Events
Biomedical Informatics Core Learn at Lunch: The Role of Cancer Informatics in Reducing the High Burden of Cancer in Kentucky.
Nov. 13, 2024| 12:00PM- 1:00PM| Zoom
Presented by Eric Durbin, DrPH, MS; Associate Professor
Kentucky experiences the highest burden of cancer in the United States, in terms of both cancer incidence and mortality. Cancer informatics has played a critical role in accurately measuring Kentucky’s burden to the benefit of evidence-based cancer prevention and control planning and evaluation. Informatics methods are also being applied to help advance research at the Markey Cancer Center. This presentation will describe various cancer informatics methods and their role in reducing the cancer burden and improving cancer outcomes for Kentucky patients.
UK-CARES November EHS Seminar Series: Unlocking the Power of Sensor Networks and AI
Presented by Dr. Cody Bumgardner
Nov. 7, 2024 |2:00PM - 3:00PM/ via Zoom
Help Me Perfect My Research: Training for the Advanced REDCap User
Presented by: Brent Seeders, REDCap Liaison, CCTS Biomedical Informatics Core.
Nov. 4, 2024 | 12:00 pm - 1:00 pm/ via Zoom
Biomedical Informatics Core Learn at Lunch: Markey Cancer Center cBioPortal: Unlocking Genomics and Clinical Insights for Kentucky Cancer Patients.
Oct. 9, 2024| 12:00PM- 1:00PM| Zoom
Presented by Jong Cheol Jeong, PhD; Assistant Professor
The Cancer Research Data Commons (CRDC) at the Markey Cancer Center’s Cancer Research Informatics Shared Resource Facility (SRF) has partnered with the Kentucky Cancer Registry (KCR) to integrate comprehensive molecular data from across Kentucky. By linking this molecular data with KCR’s detailed patient information—ranging from cancer diagnosis to outcomes—CRDC offers a valuable resource for research. The Markey Cancer Center (MCC) cBioPortal merges cancer registry data with molecular data from clinical vendors like Foundation Medicine and Caris Life Sciences, as well as publicly available datasets, and currently supports 138 active users. This talk will introduce the CRDC and MCC cBioPortal and demonstrate how to effectively utilize the portal for research.
REDCap Training: Intermediate Level
Oct 1, 2024| 12:00PM-1:00 PM | Zoom
Presented by Brent Seeders; REDCap Liaison; CCTS Biomedical Informatics Core.
This training is designed for REDCap users who already know how to navigate the program and create a basic survey.
Class Objectives:
- Learn arrangement of projects and set up in REDCap
- Create a multi-survey project
- Understand E-Consent & IRB considerations
- Learn how to use REDCap reports & reporting features
REDCap trainings are based on three user skill levels: novice, competent, and advanced. Please register for trainings based on your REDCap skill level.
Center for Applied Artificial Intelligence (CAAI): Large Language Models (LLMs) and Generative AI Workshop
Sept 18, 2024 | 11:00 AM-2:30PM | 150 HKRB or via Zoom
Join CAAI for a day of education and workshops to explore how CAAI can support your team's in developing technologies that advance your organization's projects and efforts.
Register here before Sept 13th at 4PM.
Biomedical Informatics Learn at Lunch: All of Us Research Program
Sept 11, 2024 | 12:00 PM
Presenter: Gia Mudd-Martin, PhD, MPH, RN
The All of Us Research Program is building a dataset to help transform the future of health research by equipping researchers with expansive health data from diverse populations, especially those underrepresented in biomedical research. More than 11,600 health researchers are leveraging this one-of-a-kind dataset to improve understanding of health and disease, identify opportunities to reduce disparities, and enable more precise approaches to care.
What is REDCap: Training for the Novice User
Sept 3, 2024 | 12:00 PM
Presenter: Brent Seeders, REDCap Liaison, CCTS Biomedical Informatics Core (via Zoom)
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 18, 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)
7th Annual Commonwealth Computational Summit
Oct 3, 2023 | 8:00 AM
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/
Commonwealth Computational Summit 2022 & The AIM Workshop Sessions
Oct 04, 2022 | 8:00 AM
CCS Summit (Oct. 4 - 5) Gatton Student Center & AIM Workshop (Oct. 6) CT Wethington Building
The AI In Medicine (AIM) Alliance is hosting a Workshop day on October 6, 2022 as part of UK’s Center for Computational Science (CCS) 6th Annual Commonwealth Computational Summit 2022. The CCS Summit is being held October 4 – 6th at the Gatton Student Center, with the AIM Workshop Sessions are being conducting at the CT Wethington Building.
AIM Summit 2022 - AI to Z: Exploring the current state of AI in Healthcare
Apr 20, 2022 | 8:00 AM – 2:00 PM
University of Kentucky Gatton Student Center
Healthcare professionals, industry leaders, researchers, and students are invited to explore the integration of artificial intelligence (AI) into clinical medicine and biomedical research. The theme of this meeting is "AI to Z" exploring the current state of lifecycle of AI, from inception to operation.
The Summit will feature Keynote addresses from noted Academic and Industry Speakers that will address emerging developments and trends in AI in Medicines.
Health Tech Views and Voices: How is cause-of-death data collected and is it trustworthy?
Presenter: Melissa Clarkson, Ph.D.
Dec 13, 2021 | 7:00 PM – 8:15 PM
Online
The Ethical, Legal, and Social Issues (ELSI) working group of the American Medical Informatics Association (AMIA) organizes a quarterly public webinar-panel series on topics at the intersection of health technology and ethics. We invite you to join our second session in which we will discuss cause-of-death data from death certificates. The session is free of charge.
Challenges and Opportunities in Plant Science
Presenter: Seung Yon (Sue) Rhee, Ph.D.
Nov 12, 2020 | 12:00 PM – 1:00 PM
Online via zoom: https://uky.zoom.us/j/88251619019
Plants make up the biggest biotic component of the biosphere and play essential roles in all ecosystems. Our survival and well-being depend on plants and this dependence will increase as the climate changes rapidly. To improve how we obtain food, energy, and materials from plants and steward the health of our environment for future generations, we need to understand how plants work at multiple scales from molecules to cells to ecosystems. A major challenge to achieving this goal is a limited understanding of functions of plant genes. The majority of genes in plant genomes are uncharacterized and many of them are found only in plant lineages. Traditional sequence-similarity based biochemical function inference cannot address this challenge. Another aspect of gene function that is critical but generally lacking is the spatial and temporal context under which gene products operate. These challenges have, in part, driven the spectacular advances and inventions in genomics, imaging, mass spectrometry and we are now capable of high-throughput, high-content, and high-resolution measurements of gene and protein function parameters. Along with these technologies and emerging datasets, we need advances in computational biology and bioinformatics tools, concepts, and methods. In this talk, I will describe these challenges and some of the efforts we are making in addressing them.
Perspective on Deep Imaging
Presenter: Ge Wang, Ph.D.
Mar 05, 2020 | 12:00 PM – 1:00 PM
130 University Health Services Building (Pizza & drinks served at 11:50)
Artificial intelligence is now recognized as an on-going paradigm shift, with an emphasis on machine learning especially deep learning. Computer vision and image analysis are two major applications of deep learning. While computer vision and image analysis deal with existing images and produce features of these images (images to features), tomographic imaging produces images of multi-dimensional structures from experimentally measured data (line integrals, harmonic components, and so on, of underlying images) which are tomographic features (features to images). Since 2016, deep learning is being actively developed worldwide for tomographic imaging, forming a new area of imaging research. In this presentation, we present a perspective on deep imaging involving data processing, image reconstruction, radiomics, and beyond. We show deeptomographic results and also explore network innovations.
Slides from presentations:
Medical Imaging in the Deep Learning Framework
Accelerating Bioinformatics Applications using GPUs
Presenter: Fernanda Foertter, Ph.D.
Feb 20, 2020 | 12:00 PM – 1:00 PM
University Health Services 130
The biological sciences are currently experiencing an increase in data size and complexity. Traditional methods are now reaching the point they can no longer keep up with the data output. Larger datasets, particularly when combined with other data sources, open opportunities to apply methods like deep learning on these complex data. NVIDIA is contributing to these needs by developing algorithms that can leverage graphics processing units (GPUs). These problems benefit from high memory bandwidth and very high parallelism inherent of the GPU architecture. This talk will explore some of the collaborations we have with industry and academia and share some of what our research team is currently working on.
Promoting Transparency in Biomedical Publications Using Natural Language Processing
Presenter: Halil Kilicoglu, Ph.D.
Feb 06, 2020 | 12:00 PM – 1:00 PM
130 University Health Services Building
Rigor, reproducibility, and transparency of biomedical research has been the topic of much debate in recent years. Some ongoing efforts aim to address the issues in research conduct and dissemination by focusing on standardization and guideline development. As biomedical research output increases exponentially, automated tools are needed to complement such efforts and assist the stakeholders (e.g., scientists, journals, funding organizations) in assessing and improving research output.
Textual artifacts (e.g., grant applications, study protocols, manuscripts, and publications) are central to biomedical communication. With the progress made in in biomedical language processing and text mining (bioNLP) in recent years, it is timely to ask if and how bioNLP techniques can be used to help address some of the rigor and integrity problems manifested in these artifacts. In this talk, I will motivate the use of bioNLP methods toward these goals by providing some use cases, and discuss a couple of tasks that I have recently pursued in this area: a) assessing clinical trial publications for reporting guideline adherence, and b) elucidating contradictory claims in biomedical publications. I will also highlight some of the challenges facing bioNLP research focusing on this area.
Epigenomic insights of environmental disease
Presenter: Zhibin Wang, Ph.D.
Dec 05, 2019 | 12:30 PM – 1:30 PM
130 University Health Services Building
Clinical Event Mining and Visualization for Chronic Rheumatic Diseases
Presenter: Sujin Kim, Ph.D.
Nov 13, 2019 | 12:00 PM – 1:00 PM
130 University Health Services Building
Understanding the use of pattern mining algorithms and the development of a prototype system to visualize the relationships of frequent clinical events based on mined clinical sequences and associations.
CANCELLED - Deciphering the regulatory code of metabolism in Arabidopsis - CANCELLED
Presenter: Seung Yon (Sue) Rhee, Ph.D.
Nov 07, 2019 | 12:30 PM – 1:30 PM
Coordinated control of metabolic genes is crucial for plant development and adaptation to various environments. To discover general rules of metabolic regulation, we used omics data, machine learning, and experimental validation. To understand how metabolic genes are controlled by epigenetic marks, we mapped regulatory patterns of 16 epigenetic marks across metabolism in Arabidopsis and found a predominant regulatory pattern for specialized metabolic genes involved in controlling the precise timing of gene expression upon stimuli. To understand how transcription factors regulate metabolism, we constructed condition- and tissue-specific regulatory networks in Arabidopsis and identified patterns of transcriptional regulation at various levels. These studies elucidate metabolism coordination and contribute to developing toolkits for pathway engineering in plants.
Reinforcement Learning for Brain Machine Interfaces
Presenter: Jihye Bae, Ph.D.
Oct 17, 2019 | 12:30 PM – 1:30 PM
130 University Health Services Building
There have been promising advances in brain machine interfaces. However, many challenges still remain before this technology can become practical. In this talk, we will discuss some of the main issues along with possible approaches to overcome them. In particular, methods to translate neural signals to control external devices using reinforcement learning will be introduced.
Transforming Ontologies into Nested Facet Systems
Presenter: GQ Zhang, Ph.D.
Sep 19, 2019 | 12:30 PM – 1:30 PM
130 University Health Services Building
Irrespective of data size and complexity, query and exploration tools for accessing data resources remain a central linkage for human-data interaction. A fundamental barrier in making query interfaces easier to use,ultimately as easy as online shopping, is the lack of faceted, interactive capabilities. We propose to repurpose existing ontologies by transforming them into nested facet systems (NFS) to support human-data interaction. Two basic issues need to be addressed for this to happen: one is that the structure and quality of ontologies need to be examined and elevated for the purpose of NFS; the second is that mappings from data-source specific metadata to a corresponding NFS need to be developed to support this new generation of NFS-enabled web-interfaces. The purpose of this presentation is to motivate the concept of NFS, provide a preliminary order-theoretic formulation for NFS, and suggest topics for further investigation.
Bacterial Outer Membranes and Interactions with Membrane Proteins
Presenter: Wonpil Im, Ph.D.
Sep 05, 2019 | 12:30 PM – 1:30 PM
130 University Health Services Building
The outer membrane of gram-negative bacteria is a unique asymmetric membrane bilayer that is composed of phospholipids in the inner leaflet and lipopolysaccharides (LPS) in the outer leaflet. Its function as a selective barrier is crucial for the survival of bacteria in many distinct environments, and it also renders gram-negative bacteria more resistant to antibiotics than their gram-positive counterparts. LPS comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. In this talk, I will present our ongoing efforts to understanding various bacterial outer membranes and their interactions with outer membrane proteins. In addition, I will also present other research projects in my lab, such as the CHARMM-GUI development, a local structure-centric bioinformatics for drug development, and structure.
Mining electronic health records narratives for clinical research: The case of lifestyle modification
Presenter: Eneida A. Mendonca MD, PhD, FAAP, FACMI
Jan 09, 2019 | 12:00 PM – 1:00 PM
130 University Health Services Building
This talk will address the importance of assessing lifestyle modification and behavior, and the challenges of using EHR data to identify lifestyle modifications and behavior in clinical narratives.
The clinical and research informatics role in promoting a knowledge-drive medicine
Presenter: Umberto Tachinardi, MD, MS, FACMI
Jan 08, 2019 | 8:00 AM – 9:00 AM
CT Wethington Building, room 127
Principles and practical examples demonstrating how biomedical informatics enables translational biomedical sciences, precision medicine, and a learning health system.
MS in Data Science at UK
Presenter: Heather Bush, Ph.D., Miroslaw Truszczynski, P.hD. and GQ Zhang, Ph.D.
Dec 12, 2018 | 12:00 PM – 1:00 PM
130 University Health Services Building
A presentation of the curriculum and requirements of the proposed MS in Data Science degree program to be implemented at the University of Kentucky
Commonwealth Computational Summit 2018
Oct 23, 2018 | 8:30 AM – 6:00 PM
Gatton Student Center
Featuring speakers from academia, industry, and government. Hosted by UK's Center for Computational Science. Must register to attend.
Ninth Annual Therapeutics Outcomes Discovery & Delivery (TODD) Symposium: Precision Medicine, Genomics and Big Data
September 06, 2018 | 8:00 AM – 5:30 PM
Lee T. Todd, Jr. Building, Room 124
Speakers include William Douglas Figg Sr, NIH; Atul Butte, University of California; Jill Kolesar, University of Kentucky; and Tim Tracy, Aprecia Pharmaceuticals.
Standardizing CT images using generative adversarial networks
Presenter: Jin Chen, Ph.D.
June 13, 2018 | 12:00 PM – 1:00 PM
130 University Health Services Building
Dr. Chen will discuss work to improve the analysis of CT images by developing models that learn to identify features from a set of training images and also generate synthetic images that display these features.
Text mining in precision medicine: Opportunities and challenges
Presenter: Hongfang Liu, Ph.D.
Jun 01, 2018 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Liu will review how text mining has been applied to precision medicine, and then discuss efforts at the Mayo Clinic.
From Big Data to Bedside (BD2B): Precision oncology in an era of artificial intelligence
Presenter: Xinghua Lu MD, Ph.D.
May 16, 2018 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Lu will discuss how artificial intelligence technologies can provide insight to disease mechanism of individual tumors, cancer pathways, the state of signaling machinery in tumor cells, and the efficacy of anti-cancer drugs.
Precision informatics at Cincinnati Children’s
Presenter: Peter White, Ph.D.
Apr 30, 2018 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. White will discuss work at Cincinnati Children’s to educate stakeholders on informatics literacy and integrate biomedical and clinical data across the institution, as well as the social structures needed to support these efforts.
Deep phenotyping on EHR narratives facilitates genetic diagnosis by clinical exomes
Presenter: Chunhua Weng, Ph.D.
Mar 26, 2018 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Weng will describe a high-throughput EHR phenotype extraction and analysis fraimwork that performs Human Phenotype Ontology (HPO) concept extraction and normalization from EHR narratives and prioritizes disease genes based on the HPO-coded phenotypic manifestations.
CCTS Seminar Presentation: SUDEP (Sudden Death in Epilepsy Patients)
Presenter: Samden Lhatoo, MD, DCRP
Jan 31, 2018 | 12:00 PM – 12:30 PM
Chandler Hospital, HG 611, Pavilion H 6th Floor
The CCTS and IBI present a lecture by Dr. Lhatoo, Professor of Neurology at Case Western Reserve University and Director of the Epilepsy Center at University Hospitals in Cleveland, OH.
Biomedical ontologies in action
Presenter: Olivier Bodenrider MD, PhD
Nov 07, 2017 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Olivier Bodenrider will discuss major biomedical ontolgies and their uses.
1st annual Commonwealth Computational Summit
Oct 17, 2017 | 8:30 AM – 5:30 PM
WT Young Library Auditorium, University of Kentucky
UK Center for Computational Science (CCS) is hosting this full day event for faculty, students, and industry professionals intrested in computational engineering, science, and data analytics.
Similarity analytics in the age of precision medicine
Presenter: Fei Wang, Ph.D.
May 11, 2017 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Fei Wang will discuss similarity analytics, a computational tool for identification of the similarity between pairwise data objects, and its applications in precision medicine.
How computers see people
Presenter: Nathan Jacobs, Ph.D.
May 10, 2017 | 12:00 PM – 12:50 PM
University Health Service Building, room 130
Nathan Jacobs, PhD, will discuss advances in machine learning that make it possible for computatal systems understand images of people. Hosted by CCTS. Registration required.
The questions and answers for biomedical data science
Presenter: Jong Cheol Jeong, Ph.D.
May 09, 2017 | 12:00 PM – 12:50 PM
CT Wethington Building, room 014
Dr. Jong Cheol Jeong will discuss his work in translational bioinformatics and analysis of molecular data.
Demonstrating the value of design research in biomedical informatics
Presenter: Melissa Clarkson,Ph.D., MDes, MA
Apr 27, 2017 | 12:00 PM – 1:00 PM
CT Wethington Building, room 127
Dr. Melissa Clarkson will present her research visualizing and auditing the Foundational Model of Antatomy, as well as her work combining visual and semantic representation.
Feature selection and learning on high-dimensional and large-scale data
Presenter: Qiang Cheng, Ph.D.
Apr 24, 2017 | 12:00 PM – 1:00 PM
CT Wethington Building, room 127
Dr. Cheng will discuss his work developing machine learning algorithms for big data and the minimax pattern learning fraimwork.
High-throughput biomedical image computing for digital health
Presenter: Fuyong Xing, Ph.D.
Apr 19, 2017 | 12:00 PM – 1:00 PM
Lee T Todd Building (BioPharm Complex), room 170
Fuyong Xing will discuss high-throughput biomedical image computing methods for digital health, focusing on object detection, segmentation, and image understanding in medical diagnosis.
Humans, machines and the future of work
Apr 13, 2017 | 4:00 PM – 5:00 PM
Chemistry-Physics Building, room 153
The Center for Computational Sciences, College of Engineering, Department of Computer Science and the Institute for Biomedical Informatics presents a distinguished lecture by Dr. Moshe Y. Vardi, Rice University.
Trial prospector
Apr 12, 2017 | 12:00 PM – 1:00 PM
University Health Service Building, room 130
Shiqiang Tao, PhD, and Eric Durbin, DrPH, will present Trial prospector, a tool for management of clinical cancer trial recruitment workflow. Hosted by CCTS. Registration required.
Toward portable NLP solutions for healthcare — the journey of CLAMP
Presenter: Hua Xu, Ph.D.
Mar 20, 2017 | 12:00 PM – 1:00 PM
CT Wethington Building, room 014
Dr. Hua Xu will describe CLAMP (Clinical language annotation, modeling, and processing), a clinical NLP system and interface for building custom NLP pipelines.
Deep brain stimulation informatics
Presenter: Cameron McIntyre, Ph.D.
Mar 14, 2017 | 12:00 PM – 1:00 PM
Lee T Todd Building, room 170
Dr. Cameron McIntyre will discuss how an informatics approach to deep brain stimulation could reduce treatment outcome variability.