Message from the Chief: Dear DBMI staff, trainees, faculty, and supporters:

Spring is upon us and gardens are alive in bloom buzzing with the activity of humming birds, bees, and bunnies! The foundation of that life is fertile soil steaming with nutrients and a biodiversity. A few weeks ago, with my daughter, we made a trip to the local garden store to pick up the ingredients to build our garden (i.e. seeds, soil, sprouted young shoots) and spent the day building our garden. How are we like that rich soil and what can the garden teach us about biomedical informatics?

Soil matters
Teamwork is essential
The work is not done once the garden is planted
The harvest benefits an entire community who can prosper

Soil is our substance. How does who we are impact what we are doing? What are the problems you are trying to solve? Who does it help? How does it advance the greater good for all? We are the most important part of the work that we do and who we are as we do the work matters. Commit to be the best you and bring yourself into your work.

Teamwork makes impossible dreams surmountable. Just like that garden that was daunting to toil, cultivate, and water as an individual, teams help impossible goals become achievable. Solving current challenges in healthcare access, cost, efficiency and outcomes are just a few of the daunting tasks at hand. Much admiration to all of you who join hands in collaboration to bring resources through grants and contracts to advance the efforts to modernize data driven health together.

The work is not done once the garden is planted, and everyday we step outside to pluck weeds, assess hydration, and add nutrients. Our work at hand to grow successful innovation and change is substantially the day to day efforts of trial, error, refocus. We apply what we have learned as our daily effort to advance discovery.

The harvest benefits an entire community. How can our collective efforts advance the common good through the advancement of health outcomes for all? Our aims should be audacious and you are all the individuals with heart, hands, and refined depth of expertise to address the most pressing challenges that face our world.

Amy M. Sitapati, MD

Interim Chief, Division of Biomedical Informatics, UCSD

Interim Chair, Department of Biomedical Informatics, UCSDH

Pronouns: she/her/hers

DBMI Interim Chief, Amy Sitapati, MD and faculty member, Mike Hogarth, MD are excited to be finalizing the CalIVRS contract renewal with CDPH that would extend DBMI’s relationship through June of 2027. The renewal marks a significant milestone as it continues UC's 43-year history of supporting, maintaining, and innovating California's vital statistics data systems, one of the most advanced vital records systems in the world. The planned enhancements will help CalIVRS integrate with birthing centers, medical examiners, coroners, and federal partners. New initiatives in data modernization will also help leverage years of collected data to support public health research and surveillance. We're immensely proud of the collaborative efforts that have brought us to this moment and look forward to the positive impact our continued partnership will have on shaping the future of public health in California and beyond.

DBMI PhD student, Aaron Boussina, alongside DBMI faculty, Robert El-Kareh, MD, MS, MPH, Christopher Longhurst, MD, MS., and Shamim Nemati, PhD, co-authored a study on the benefits in the use of AI in detecting early Sepsis. In a prospective, pre-post study, the group and their team found that an AI algorithm they’d developed can more quickly and accurately identify patients at risk for the serious blood infection sepsis while limiting false positives better than existing protocols. The algorithm, COMPOSER, yielded exceptional results in producing an absolute 1.9% decrease in mortality corresponding to a 17% relative decrease across the two hospital emergency departments where it was used. In a sit-down interview with Fortune Magazine, Mr. Boussina and Dr. Nemati share more on their discovery in detail.

DBMI faculty, Tiffany Amariuta, PhD has been awarded the National Science Foundation (NSF) CAREER award to advance their research in the areas of genetic regulation of gene expression and algorithmic/bioinformatic development. The NSF CAREER award is the National Science Foundation's most prestigious awards in support of early-career faculty who have the potential to serve as academic role models in research and education and to lead advances in the mission of their department or organization. There are only 500 awards across different NSF disciplines made each year, and PIs only have three chances to apply. Dr. Amariuta shares that beyond research, they aim to use the grant to implement a 3-week summer residential camp at UCSD consisting of a coding boot-camp and in-lab research experience that would specifically serve high school students from under-resourced school districts. In addition, they also aim to design a statistical genetics course that meets an unmet need here at UCSD.

DBMI Alumni and Faculty, Sally Baxter, MD, MSc, has been highlighted for her participation in the All of Us Research Program. In their recent newsletter, the All of Us Research Program chronologizes Dr. Baxter's path to her career in ophthalmology. As a physician-scientist and program participant, Dr. Baxter uses All of Us data to study vision loss and glaucoma. In college, Dr. Baxter interned at a mobile clinic that gave vision screenings to children in underserved communities. Now, with the utilization of All of Us' unique and diverse data set, she studies ways to predict risk for glaucoma with hopes of highlighting and explaining disparities in health care.

DBMI Faculty, Ming Tai-Seale, PhD, MPH, Sally Baxter, M.D, MSc, Amy Sitapati, MD, Marlene Millen, MD, and Christopher Longhurst, MD, MS co-authored a study on evaluating the use of AI-generated physician messaging. As one of the first health systems to integrate the use of AI in healthcare, the UCSD Health study focused on whether the use of AI-generated replies could aid in decreasing time spent for physician response. Although the team found that AI-generated replies did not reduce physician response time, they were beneficial in relieving cognitive burden by creating an empathetic draft physicians tailor as needed. We welcome you to read more here.

Kevin Kunkel Celebrates 20 Years at the University of California

Kevin Kunkel, a Technical Project Management Professional, recently marked a significant milestone — his 20th anniversary with the University of California system. His journey began in 2004 at UC Davis, where he started as an Information Systems Analyst. Kevin played a pioneering role by supporting the California Electronic Death Registration System, a groundbreaking initiative developed by the UC for the California Department of Public Health under Dr. Michael Hogarth's leadership. In 2020, Kevin, along with other CalIVRS team members from UCD, transitioned to UC San Diego. Throughout his career, Kevin's contributions have been invaluable in ensuring reliable and responsive service for the state.

The Kunkel family's dedication to the UC extends beyond Kevin. His mother, Martha Kunkel, served as a Clinical Lab Specialist in Pathology at the UCD Medical Center for an impressive 32 years. Martha's commitment began even earlier, at the Sacramento County Hospital (later renamed Sacramento Medical Center), six years before the University acquired it and established it as the UC Davis Medical Center. A dedicated professional, Martha also held a Bachelor's degree in Nursing from the University of Washington. We mourn her passing earlier this year in January.

The University of California is deeply grateful for the enduring service of the Kunkel family.

As faculty Tim Kuo, PhD, embarks on a new chapter at Yale University, we want to take a moment to bid him a fond farewell. Dr. Kuo’s work as an Associate Professor has been integral to DBMI. In addition to his research in the areas of Predictive Modeling and Personalized Medicine; Privacy Technology, Data Sharing, and Big Data Analytics, he has served as the Associate Director of our NLM Fellowship and Co-Director for our Summer Internship Program. An alumni of our Summer Internship Program turned faculty, Tim’s dedication and kindness is something notable we all will truly miss.

DBMI Faculty and Staff headed out to catch the 2024 eclipse!

DBMI Post Doc fellow Alina Arseniev-Koehler, PhD has recently been awarded the AnalytiXIN Fellowship. AnalytiXIN is an academic-industry initiative based in Indianapolis, established to develop a digital community, including a collaboration location in Indianapolis. The program is aimed at strengthening engagement among academic researchers with their industry counterparts. In affiliation with Purdue University’s Office of Research, Dr. Arseniev-Koehler joins 8 others as faculty research fellows. Their research will continue to focus on computational and cultural sociology.

DBMI hosted its annual student retreat with all thanks for Pre-doc student, Brian Johnson as organizer. The retreat included flash talks from DBMI faculty and student faculty networking. We want to give a special thanks for Brian for organizing such a successful retreat and to all who attended!

We want to take time to celebrate the following students for successfully defending their dissertations!

Alexander Wenzel
"Expanding the applicability of gene set enrichment analysis with data-driven gene set refinement and adaptation for sparse data"

Jennifer P. Nguyen “Using multi-omic QTL analysis in fetal-like pancreatic progenitor cells to characterize diabetes-associated regulatory variants during early development”

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.

Do you have an event you would like to share on our calendar? Let us know at DBMI_Events@health.ucsd.edu.

Have your presented a poster recently? Please provide an electronic copy to

Maria (M1Triplett@health.ucsd.edu) so we can include it in our next newsletter

and promote your great work across campus.

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

Ayers JW, Poliak A, Dredze M, Leas EC, Zhu Z, Kelley JB, Faix DJ, Goodman AM, Longhurst CA, Hogarth M, Smith DM. Comparing Physician and Artificial Intelligence Chatbot Responses to Patient Questions Posted to a Public Social Media Forum. JAMA Intern Med. 2023 Apr 28:e231838. doi: 10.1001/jamainternmed.2023.1838. Online ahead of print. PMID: 37115527

Wardi G, Owens R, Josef C, Malhotra A, Longhurst C, Nemati S. Bringing the Promise of Artificial Intelligence to Critical Care: What the Experience With Sepsis Analytics Can Teach Us. Crit Care Med. 2023 Apr 26. doi: 10.1097/CCM.0000000000005894. Online ahead of print. PMID: 37098790 No abstract available.

Wang X, Ryu J, Kim J, Ramirez A, Mayo KR; All of Us Research Program; Condon H, Vaitinadin NS, Ohno-Machado L, Talavera GA, Ellinor PT, Lubitz SA, Choi SH. Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program. J Hum Genet. 2023 Apr 18. doi: 10.1038/s10038-023-01147-z. Online ahead of print. PMID: 37072623

Boussina A, Langouche L, Obirieze AC, Sinha M, Mack H, Leineweber W, Aralar A, Pride DT, Coleman TP, Fraley SI. Machine learning based DNA melt curve profiling enables automated novel genotype detection. BMC Bioinformatics. 2024 May 10;25(1):185. doi: 10.1186/s12859-024-05747-0. PMID: 38730317

Goldhaber NH, Jacobs MB, Laurent LC, Knight R, Zhu W, Pham D, Tran A, Patel SP, Hogarth M, Longhurst CA. Integrating clinical research into electronic health record workflows to support a learning health system. JAMIA Open. 2024 May 15;7(2):ooae023. doi: 10.1093/jamiaopen/ooae023. eCollection 2024 Jul. PMID: 38751411

Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Matsen Iv FA, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Random-effects substitution models for phylogenetics via scalable gradient approximations. Syst Biol. 2024 May 7:syae019. doi: 10.1093/sysbio/syae019. Online ahead of print. PMID: 38712512

Leas EC, Ayers JW, Desai N, Dredze M, Hogarth M, Smith DM Using Large Language Models to Support Content Analysis: A Case Study of ChatGPT for Adverse Event Detection. J Med Internet Res. 2024 May 2;26:e52499. doi: 10.2196/52499. PMID: 38696245

Okeke N, Hennessey KC, Sitapati AM, Weisshaar D, Shah NP, Alicki R, Haft H. Sustainable Approach to Justice, Equity, Diversity, and Inclusion Through Better Quality Measurement. Circ Cardiovasc Qual Outcomes. 2024 Apr 15:e010791. doi: 10.1161/CIRCOUTCOMES.123.010791. Online ahead of print. PMID: 38618717 Review.

Pham TT, Loo TM, Malhotra A, Longhurst CA, Hylton D, Dameff C, Tully J, Wardi G, Sell RE, Pearce AK. Ransomware Cyberattack Associated With Cardiac Arrest Incidence and Outcomes at Untargeted, Adjacent Hospitals. Crit Care Explor. 2024 Apr 10;6(4):e1079. doi: 10.1097/CCE.0000000000001079. eCollection 2024 Apr. PMID: 38605720

Baxter SL, Longhurst CA, Millen M, Sitapati AM, Tai-Seale M. Generative artificial intelligence responses to patient messages in the electronic health record: early lessons learned. JAMIA Open. 2024 Apr 10;7(2):ooae028. doi: 10.1093/jamiaopen/ooae028. eCollection 2024 Jul. PMID: 38601475

Goldhaber NH, Mehta S, Longhurst CA, Malachowski E, Jones M, Clary BM, Schaefer RL, McHale M, Rhodes LP, Mekeel KL, Reeves JJ. Call me Ishmael: addressing the white whale of team communication in the operating room with labelled surgical caps at an academic medical centre. BMJ Open Qual. 2024 Apr 8;13(2):e002453. doi: 10.1136/bmjoq-2023-002453. PMID: 38589054

Zhang M, Kuo TT. Early prediction of long hospital stay for Intensive Care units readmission patients using medication information. Comput Biol Med. 2024 Apr 8;174:108451. doi: 10.1016/j.compbiomed.2024.108451. Online ahead of print. PMID: 38603899

Voices of All of Us: Dr. Sally Baxter: A Bold Vision for Big Data and Health Equity Sally Baxter, M.D., MSc., is a physician-scientist using All of Us data to study vision loss. She’s also a program participant. In college, Dr. Baxter interned at a mobile clinic that gave vision screenings to children in underserved communities. Now, she studies ways to predict risk for glaucoma—one of the leading causes of blindness. And she’s spreading her passion for learning and growth to the early-career researchers she trains. Article Link: March 2024 | Join All of Us

Patel SP, Wang R, Zhou SQ, Sheinson D, Johnson A, Lee JS. Validation of an Updated Algorithm to Identify Patients With Incident Non-Small Cell Lung Cancer in Administrative Claims Databases. JCO Clin Cancer Inform. 2024 Mar;8:e2300165. doi: 10.1200/CCI.23.00165. PMID: 38502111

Krause M, Mehdipour S, Veerapong J, Baumgartner JM, Lowy AM, Gabriel RA. Development of a predictive model for risk stratification of acute kidney injury in patients undergoing cytoreductive surgery with hyperthermic intraperitoneal chemotherapy. Sci Rep. 2024 Mar 19;14(1):6630. doi: 10.1038/s41598-024-54979-w. PMID: 38503776

Christopher M, Hallaj S, Jiravarnsirikul A, Baxter SL, Zangwill LM. Novel Technologies in Artificial Intelligence and Telemedicine for Glaucoma Screening. J Glaucoma. 2024 Mar 20. doi: 10.1097/IJG.0000000000002367. Online ahead of print. PMID: 38506792

Garcia P, Ma SP, Shah S, Smith M, Jeong Y, Devon-Sand A, Tai-Seale M, Takazawa K, Clutter D, Vogt K, Lugtu C, Rojo M, Lin S, Shanafelt T, Pfeffer MA, Sharp C. Artificial Intelligence-Generated Draft Replies to Patient Inbox Messages. JAMA Netw Open. 2024 Mar 4;7(3):e243201. doi: 10.1001/jamanetworkopen.2024.3201. PMID: 38506805

Stults CD, Mazor KM, Cheung M, Ruo B, Li M, Walker A, Saphirak C, Vaida F, Singh S, Fisher KA, Rosen R, Yood R, Garber L, Longhurst C, Kallenberg G, Yu E, Chan A, Millen M, Tai-Seale M. Patients' Perspectives on Plans Generated During Primary Care Visits and Self-Reported Adherence at 3 Months: Data From a Randomized Trial. J Particip Med. 2024 Mar 14;16:e50242. doi: 10.2196/50242. PMID: 38483458

Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN; iPSCORE Consortium; Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, Frazer KA. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. Nat Commun. 2024 Feb 23;15(1):1664. doi: 10.1038/s41467-024-45506-6. PMID: 38395976

Nibbelink CW, Dunn Lopez K, Reeves JJ, Horman S, El-Kareh RE. Nurse and Physician Perceptions and Decision Making During Interdisciplinary Communication: Factors That Influence Communication Channel Selection. Comput Inform Nurs. 2024 Feb 12. doi: 10.1097/CIN.0000000000001108. Online ahead of print. dPMID: 38335993

Kwan B, Bell JF, Longhurst CA, Goldhaber NH, Clay B. Implementation of an electronic health record-integrated instant messaging system in an academic health system. J Am Med Inform Assoc. 2024 Jan 29:ocad253. doi: 10.1093/jamia/ocad253. Online ahead of print. PMID: 38287641

Boussina A, Shashikumar SP, Malhotra A, Owens RL, El-Kareh R, Longhurst CA, Quintero K, Donahue A, Chan TC, Nemati S, Wardi G. Impact of a deep learning sepsis prediction model on quality of care and survival. NPJ Digit Med. 2024 Jan 23;7(1):14. doi: 10.1038/s41746-023-00986-6. PMID: 38263386

Kwan B, Engel J, Steele B, Oyama L, Longhurst CA, El-Kareh R, Daniel M, Goldberg C, Clay B. An Automated System for Physician Trainee Procedure Logging via Electronic Health Records. JAMA Netw Open. 2024 Jan 2;7(1):e2352370. doi: 10.1001/jamanetworkopen.2023.52370. PMID: 38265802

Boussina A, Chan T, Donahue A, El-Kareh R, Malhotra A, Owens R, Quintero K, Shashikumar S. Study: AI Surveillance Tool Successfully Helps to Predict Sepsis, Saves Lives (ucsd.edu) The study was funded, in part, by the National Institutes of Health (grants K23GM146092, R01LM013998, R42AI177108 and R35GM143121), the National Library of Medicine (grant 2T15LM011271-11), and the Joan and Irwin Jacobs Center for Health Innovation at UC San Diego Health.

Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC; SEARCH Alliance; Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting. Clin Infect Dis. 2024 Jan 16:ciad738. doi: 10.1093/cid/ciad738. Online ahead of print. PMID: 38227643

Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H. Predictive analyses of regulatory sequences with EUGENe. Nat Comput Sci. 2023 Nov;3(11):946-956. doi: 10.1038/s43588-023-00544-w. Epub 2023 Nov 16. PMID: 38177592

Somayajula SA, Litake O, Liang Y, Hosseini R, Nemati S, Wilson DO, Weinreb RN, Malhotra A, Xie P. Improving long COVID-related text classification: a novel end-to-end domain-adaptive paraphrasing framework. Sci Rep. 2024 Jan 2;14(1):85. doi: 10.1038/s41598-023-48594-4. PMID: 38168099

Singh K, Kashani K, Awdishu L, Bagshaw S, Barreto E, Evans B, Forni L, Ghosh E, et al, Digital health and acute kidney injury: consensus report of the 27th Acute Disease Quality Initiative workgroup. PMID: 37580570 DOI: 10.1038/s41581-023-00744-7