Dear DBMI staff, trainees, faculty, and supporters:
We are seeing an unprecedented time where technology is working through biomedical informatics to transform medicine in what the National Library of Medicine Director Dr. Patti Brennan has called ‘Data Powered Health.’ We are the blacksmiths of this transformation — welding, molding, and shaping data to drive improvements in health. We are each uniquely poised to bring our hearts, hands, and intellect to serve the common good — intentionally lifting the vision beyond our walls and thinking ‘big.’ I invite you all to look at the news and all that is going on in healthcare informatics and truly reflect. We are on the verge of change that will be as exciting as the decoding of the genome!
Along this journey to transform medicine, we must intentionally think about unintended biases we have, our lack of inclusion, or if we are just working on the wrong problem. The new tools in the blacksmith shop must be sharpened and tuned to solve problems for all, including those individuals who are often last to get to the visit, least health literate, and disabled. Think forward, empower those with access and health literacy, support those who need help, and lean in to new solutions that help those least likely to have healthy outcomes. You, friends and colleagues, can define the future of data powered health, and your pivotal insights and discoveries will create the biomedical informatics of the future. Summer is a time for growth, play, and discovery; look to the sky, watch the clouds and dream up new possibilities that seem simply to be science fiction. You are tomorrow, and your dreams just might result in that little discovery that advances healthcare by one lightyear! I look forward to connecting and seeing what ideas you nurture to fruition.
Amy M. Sitapati, MD
Interim Chief, Department of Biomedical Informatics, UCSD Health
Generative AI — What UC San Diego Researchers Need to Know
Generative Artificial Intelligence or “GenAI” is a class of machine learning-based AI that create things using massive underlying data – hence the name “generative.” GenAI has great potential to assist with biomedical research and can be used to ease administrative burdens. For example, GenAI can be used to assist with the creation of research protocols and participant information sheets. It can also be used to generate programming code and has even been used in novel drug design.
Using GenAI for research is not without risks. Public GenAI systems, such as ChatGPT and DALL-E, may incorporate input data into their underlying data, therefore using protected health information (PHI) with these type of programs is a HIPAA violation. GenAI programs are still new and may contain incorrect or biased information. Any data generated by GenAI should always be verified and checked for accuracy. To understand the operations and research guidelines for using GenAI at UC San Diego Health, please visit the GenAI Pulse page.
If you are interested in using GenAI for your research, ACTRI offers a secure environment (the UCSD Nightingale Platform) that includes non-public GenAI models. That environment also has a pre-extracted de-identified data set of UCSD patient records available for machine learning AI model development. You can request use of this data environment and data set through the ACTRI Bioinformatics request page.
Mike Hogarth, MD, Clinical Research Information Officer, recently gave an overview of using GenAI for research at the GenAI Town Hall. If you were unable to attend that meeting, please view the recording of the meeting or check out the slide deck.
We are at the dawn of GenAI in biomedical research and with caution and thorough testing, these tools can provide a plethora of possibilities to enhance research.
Featured on Amazon Science: Supreeth Shashikumar
Supreeth Shashikumar, a research scientist at the University of California, San Diego, whose Amazon Research Award supports his research on using machine learning models to predict the onset of sepsis.
We are thrilled to highlight the work of Supreeth Shashikumar, PhD, which has been featured in a recent article on Amazon Science. The article delves into his groundbreaking work within the realm of biomedical signal processing and predictive models for sepsis detection. We invite you to read the full article here and explore his fascinating insights and accomplishments. Kudos to Dr. Shashikumar for his outstanding contributions that continue to elevate our field!
From more than 1,400 submissions, we're thrilled to share some exciting news — the abstract Using a Blockchain to Immutably Preserve Digital-Only Birth Certificates, co-authored by Edwin Bean, MS, Tsung-Ting Kuo, PhD, and Mike Hogarth, MD, has been accepted for presentation at the upcoming AMIA 2023 Annual Symposium. This marks a groundbreaking exploration into incorporating birth certificates into a blockchain — a first of its kind.
Our DBMI team has also made its mark with another accepted abstract: Blockchain-based Biomedical Training Certificate Management System, co-authored by Yufei Yu, Joseph Edmonston, Czarlyn Camba, and Tsung-Ting Kuo, PhD. This study delves into the realm of blockchain's role in efficient training certificate management.
Furthermore, we're proud to announce that Standards for Ophthalmology Trauma and Infection Concept Coverage, co-authored by Mike Hogarth, MD, Sally Baxter, MD, and others, and has been recognized among the accepted abstracts. Amy Sitapati, MD, will enlighten us during her presentation titled, Empowering Justice, Equity, Diversity, and Inclusion (JEDI) through the '5' Core Clinical Informatics Electronic Health Record Domains. This November, get ready to be captivated not only by these remarkable presentations but also by a diverse range of talks in New Orleans. Secure your spot and register for AMIA here.
New Award for C. Diff. Test Prediction
The UCSD Academic Senate recently awarded a grant (RG114001) for a research project titled Positive Clostridioides Difficile Test Results Prediction, which aims to predict positive Clostridioides Difficile (C. Diff.) test results. This project is led by Principal Investigator Tsung-Ting Kuo, PhD, with Co-Investigators Robert El-Kareh, MD, Frank Myers, MA, and Lucila Ohno-Machado, MD, PhD, as well as predoc trainee Anh Pham.
Graduating House Staff Teaching Awards
The UCSD Health Internal Medicine and Medicine/Pediatrics graduating residents have recognized Amy Sitapati, MD, as one of its recipients of the Graduating House Staff Teaching Awards. Joining her in this honor are Constance Chace, MD, Meghan Sebasky, MD, and Supraja Thota, MD. A heartfelt congratulations is extended to all these deserving recipients!
With appreciation, we take this moment to acknowledge and extend our congratulations to Morgan Von Ebke for accomplishing a remarkable milestone — a decade of dedicated service to UC San Diego. Your loyalty, commitment, and diligent efforts have been instrumental in shaping DBMI's success. As you celebrate this impressive achievement, we want to express our sincere thanks for your enduring dedication.
Celebrating Faculty Advancements
We are thrilled to celebrate the exceptional achievement of Jejo Koola, MD, as he advances from the role of Assistant Clinical Professor to the position of Associate Clinical Professor. His dedication to his field, unwavering commitment to his students, and his contributions have been truly commendable. As an Associate Clinical Professor, we look forward to witnessing Dr. Koola's continued growth and influence, inspiring both colleagues and trainees alike. Congratulations on this significant career milestone!
Recognizing J. Yang Scholarship Recipient
Congratulations are in order for Kuan-Hung (Peter) Yeh, one of Dr. Tiffany Amariuta's incoming PhD students, who has been awarded a $25,000 scholarship from the J. Yang Foundation. Kuan-Hung's scholarly pursuits are currently centered around developing novel statistical approaches to integrate genetic data across millions of individuals with diverse ancestries and enhance the generalizability of disease risk models, which is necessary for the clinical implementation of personalized preventive medicine.
New Staff Member Maria Triplett
Welcome to DBMI, Maria Triplett! Maria recently stepped into the role of Academic and Research Coordinator. A proud alumna of UCSD, Maria holds a B.S. in Public Health accompanied by a minor in Ethnic Studies. Her academic journey continued to University of Southern California (USC), where she is currently wrapping up her MPH. Maria is a San Diego native who enjoys hiking, weightlifting, and journaling. When she's not trying new restaurants or coffee shops, Maria is enjoying her favorite shows — The Bear and Abbott Elementary.
As Faten Taha embarks on a new chapter at UCSD beyond our department, we want to take a moment to bid her a fond farewell. Faten’s work was instrumental in completing the Strongheart (SHS) Research Portal as well as the related Community Dashboard, adding interactive graphing capabilities to both. She also supported a host of websites including RADx-DCC, SHS-iDASH and UCSD’s local All of Us website. Most recently, she was one of the main contributors to Dr. Sitapati’s Strength project, establishing data pipelines to visualize UCSD Health’s employee vaccine efforts on Tableau.
Adding on to her expertise in building scientific web applications, Faten has decided to join Dr. Jeffrey Grethe's team in Neuroscience to contribute to their effort in developing new and innovative research tools.
Welcome New Arrival Everett Nemati
Amidst the hustle and bustle of our work, we are overjoyed to share in a moment of pure happiness – the arrival of a baby in DBMI! Everett Jules Nemati made a heartwarming entrance into the world in June 2023. He weighed 7 pounds and 9 ounces, and measured 19 inches long. Everett's dad Shamim Nemati, mom, and sister are grateful for this wonderful blessing and wish to thank you for your love and support.
Giving Recognition and Feedback
Did you know that you can give recognition to another UCSD Health employee using the MyPerformance system? Go into MyPerformance (Blink > Personal > UCLearning > MyPerformance > Continuous Feedback > Provide Recognition) to give them a shout-out. The staff member will receive notice of the positive recognition, and their supervisor will be cc’ed. If you received fantastic service from someone in IT, HR, housekeeping, or a colleague, don’t hesitate to use the system to thank them.
Did you know that DBMI has a virtual suggestion box where you can provide anonymous feedback? You can access that here. You can also access the virtual suggestion box on the DBMI website – scroll to the bottom of the homepage and click on the feedback link.
New Articles by Faculty, Staff, & Trainees
Acuff K, Radha Saseendrakumar B, Wu JH, Weinreb RN, Baxter SL. Racial, Ethnic, and Socioeconomic Disparities in Glaucoma Onset and Severity in A Diverse Nationwide Cohort in the United States. J Glaucoma. 2023 Jul 18. doi: 10.1097/IJG.0000000000002261. Online ahead of print. PMID: 37523618
Tai-Seale M, Baxter S, Millen M, Cheung M, Zisook S, Çelebi J, Polston G, Sun B, Gross E, Helsten T, Rosen R, Clay B, Sinsky C, Ziedonis DM, Longhurst CA, Savides TJ. Association of physician burnout with perceived EHR work stress and potentially actionable factors. J Am Med Inform Assoc. 2023 Jul 20:ocad136. doi: 10.1093/jamia/ocad136. Online ahead of print. PMID: 37475168
Keeler Bruce L, Paul P, Kim KK, Kim J, Keegan THM, Hiatt RA, Ohno-Machado L; All of Us Research Program Investigators. Family and personal history of cancer in the All of Us research program for precision medicine. PLoS One. 2023 Jul 17;18(7):e0288496. doi: 10.1371/journal.pone.0288496. eCollection 2023. PMID: 37459328
Bhanvadia S, Radha Saseendrakumar B, Guo J, Daniel M, Lander L, Baxter SL Evaluation of Bias in Medical Student Clinical Clerkship Evaluations Using Natural Language Processing. Acad Med. 2022 Nov 1;97(11S):S154. doi: 10.1097/ACM.0000000000004807. Epub 2022 Oct 18. PMID: 37460500
Tavakoli K, Kalaw FGP, Bhanvadia S, Hogarth M, Baxter SL Concept Coverage Analysis of Ophthalmic Infections and Trauma among the Standardized Medical Terminologies SNOMED-CT, ICD-10-CM, and ICD-11. Ophthalmol Sci. 2023 May 25;3(4):100337. doi: 10.1016/j.xops.2023.100337. eCollection 2023 Dec. PMID: 37449050
El-Kareh R, Brenner DA, Longhurst CA Developing a highly-reliable learning health system. Learn Health Syst. 2022 Oct 27;7(3):e10351. doi: 10.1002/lrh2.10351. eCollection 2023 Jul. PMID: 37448457
Tully JL, Zhong W, Simpson S, Curran BP, Macias AA, Waterman RS, Gabriel RA. Machine Learning Prediction Models to Reduce Length of Stay at Ambulatory Surgery Centers Through Case Resequencing. J Med Syst. 2023 Jul 10;47(1):71. doi: 10.1007/s10916-023-01966-9. PMID: 37428267
Seng EC, Mehdipour S, Simpson S, Gabriel RA. Tracking persistent postoperative opioid use: a proof-of-concept study demonstrating a use case for natural language processing. Reg Anesth Pain Med. 2023 Jul 6:rapm-2023-104629. doi: 10.1136/rapm-2023-104629. Online ahead of print. PMID: 37419509
Vuyyuru SK, Solitano V, Hogan M, MacDonald JK, Zayadi A, Parker CE, Sands BE, Panaccione R, Narula N, Feagan BG, Singh S, Jairath V, Ma C. Efficacy and Safety of IL-12/23 and IL-23 Inhibitors for Crohn's Disease: Systematic Review and Meta-Analysis. Dig Dis Sci. 2023 Jun 28. doi: 10.1007/s10620-023-08014-z. Online ahead of print. PMID: 37378711
Lu B, Curtius K, Graham TA, Yang Z, Barnes CP. CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples. Genome Biol. 2023 Jun 20;24(1):144. doi: 10.1186/s13059-023-02983-0. PMID: 37340508
Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet. 2023 Jun 13:S0002-9297(23)00170-2. doi: 10.1016/j.ajhg.2023.05.013. Online ahead of print. PMID: 37339630
Gabriel RA, Park BH, Mehdipour S, Bongbong DN, Simpson S, Waterman RS. Leveraging a Natural Language Processing Model (Transformers) on Electronic Medical Record Notes to Classify Persistent Opiod Use After Surgery. 2023 Jun 20. doi: 10.1213/ANE.0000000000006579. Online ahead of print. PMID: 37339081 No abstract available.
Ayers JW, Zhu Z, Poliak A, Leas EC, Dredze M, Hogarth M, Smith DM. Evaluating Artificial Intelligence Responses to Public Health Questions. JAMA Netw Open. 2023 Jun 1;6(6):e2317517. doi: 10.1001/jamanetworkopen.2023.17517. PMID: 37285160
Wu JH, Radha Saseendrakumar B, Moghimi S, Sidhu S, Kamalipour A, Weinreb RN, Baxter SL. Heliyon. Epidemiology and factors associated with cannabis use among patients with glaucoma in the All of Us Research Program. 2023 Apr 25;9(5):e15811. doi: 10.1016/j.heliyon.2023.e15811. eCollection 2023 May. PMID: 37215923 Free PMC article.
Dameff C, Tully J, Chan TC, Castillo EM, Savage S, Maysent P, Hemmen TM, Clay BJ, Longhurst CA. Ransomware Attack Associated With Disruptions at Adjacent Emergency Departments in the US. JAMA Netw Open. 2023 May 1;6(5):e2312270. doi: 10.1001/jamanetworkopen.2023.12270. PMID: 37155166
Hogarth M, John D, Li Y, Wang-Rodriguez J, Chakladar J, Li WT, Mehta SR, Jain S, Ongkeko WM. Clinical Characteristics and Comorbidities associated with SARS-CoV-2 breakthrough infection in the California Healthcare Systems. Am J Med Sci. 2023 May 3:S0002-9629(23)01166-7. doi: 10.1016/j.amjms.2023.04.019. Online ahead of print. PMID: 37146904
Lam JY, Richardson A, Kanegaye JT, Tremoulet AH, Shimizu C, Stadnick NA, Burns JC, Nemati S, Gardiner MA Implementation of KIDMATCH: A Clinical Decision Support Tool for Diagnosing Pediatric Patients with Multisystem Inflammatory Syndrome and Kawasaki Disease. Lam JY, AMIA Annu Symp Proc. 2023 Apr 29;2022:653-661. eCollection 2022. PMID: 37128449
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