PheWAS Reveals Post-COVID-19 Diagnoses

A high-throughput informatics technique developed at Vanderbilt University Medical Center that reveals associations between genetic variations and medical conditions in the electronic health record (EHR) also can identify new “post-COVID” diagnoses, according to a report in the Journal of the American Medical Informatics Association. 

VUMC's Dan Roden Leads Effort to Map Heart Disease-Causing Genetic Variations

One in 100 people have genetic variations that can cause potentially life-threatening heart conditions, including high cholesterol (lipid disorders), heart muscle disease (cardiomyopathies), and abnormal heart rhythms (arrhythmias). Yet the functional impact of most of these cardiovascular genetic variants — whether they disrupt normal function or are harmless — is unknown. That is about to change.

NATURE: Cosmin Adi Bejan uses Natural Language Processing (NLP) to improve how well we identify (“ascertain”) suicidal thoughts and behaviors in healthcare data.

Methods relying on diagnostic codes to identify suicidal ideation and suicide attempt in Electronic Health Records (EHRs) at scale are suboptimal because suicide-related outcomes are heavily under-coded. We propose to improve the ascertainment of suicidal outcomes using natural language processing (NLP). We developed information retrieval methodologies to search over 200 million notes from the Vanderbilt EHR. Suicide query terms were extracted using word2vec. A weakly supervised approach was designed to label cases of suicidal outcomes.

DBMI Digest August 2022 Issue—Now Available!

The Vanderbilt University Medical Center (VUMC) Department of Biomedical Informatics's (DBMI) monthly newsletter, DBMI Digest, is now available to view. Read the August 2022 DBMI Digest here. Each DBMI Digest features department & faculty announcements, awards & appointments, educational & HR updates, funding opportunities and more. Each issue also includes a profile of one of our faculty, staff, postdocs and students. 

Laura Zahn

Laura
Zahn
Senior Project Manager
2525 West End Avenue
laura.a.zahn@vumc.org

Chao Yan, PhD, MS

Chao
Yan
Research Instructor
Department of Biomedical Informatics
2525 West End Avenue
Nashville
Tennessee
37203
chao.yan.1@vumc.org

Chao Yan, PhD, MS, joined as Research Instructor in the Department of Biomedical Informatics in Feb. 2025. Prior to his primary faculty appointment, Dr. Yan completed a postdoctoral fellowship in the Department of Biomedical Informatics, Vanderbilt University Medical Center. Dr. Yan’s research focuses on synthetic health data generation and evaluation, predictive modeling, differential medical AI outcomes across groups, and privacy protection in health data use.

He received his PhD in Computer Science from Vanderbilt University in 2022. Dr. Yan has received multiple research honors, including one of the best article on clinical research informatics published in 2020, which was included in the 2021 International Medical Informatics Association Yearbook, and the distinguished paper award in 2019 AMIA Annual Symposium. He has been invited to give multiple presentations on his research, including the JAMIA Journal Club Webinar. Dr. Yan was a member of the JAMIA Student Editorial Board.

Technical and Legal Specialists Team Up to Address Security of Genomic Data

An explosive increase in the quantity of genomic data being collected, used and shared is propelling current and ongoing research into privacy protections related to personal genetic information. A team at Vanderbilt University Medical Center has reexamined the literature surrounding online threats and protections against genomic data leaks from both a legal and technical perspective.

Mohammed Ali Al-Garadi, PhD

Mohammed
A
Al-Garadi
Research Assistant Professor
Department of Biomedical Informatics

Dr. Mohammed Al-Garadi is a Research Assistant Professor in the Department of Biomedical Informatics at Vanderbilt University Medical Center. He previously worked as a Postdoctoral Researcher at Emory University, focusing on natural language processing (NLP), machine learning (ML), deep learning and large language models (LLMs) for healthcare applications. His research focuses on extracting insights from unstructured healthcare data, particularly unstructured notes, using NLP and machine learning techniques. By developing modules and pipelines, he has created systems to efficiently process diverse healthcare data streams. He worked on NIH and CDC grants involving the application of NLP and machine learning to analyze large-scale clinical narratives and public health data. 

To date, Dr. Al-Garadi has authored and co-authored over 50 papers in high-impact scientific journals. Currently, Dr. Al-Garadi is exploring the potential of NLP, ML, and LLMs on unstructured EHR clinical notes for various healthcare applications. These include extracting, predicting, and detecting causes of death, postoperative infections, COPD exacerbations, kidney disease, peripheral artery disease, and tele-dermatology conditions and outcomes. He is working on projects supported by the NIH, Department of Veterans Affairs, and FDA.

Twitter: https://twitter.com/AliAlgaradi
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