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

Beauty is all around us and envelops us with data. We see streams of data as bits and bytes of information that inform and transform health. You, my colleagues, are pushing evolution outside of our genome and into the digital ecosystem that strengthens and supports health.

The Division and Department of Biomedical Informatics is currently at this juncture of opportunity. Ready and poised to contribute with our local, regional, and national colleagues to transform healthcare inclusive of dimensions of equity, security, transparency, and trustworthiness. Seek new ventures to collaborate and innovate. For those of you who attend meetings during fall to learn newly emerging approaches to methods and intervention — take notes, commit to a new idea, and share those ideas with your colleagues, trainees, and fellow staff. Team science requires team learning — we seek to stretch and strengthen our minds to lead this endeavor.

Next time you sit down to type on a keyboard, pause, and feel informatics — how is your compassion and intent — actively working to better health for the common good, one keystroke at a time?

Amy M. Sitapati, MD

Interim Chief, Division of Biomedical Informatics, UCSD

Interim Chair, Department of Biomedical Informatics, UCSD Health

In a recent issue of Nature Genetics, DBMI Assistant Professor Tiffany Amariuta, PhD, and co-authors develop a new statistical method to infer causal cell types for polygenic diseases and complex traits . Genome-wide association studies have identified hundreds of thousands of disease-associated variants, but it is unclear which genes and cell types mediate the effects of these variants. In this study, the authors disentangle genetic effects between closely related cell types to identify tissue-specific contributions to the genetics of 78 diseases and complex traits and to the genetic correlations of 262 pairs of diseases/traits with high genetic correlation. The authors provide software for the greater genomics community to engage with this new method.

Kathleen Curtius, PhD, and her team published a paper titled cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory in the journal Bioinformatics this month. DBMI PhD student Brian Johnson is first author on the paper, and both collaborated with researchers in the UCSD Math department to derive analytical methods for measuring growth rates of clonal populations in the human body. When applied to hematopoietic data, they show that their estimates may have broad applications to improve prognostic ability. For example, they found that stratifying patients with a myeloproliferative neoplasm (MPN) by the growth rate of their fittest clone shows that higher growth rates are significantly associated with shorter time to MPN diagnosis. Brian also created a freely accessible R package called cloneRate to apply these methods to your own single-cell sequencing data.

DBMI has been awarded a new grant (1R01CA270235) from the National Cancer Institute titled Multiscale modeling of spatiotemporal evolution in Barrett's esophagus. Kathleen Curtius, PhD, is the PI and key co-investigator contributors are located at the William Grady Lab at the Fred Hutchinson Cancer Research Center and the Shibata Lab at USC. As background, Barrett’s esophagus (BE) is the precursor to esophageal adenocarcinoma (EAC). Therefore, patients undergo surveillance exams to detect early cancers. Dr. Curtius and team’s study proposed experiments and analyses will define a BE patient’s “tissue phylogeography", including significant features of clonal expansions that are predictive of BE progressing to future EAC. To this end, they will leverage a rich set of serially collected tissue samples and genomic data from patients in the Seattle BE natural history cohort that includes cancer outcome patients and an age-matched group of patients with non-cancer outcomes, sampled at multiple time points. This R01 funding is for 5 years.

Congratulations are in order for Brian Fox and Edwin (Ed) Bean, MS as we celebrate their anniversaries. As of May 2023, Brian has been dedicated to serving UCSD for 10 years! We want to take this time to extend our appreciation and gratitude to Brian for his commitment to DBMI. Additionally, we want to congratulate Ed for his upcoming anniversary in November as he celebrates 15 years at UCSD! We want to take time to thank you Ed for your loyalty and devotion as you approach this exceptional milestone. You both are invaluable members of our team and your presence and hard work has been vital in DBMI's success. It’s been an honor to share in your achievements; here's to many more!

During the past year, the All of Us Research Program held a program-wide initiative to meet elevated objectives during special weeks. These "enrollment sprints" encouraged the All of Us team here at DBMI to think big and unite in a shared commitment for the program's success. All of Us CEO Josh Denny has recognized Jamie Le and Teresa Magdaleno Perez for their dedication and contributions to the All of Us May Elevate Initiative. Congratulations are in order for their hard work and achievement! While Jamie and Teresa may have received the appreciation awards, it's important to acknowledge that this achievement was made possible through the collective hard work and determination of the entire team.

We're delighted to share some uplighting news — a new baby arrived in the DBMI family in July 2023! Congratulations to Angelina Cordaro on the birth of her little one, Ella Cordaro Marker, who came into the world weighing 8 pounds and 6 ounces with a head full of hair! Join us in sending our warmest wishes and congratulations to the Cordaro family.

Say hello to DBMI's newest fur baby, Leo! Mathi Ganapathi and family adopted the Maltipoo in August 2023. He is now 15 weeks old and his current hobbies include chewing his brothers' shoes, taking long walks, and getting zoomies after potty breaks!

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.

Isakari M, Sanchez A, Conic R, Peretti J, Saito K, Sitapati AM, Millen M, Longhurst C. Benefits and Challenges of Transitioning Occupational Health to an Enterprise Electronic Health Record. J Occup Environ Med. 2023 Apr 12. doi: 10.1097/JOM.0000000000002864. Online ahead of print. PMID: 37043385

Ohno-Machado L, Jiang X, Kuo TT, Tao S, Chen L, Ram PM, Zhang GQ, Xu H. A Hierarchical Strategy to Minimize Privacy Risk when Linking "De-identified" Data in Biomedical Research Consortia. J Biomed Inform. 2023 Feb 16:104322. doi: 10.1016/j.jbi.2023.104322. Online ahead of print. PMID: 36806328

Rogers P, Boussina AE, Shashikumar SP, Wardi G, Longhurst CA, Nemati S. J Med Internet Res. Optimizing the Implementation of Clinical Predictive Models to Minimize National Costs: Sepsis Case Study. 2023 Feb 13;25:e43486. doi: 10.2196/43486. PMID: 36780203

Lee TC, Radha-Saseendrakumar B, Delavar A, Ye GY, Ting MA, Topilow NJ, Bass J, Korn BS, Kikkawa DO, Baxter SL, Liu CY. Evaluation of Depression and Anxiety in a Diverse Population With Thyroid Eye Disease Using the Nationwide NIH All of Us Database. Ophthalmic Plast Reconstr Surg. 2023 Jan 24. doi: 10.1097/IOP.0000000000002318. Online ahead of print. PMID: 36727790

Fatemeh Amrollahi, Supreeth P Shashikumar, Angela Meier, Lucila Ohno-Machado, Shamim Nemati, Gabriel Wardi, All of Us Data Helps Better Predict Hospital Readmission for Patients With Sepsis, National Institue of Health All of Us Research Program, October 4, 2022

Fatemeh Amrollahi, Supreeth P Shashikumar, Angela Meier, Lucila Ohno-Machado, Shamim Nemati, Gabriel Wardi, Inclusion of social determinants of health improves sepsis readmission prediction models, Journal of the American Medical Informatics Association, Volume 29, Issue 7, July 2022, Pages 1263–1270

Kuo, TT, Ohno-Machado L. Transforming Biomedical Informatics and Health Information Access: Don Lindberg and the U.S. National Library of Medicine, 978-1-64368-238-9 (print) | 978-1-64368-239-6 (online)

Tong EK, Zhu SH, Anderson CM, Avdalovic MV, Amin AN, Diamant AL, Fong TW, Clay B, El-Kareh R, Sankaran S, Bonniot C, Kirby CA, Mayoral A, Sarna L. Implementation, Maintenance, and Outcomes of an Electronic Referral to a Tobacco Quitline Across Five Health Systems. Nicotine Tob Res. 2023 Mar 29:ntad008. doi: 10.1093/ntr/ntad008. Online ahead of print.PMID: 36977494

Kuo TT, Pham A, Edelson ME, Kim J, Chan J, Gupta Y, Ohno-Machado L; Blockchain-Enabled Immutable, Distributed, and Highly Available Clinical Research Activity Logging System for Federated COVID-19 Data Analysis from Multiple Institutions. J Am Med Inform Assoc. 2023 Mar 14:ocad049. doi: 10.1093/jamia/ocad049. Online ahead of print. PMID: 36916740

Nakagawa K, Moukheiber L, Celi LA, Patel M, Mahmood F, Gondim D, Hogarth M, Levenson R. AI in Pathology: What could possibly go wrong? Semin Diagn Pathol. 2023 Mar 2:S0740-2570(23)00017-5. doi: 10.1053/j.semdp.2023.02.006. Online ahead of print. PMID: 36882343 Review.

D'Antonio M, Nguyen JP, Arthur TD; Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. iPSCORE Consortium; Matsui H, D'Antonio-Chronowska A, Frazer KA. Nat Commun. 2023 Feb 28;14(1):1132. doi: 10.1038/s41467-023-36638-2. PMID: 36854752

Ohno-Machado L, Jiang X, Kuo TT, Tao S, Chen L, Ram PM, Zhang GQ, Xu H.A Hierarchical Strategy to Minimize Privacy Risk when Linking "De-identified" Data in Biomedical Research Consortia. J Biomed Inform. 2023 Feb 16:104322. doi: 10.1016/j.jbi.2023.104322. Online ahead of print. PMID: 36806328

Rogers P, Boussina AE, Shashikumar SP, Wardi G, Longhurst CA, Nemati S. Optimizing the Implementation of Clinical Predictive Models to Minimize National Costs: Sepsis Case Study. J Med Internet Res. 2023 Feb 13;25:e43486. doi: 10.2196/43486. PMID: 36780203

Lee TC, Radha-Saseendrakumar B, Delavar A, Ye GY, Ting MA, Topilow NJ, Bass J, Korn BS, Kikkawa DO, Baxter SL, Liu CY. Evaluation of Depression and Anxiety in a Diverse Population With Thyroid Eye Disease Using the Nationwide NIH All of Us Database. Ophthalmic Plast Reconstr Surg. 2023 Jan 24. doi: 10.1097/IOP.0000000000002318. Online ahead of print. PMID: 36727790.

Baxter, SL., Representation Matters - Diversity in Retina Clinical Trails. PMID: 36201217, DOI: 10.1001/jamaophthalmol.2022.3930

Matthews, B, Fredrickson, M, El-Kareh, R Structured case reviews for organizational learning about diagnostic vulnerabilities: initial experiences from two medical centers.& Diagnosis (Berl) 2020 Jan 28;7(1):27-35. doi: 10.1515/dx-2019-0032.

Ohno-Machado L, Xu H. Coronavirus: indexed data speed up solutions. Nature 584, 192 (2020)