on AI in Education, Medicine, and Research. Location: Gatton Student Center Ballroom and Conference Facilities, University of Kentucky, 160 Avenue of Champions, Lexington, KY 40508.
This “LIVE” two-day Summit event will take place at the University of Kentucky Gatton Student Center Ballroom and meeting facilities. If you are interested in any aspect of Artificial Intelligence, research or education, methods, tools, or technologies, including generative AI, machine learning, deep learning and neural networks, expert systems and decision support, autonomous control, robotics, natural language processing, textual analysis, image recognition, speech recognition, large language models, virtual agents, or chatbots, then come join us at the Commonwealth Computational Summit! This event is open to all university faculty and graduate students across the Commonwealth (and our region) as well as to industry professionals. And it is FREE!
October 16-17, 2023 AI in Education, Medicine, and Research
October 16 – AI in Education & Industry Day – Tech Talks, Tutorials and Workshops
October 17 – Keynotes, AI in Research, AI in Medicine, Poster Competition
Note: Both days will offer a continental breakfast, lunch, break refreshments, and a closing day reception.
More information on Summit web pages – sign up for FREE! https://summit.ccs.uky.edu/ccs_summit/
IBI Launches New Center for Applied Artificial Intelligence
Sept 29, 2023
The Center for Applied Artificial Intelligence (CAAI) within the UK Institute for Biomedical Informatics launched today from the past two years of effort in the Artificial Intelligence in Medicine Alliance. The Alliance brought together researchers across campus to explore the potential of AI to transform healthcare. The establishment of CAAI will allow us to build on this foundation and accelerate AI innovation and translation.
CAAI will focus on developing AI tools for improving disease diagnosis, treatment personalization, clinical workflow optimization, and more. Potential high impact application areas include medical imaging, digital pathology, population health informatics, and precision medicine. We believe AI holds immense promise to augment clinician capabilities, increase access to care, reduce costs, and ultimately improve patient outcomes.
Under the leadership of Dr. Cody Bumgardner as Director, CAAI will host collaborative projects, share computing resources, provide educational opportunities, and foster an interdisciplinary community of AI researchers. We aim to develop strong partnerships between our clinicians, basic scientists, informaticians, and engineers to drive impactful work.
CAAI will build on existing strengths at our academic medical center while expanding the scope of AI application. We are excited by the breadth of talent and potential at UK to be leaders in validating, translating, and ethically implementing AI technologies. Please reach out if you are interested in learning more and participating in CAAI activities. Together we can harness AI to solve major challenges in 21st century medicine and healthcare.
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data
Jul 23, 2023
Christian D. Powell & Hunter N. B. Moseley. BMC Bioinformatics volume 24, Article number: 299 (2023).
An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.
MESSES: Software for Transforming Messy Research Datasets into Clean Submissions to Metabolomics Workbench for Public Sharing
Jul 12, 2023
P. Travis Thompson1 and Hunter N. B. Moseley. Metabolites 2023, 13(7), 842; https://doi.org/10.3390/metabo13070842
In recent years, the FAIR guiding principles and the broader concept of open science has grown in importance in academic research, especially as funding entities have aggressively promoted public sharing of research products. Key to public research sharing is deposition of datasets into online data repositories, but it can be a chore to transform messy unstructured data into the forms required by these repositories. To help generate Metabolomics Workbench depositions, we have developed the MESSES (Metadata from Experimental SpreadSheets Extraction System) software package, implemented in the Python 3 programming language and supported on Linux, Windows, and Mac operating systems. MESSES helps transform tabular data from multiple sources into a Metabolomics Workbench specific deposition format. The package provides three commands, extract, validate, and convert, that implement a natural data transformation workflow. Moreover, MESSES facilitates richer metadata capture than is typically attempted by manual efforts. The source code and extensive documentation is hosted on GitHub and is also available on the Python Package Index for easy installation.
New faculty Yuan Wen joins IBI
Jul 01, 2023
We would like to welcome Dr. Yuan Wen, PhD, Assistant Professor in the Division of Biomedical Informatics, Department of Internal Medicine. Dr. Wen's career goal is to develop novel and effective tools and therapeutics so that more people can be cured faster. He started out as a chemist at the University of Pennsylvania before coming back to UK, where he graduated from the MD/PhD Program in 2020. Currently, Dr. Wen is focused on the application of computation and AI technologies to improve medical care for patients. His research program mainly includes molecular mechanisms of protein synthesis, cellular physiology, and animal models of health and disease. The plan is to extend the findings from these projects into translational and clinical applications to benefit patients in the ICU or suffering from genetic diseases such as muscular dystrophy.
New faculty Cody Steely joins IBI
Jul 01, 2023
We would like to welcome Dr. Cody Steely, PhD, Assistant Professor in the Division of Biomedical Informatics, Department of Internal Medicine. His work is focused on using sequencing data and bioinformatics to study age-related disorders like neurodegeneration and cancer. Dr. Steely is currently working to understand how the genome changes as individuals age and how the somatic mutations accrued over time might impact disease risk. Dr. Steely is also interested in the role of repetitive DNA (transposable elements and tandem repeats) in Alzheimer’s Disease and cancer.
A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data
Jun 23, 2023
Rance Nault, Matthew C. Cave, Gabriele Ludewig, Hunter N.B. Moseley, Kelly G. Pennell, and Tim Zacharewski
Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise.
A proposed FAIR approach for disseminating geospatial information system maps
Jun 16, 2023
P. Travis Thompson, Sweta Ojha, Christian D. Powell, Kelly G. Pennell & Hunter N. B. Moseley. Scientific Data volume 10, Article number: 389 (2023).
We present a draft Minimum Information About Geospatial Information System (MIAGIS) standard for facilitating public deposition of geospatial information system (GIS) datasets that follows the FAIR (Findable, Accessible, Interoperable and Reusable) principles. The draft MIAGIS standard includes a deposition directory structure and a minimum javascript object notation (JSON) metadata formatted file that is designed to capture critical metadata describing GIS layers and maps as well as their sources of data and methods of generation. The associated miagis Python package facilitates the creation of this MIAGIS metadata file and directly supports metadata extraction from both Esri JSON and GEOJSON GIS data formats plus options for extraction from user-specified JSON formats. We also demonstrate their use in crafting two example depositions of ArcGIS generated maps. We hope this draft MIAGIS standard along with the supporting miagis Python package will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community as well as a future public repository for GIS datasets.
Students@SC Chair Sally Ellingson Shines Her Guiding Light
Apr 11, 2023
The Students@SC program is a perfect example of what SC is all about – bringing people together to talk tech. Open to everyone from high school to graduate students, the program provides vital career-growing tools, such as a job fair, alumni networking event, various workshops and skill-building activities, and so much more.
Rama Kavuluru receives best paper award at IEEE ICHI
Mar 29, 2023
The 11th IEEE International Conference on Healthcare Informatics awarded Dr. Kavuluru's article entitled, "End-to-End n-ary Relation Extraction for Combination Drug Therapies" as best paper.
Relations linking various biomedical entities constitute a crucial resource that enables biomedical data science applications and knowledge discovery. Relational information spans the translational science spectrum going from biology (e.g., protein–protein interactions) to translational bioinformatics (e.g., gene–disease associations), and eventually to clinical care (e.g., drug–drug interactions). Scientists report newly discovered relations in nat- ural language through peer-reviewed literature and physicians may communicate them in clinical notes. More recently, patients are also reporting side-effects and adverse events on social media. With exponential growth in textual data, advances in biomedical natural language processing (BioNLP) methods are gaining prominence for biomedical relation extraction (BRE) from text.
Sally Ellingson, Ph.D., is a computational scientist working at the intersection of computational biology and high-performance computing.
Mar 15, 2023
Throughout March, the University of Kentucky is spotlighting Women Making History during Women’s History Month. These women are leading their fields of research and impacting the lives of Kentuckians.
Their work addresses key issues impacting the Commonwealth, like cancer, Alzheimer’s disease and diabetes. They also offer new perspectives on history by finding ways to preserve our collective memory and better understand it.
When you think of how scientists test new drugs to fight cancers, you probably think of a traditional lab setting. However, one UK researcher is using computers to evaluate how those drugs work in the body.
kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes
Mar 4, 2023
Erik Huckvale & Hunter N. B. Moseley. BMC Bioinformatics volume 24, Article number: 78 (2023).
The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and reusable (FAIR) by providing RESTful access to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software package support available in a given programming language. While R library support for KEGG is fairly strong, Python library support has been lacking. Moreover, there is no software that provides extensive command line level support for KEGG access and utilization.
New faculty Yasminka Jakubek Swartzlander joins 3rd cohort of the Research Scholars Program
Mar 01, 2023
We welcome Yasminka Jakubek Swartzlander to the third cohort of the Research Scholars Program (RSP). The program is aimed at ensuring diversity, equity and inclusion in research by promoting faculty success.
Eric Durbin's research seeks to understand Appalachia’s childhood cancer disparity
Feb 07, 2023
When Eric Durbin, Dr.PH., director of the Cancer Research Informatics Shared Resource Facility at the University of Kentucky Markey Cancer Center, began mapping childhood cancer incidence rates, he noticed a troubling trend: Brain cancer rates appeared to be higher in the Appalachian region of Kentucky. That led Durbin, who is also the director of the Kentucky Cancer Registry, to conduct a broader study that looked at all childhood brain cancers across the U.S. The goal of this study was to see if there were differences between Appalachian children and children outside Appalachia.
Kavuluru becomes chartered member of NIH study section
Jul 05, 2022
Ramakanth (Rama) Kavuluru, PhD, Associate Professor, has become a chartered member of the National Institute of Health’s Clinical Data Management and Analysis (CDMA) Study Section. This study section meets three times a year to review grant applications that "develop computing technology, simulation/data models, data analytics, and technical software intended for eventual translation of research or novel findings for clinical use.” His term will expire in 2026.
Dr. George Shih delivers keynote address at AIM Summit 2022
May 17, 2022
On April 20, 2022, the AIM Alliance hosted the inaugural AIM Summit, a half-day conference focusing on AI in Medicine. Dr. George Shih from Weill Cornell Medicine addressed the inaugural AIM Summit as the keynote speaker and delivered his presentation "AI Bias and Fairnes"
AI in Medicine Alliance announces AIM Summer Undergraduate Research Fellowship
Mar 11, 2022
The AIM Fellowship, sponsored by the AI in Medicine (AIM) Alliance, Institute for Biomedical Informatics (IBI), and UK Center for Clinical and Translational Science (CCTS) seeks to ensure the inclusion of a diverse population of undergraduate students pursuing mentored research in artificial intelligence and medicine.
Clarkson awarded NIH grant to develop standardized graphic libraries for anatomy
Jul 01, 2021
Dr. Melissa Clarkson has been awarded four years of funding from the National Institute of Dental and Craniofacial Research for her project "Developing standardized graphic libraries for anatomy: A focus on human craniofacial anatomy and phenotypes". Her team will be developing "semantically-enabled" graphics depicting anatomy of the human head, including developmental stages, phenotypes, and malformations. You can preview their work at the Endless Forms Studio website.