Biomedical Informatics Publication

Azenkot T, Rivera DR, Stewart MD, Patel SP. Artificial Intelligence and Machine Learning Innovations to Improve Design and Representativeness in Oncology Clinical Trials. Am Soc Clin Oncol Educ Book. 2025 Jun;45(3):e473590. doi: 10.1200/EDBK-25-473590. Epub 2025 May 22. PMID: 40403202 Review.
Chae YK, Othus M, Patel SP, Aljumaily R, Win KZ, Pejovic T, Thomas SS, Robinson WR 3rd, Kim HS, Chung LI, McLeod CM, Chen HX, Sharon E, Streicher H, Ryan CW, Blanke CD, Kurzrock R. A phase II basket trial of dual anti-CTLA-4 and anti-PD-1 blockade in rare tumors (DART) SWOG S1609: durable responses and delayed pseudoprogression in small cell carcinoma of the ovary, hypercalcemic type cohort. Cancer Commun (Lond). 2025 May 22. doi: 10.1002/cac2.70020. Online ahead of print. PMID: 40402690
Manjanatha D, Pippard N, Bloss CS. Self-compassion as a protective factor against adverse consequences of social media use: A scoping review. PLoS One. 2025 May 21;20(5):e0322227. doi: 10.1371/journal.pone.0322227. eCollection 2025. PMID: 40397849 Free PMC article.
Singh A, Farmer PE, Tully JL, Waterman RS, Gabriel RA. Forecasting Surgical Bed Utilization: Architectural Design of a Machine Learning Pipeline Incorporating Predicted Length of Stay and Surgical Volume. J Med Syst. 2025 May 21;49(1):67. doi: 10.1007/s10916-025-02201-3. PMID: 40397217 Free PMC article.
Shashikumar SP, Mohammadi S, Krishnamoorthy R, Patel A, Wardi G, Ahn JC, Singh K, Aronoff-Spencer E, Nemati S. Development and prospective implementation of a large language model based system for early sepsis prediction. NPJ Digit Med. 2025 May 17;8(1):290. doi: 10.1038/s41746-025-01689-w. PMID: 40379845 Free PMC article.
Domingo MR, Do DD, Conlin CC, Bagrodia A, Barrett T, Baxter MT, Cooperberg M, Feng F, Hahn ME, Harisinghani M, Hollenberg G, Javier-Desloges J, Kallis K, Kamran S, Kane CJ, Kessler D, Kuperman J, Lee KL, Levine J, Liss MA, Margolis DJ, Matthews I, Murphy PM, Nakrour N, Ohliger M, Ollison C, Osinski T, Pamatmat AJ, Pompa IR, Rakow-Penner R, Roberts JL, Shabaik AS, Song Y, Song D, Tempany CM, Trecarten S, Wehrli N, Weinberg EP, Woolen S, Xu G, Zhong AY, Dale AM, Seibert TM. Restriction Spectrum Imaging as a quantitative biomarker for prostate cancer with reliable positive predictive value. J Urol. 2025 May 16:101097JU0000000000004611. doi: 10.1097/JU.0000000000004611. Online ahead of print. PMID: 40377262
Dennis MJ, Abrahami D, Vieira MC, Benjumea D, Boyd M, Shao A, Kelton J, Patel SP. Real-World Analysis of Disparities in Biomarker Testing and Use of Recommended Targeted Therapies in Metastatic Non-Small Cell Lung Cancer in the United States. JCO Precis Oncol. 2025 May;9:e2400449. doi: 10.1200/PO-24-00449. Epub 2025 May 15. PMID: 40373260
Tully JL, Gabriel RA, Waterman RS, Dameff CJ. Digital Disasters: The Growing Threat of Healthcare Ransomware. Anesthesiology. 2025 Jun 1;142(6):1005-1008. doi: 10.1097/ALN.0000000000005442. Epub 2025 May 13. PMID: 40358336 Review.
Zhou YQ, Litake O, Meineke MN, Tully JL, Xu N, Abdou W, Gabriel RA. A Large Language Model Approach to Identifying Preoperative Frailty Among Older Adults From Clinical Notes. J Am Geriatr Soc. 2025 May 15. doi: 10.1111/jgs.19545. Online ahead of print. PMID: 40372061
Dennis MJ, Abrahami D, Vieira MC, Benjumea D, Boyd M, Shao A, Kelton J, Patel SP. Real-World Analysis of Disparities in Biomarker Testing and Use of Recommended Targeted Therapies in Metastatic Non-Small Cell Lung Cancer in the United States. JCO Precis Oncol. 2025 May;9:e2400449. doi: 10.1200/PO-24-00449. Epub 2025 May 15. PMID: 40373260
Wardi G, Longhurst CA. Unreasonable effectiveness of training AI models locally. BMJ Qual Saf. 2025 May 8:bmjqs-2025-018543. doi: 10.1136/bmjqs-2025-018543. Online ahead of print. PMID: 40345681 No abstract available.
Weinreb RN, Lee AY, Baxter SL, Lee RWJ, Leng T, McConnell MV, El-Nimri NW, Rhew DC. Application of Artificial Intelligence to Deliver Healthcare From the Eye. JAMA Ophthalmol. 2025 May 8. doi: 10.1001/jamaophthalmol.2025.0881. Online ahead of print. PMID: 40338607
Ramesh G, Kobayashi E, Sharma N, Majithia AR, Kulasa K, Boeder SC. Accuracy of Factory-Calibrated Continuous Glucose Monitors in Critically Ill Patients Receiving Intravenous Insulin: A Prospective Clinical Trial of Two Leading Systems. J Diabetes Sci Technol. 2025 May 8:19322968251338865. doi: 10.1177/19322968251338865. Online ahead of print. PMID: 40337990
Pekar JE, Lytras S, Ghafari M, Magee AF, Parker E, Wang Y, Ji X, Havens JL, Katzourakis A, Vasylyeva TI, Suchard MA, Hughes AC, Hughes J, Rambaut A, Robertson DL, Dellicour S, Worobey M, Wertheim JO, Lemey P. The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. Cell. 2025 May 7:S0092-8674(25)00353-8. doi: 10.1016/j.cell.2025.03.035. Online ahead of print. PMID: 40339581
Díaz LA, Alazawi W, Agrawal S, Arab JP, Arrese M, Idalsoaga F, Barreyro FJ, Gadano A, Marciano S, Morales JM, Villela-Nogueira C, Leite N, Couto CA, Theodoro R, Joyner de Sousa Dias Monteiro M, Oliveira CP, Pessoa MG, Alvares-da-Silva MR, Madamba E, Bettencourt R, Richards LM, Majithia AR, Khera AV, Loomba R, Ajmera V. High inherited risk predicts age-associated increases in fibrosis in patients with MASLD. J Hepatol. 2025 May 5:S0168-8278(25)00294-6. doi: 10.1016/j.jhep.2025.04.035. Online ahead of print. PMID: 40334848
Pagadala MS, Teerlink CC, Jasuja GK, Palnati M, Anglin-Foote T, Chang NN, Deka R, Lee KM, Agiri FY, Amariuta T, Seibert TM, Rose BS, Pridgen KM, Lynch JA, Carter HK, Panizzon MS, Hauger RL. Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men. Nat Commun. 2025 May 2;16(1):4104. doi: 10.1038/s41467-025-57372-x. PMID: 40316537 Free PMC article.
Mathis MR, Mentz GB, Cao J, Balczewski EA, Janda AM, Likosky DS, Schonberger RB, Hawkins RB, Heung M, Ailawadi G, Ladhania R, Sjoding MW, Kheterpal S, Singh K; MPOG Collaborators. Hospital and Clinician Practice Variation in Cardiac Surgery and Postoperative Acute Kidney Injury. JAMA Netw Open. 2025 May 1;8(5):e258342. doi: 10.1001/jamanetworkopen.2025.8342. PMID: 40314957 Free PMC article.
McCurdy JD, Macdonald B, Rosenfeld G, Bessissow T, Jairath V, Bruining DH, Singh S. Editorial: Seton Use in Perianal Fistulising Crohn's Disease. Authors' Reply. Aliment Pharmacol Ther. 2025 Apr 27. doi: 10.1111/apt.70170. Online ahead of print. PMID: 40289278 No abstract available.

Le J, Huynh J, Vo B, Mai A, Mak RH, Momper JD, Capparelli EV, Harvey H, Avedissian S, Bradley E, Sitapati A, Singh K, Bradley JS. Variability in Meropenem Distribution and Clearance in Children with Sepsis: Population-Based Pharmacokinetics with Assessment of Renal Biomarkers. Clin Pharmacokinet. 2025 Apr 24. doi: 10.1007/s40262-025-01495-3. Online ahead of print. PMID: 40272699
Du AL, Macias AA, Burton BN, Gabriel RA. Association of Race, Ethnicity, and Outcomes Following Pediatric Firearm Injury: A United States Population Study. J Intensive Care Med. 2025 Apr 23:8850666251337399. doi: 10.1177/08850666251337399. Online ahead of print. PMID: 40267291
Johnson B, Bath T, Huang X, Lamm M, Earles A, Eddington H, Dornisch AM, Jih LJ, Gupta S, Shah SC, Curtius K. Large language models for extracting histopathologic diagnoses of colorectal cancer and dysplasia from electronic health records. medRxiv [Preprint]. 2025 Apr 22:2024.11.27.24318083. doi: 10.1101/2024.11.27.24318083. PMID: 40313292 Free PMC article. Preprint.
McCurdy JD, Macdonald B, Rosenfeld G, Bessissow T, Jairath V, Bruining DH, Singh S. Letter: Re-Examining Seton Efficacy in Perianal Crohn's Disease-Critical Considerations for Outcome Measurement and Clinical Interpretation. Authors' Reply. Aliment Pharmacol Ther. 2025 Apr 25. doi: 10.1111/apt.70153. Online ahead of print. PMID: 40276820 No abstract available.
Jung J, Kang S, Choi J, El-Kareh R, Lee H, Kim H. Evaluating the impact of explainable AI on clinicians' decision-making: A study on ICU length of stay prediction. Int J Med Inform. 2025 Apr 21;201:105943. doi: 10.1016/j.ijmedinf.2025.105943. Online ahead of print. PMID: 40318498
Morrison J, Le JP, Malhotra A, Nemati S, Wardi G, Ford JS. A Snapshot of National Institutes of Health Funding for Sepsis Research: 2019-2023. Ann Emerg Med. 2025 Apr 15:S0196-0644(25)00139-8. doi: 10.1016/j.annemergmed.2025.03.011. Online ahead of print. PMID: 40237685 No abstract available.
Umeh UO, Kalsi MS, Tailor M, Zhong H, Mehta S, Jain N, Pai P, Pulos B, Gabriel R, Joseph RS Jr, Lauzadis J, Hargett MJ, Rosenblatt MA. A cross-sectional study of diversity in regional anesthesia and acute pain medicine fellowships. Can J Anaesth. 2025 Apr 12. doi: 10.1007/s12630-025-02947-x. Online ahead of print. PMID: 40216689 English
Hallaj S, Halfpenny W, Radgoudarzi N, Boland MV, Swaminathan SS, Wang SY, Xu BY, Amarasekera DC, Stagg B, Chen A, Hribar M, Thakoor KA, Goetz KE, Myers JS, Lee AY, Christopher MA, Zangwill LM, Weinreb RN, Baxter SL. Gap Analysis of Standard Automated Perimetry Concept Representation in Medical Terminologies. J Glaucoma. 2025 Apr 8. doi: 10.1097/IJG.0000000000002575. Online ahead of print. PMID: 40193233
Melmed GY, Oliver B, Kennedy A, Hou JK, Lum D, Singh S, van Deen WK, Oberai R, Weaver SA, Testaverde J, Siegel CA; IBD Qorus. LONG-TERM SUSTAINED IMPROVEMENT IN UNPLANNED HEALTHCARE UTILIZATION IN PATIENTS WITH INFLAMMATORY BOWEL DISEASE. Am J Gastroenterol. 2025 Apr 7. doi: 10.14309/ajg.0000000000003454. Online ahead of print. PMID: 40192134
Chung S, Saberzadeh-Ardestani B, Nigam G, Yuan Y, Singh S, Shung D. Large Language Model-supported Systematic Reviews to Augment Clinical Guideline Development: An AGA Pilot. Gastroenterology. 2025 Apr 6:S0016-5085(25)00605-5. doi: 10.1053/j.gastro.2025.03.034. Online ahead of print. PMID: 40199387 No abstract available.
Singh S, Nguyen JD, Fudman DI, Gerich ME, Shah SA, Hudesman D, McConnell RA, Lukin DJ, Flynn AD, Hwang C, Sprung B, Gaidos JKJ, Mattar MC, Rubin DT, Hashash JG, Metwally M, Ali T, Ma C, Hoentjen F, Narula N, Bessissow T, Rosenfeld G, McCurdy JD, Ananthakrishnan AN, Cross RK, Rodriguez Gaytan JR, Gurrola ES, Patel S, Siegel CA, Melmed GY, Weaver SA, Power S, Zou G, Jairath V, Hou JK. Treat-to-target of endoscopic remission in patients with inflammatory bowel disease in symptomatic remission on advanced therapies (QUOTIENT): rationale, design and protocol for an open-label, multicentre, pragmatic, randomised controlled trial. BMJ Open Gastroenterol. 2025 Mar 31;12(1):e001615. doi: 10.1136/bmjgast-2024-001615. PMID: 40164445 Free PMC article.
Sawas T, Jones AR, Alsawas R, Talluri R, Rogers H, Bardhi O, Spezia-Lindner D, Gerberi D, Singh S, Murad MH, Shaheen NJ, Katzka DA, Wani S. Overall and Cause-Specific Mortality in Patients with Barrett's Esophagus: A Systematic Review and Meta-Analysis of Population-Based Studies. Am J Gastroenterol. 2025 Mar 31. doi: 10.14309/ajg.0000000000003456. Online ahead of print. PMID: 40162666
Dziegielewski C, Yuan Y, Ma C, Boland BS, Chang JT, Syal G, Vuyyuru SK, Peyrin-Biroulet L, Jairath V, Singh S. IL-23p19 Antagonists vs. Ustekinumab for Treatment of Crohn's Disease: A Meta-analysis of Randomized Controlled Trials. Am J Gastroenterol. 2025 Mar 12. doi: 10.14309/ajg.0000000000003406. Online ahead of print. PMID: 40071763
Filipovski I, Vesterdahl F, Curran BP, Gabriel RA. Treatment of Chronic Pain Due to Slipping Rib Syndrome Using Ultrasound-Guided Intercostal Cryoneurolysis: A Case Report. Case Rep Anesthesiol. 2025 Mar 11;2025:8800687. doi: 10.1155/cria/8800687. eCollection 2025. PMID: 40226487 Free PMC article.
Shashikumar SP, Mohammadi S, Krishnamoorthy R, Patel A, Wardi G, Ahn JC, Singh K, Aronoff-Spencer E, Nemati S. Development and Prospective Implementation of a Large Language Model based System for Early Sepsis Prediction. medRxiv [Preprint]. 2025 Mar 11:2025.03.07.25323589. doi: 10.1101/2025.03.07.25323589. PMID: 40162268 Free PMC article. Preprint.
Abushamma S, Yadete T, Nero N, Falloon K, Parker CE, Abreu MT, Ahuja V, Armuzzi A, Bemelman W, Bruining DH, Deepak P, Dignass A, Dotan I, Feagan BG, Fulmer C, Halfvarson J, Hart A, Holubar SD, Leong RW, Ma C, Magro F, McCurdy JD, Narula N, Panés J, Raine T, Regueiro M, Rogler G, Singh S, Sparrow MP, Spinelli A, Van Koughnett JA, Vuyyuru SK, Solitano V, Yuan Y, Jairath V, Rieder F. Definitions, Diagnosis and Management of Postoperative Recurrence in Crohn's Disease Patients with Permanent Ileostomy - A Systematic Review and Meta-Analysis. J Crohns Colitis. 2025 Mar 10:jjaf041. doi: 10.1093/ecco-jcc/jjaf041. Online ahead of print. PMID: 40066499
Moussa K, Virk JS, Paciotti B, Durbin-Johnson BP, Shantha JG, Tsui E, Sun CQ, Baxter SL, Gore C, Yiu GY. Adherence to Hydroxychloroquine Dosing Guidelines at the University of California. Ophthalmol Retina. 2025 Mar 10:S2468-6530(25)00100-9. doi: 10.1016/j.oret.2025.03.003. Online ahead of print. PMID: 40074061
Kepner W, Yang KH, Dionicio P, Bailey K, Satybaldiyeva N, Moore A, Han BH, Palamar JJ. Prevalence and Correlates of Lifetime Ecstasy/MDMA Use Among Asian American and Pacific Islander Adult Populations in the United States, 2015-2020. J Psychoactive Drugs. 2025 Mar 3:1-9. doi: 10.1080/02791072.2025.2474243. Online ahead of print. PMID: 40033160
Parsons GR, Parvathinathan G, Etemadi A, Liu S, Ross E, Jones WS, Stedman MR, Chang TI. Identifying peripheral artery disease in persons with and without chronic kidney disease from electronic health records.Vasc Med. 2025 Mar 3:1358863X251322182. doi: 10.1177/1358863X251322182. Online ahead of print. PMID: 40028756 No abstract available.
Arseniev-Koehler A, Tai-Seale M, Cené CW, Grunvald E, Sitapati A. Leveraging diagnosis and biometric data from the All of Us Research Program to uncover disparities in obesity diagnosis. Obes Pillars. 2025 Feb 7;13:100165. doi: 10.1016/j.obpill.2025.100165. eCollection 2025 Mar. PMID: 40028616 Free PMC article.
Chilakapati N, Timple L, Pizzi S, Fine JF, Makhija H, Bruce LK, Owens RL, Alden D, Malhotra A, Martin JL, Kamdar BB. Light levels in a modern intensive care unit: Impact of time of year, window directionality, and outdoor light levels. Chronobiol Int. 2025 Feb 24:1-9. doi: 10.1080/07420528.2025.2469885. Online ahead of print. PMID: 39994888
Pekar JE, Moshiri N, Lemey P, Crits-Christoph A, Débarre F, Goldstein SA, Hensel Z, Rambaut A, Worobey M, Holmes EC, Wertheim JO. Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived.Virus Evol. 2025 Feb 22;11(1):veaf008. doi: 10.1093/ve/veaf008. eCollection 2025. PMID: 40040925 Free PMC article.

Lubrano S, Cervantes-Villagrana RD, Faraji F, Ramirez S, Sato K, Adame-Garcia SR, Officer A, Arang N, Rigiracciolo DC, Anguiano Quiroz PY, Martini C, Wang Y, Ferguson FM, Bacchiocchi A, Halaban R, Coma S, Holmen SL, Pachter JA, Aplin AE, Gutkind JS. FAK inhibition combined with the RAF-MEK clamp avutometinib overcomes resistance to targeted and immune therapies in BRAF V600E melanoma. Cancer Cell. 2025 Feb 20:S1535-6108(25)00053-4. doi: 10.1016/j.ccell.2025.02.001. Online ahead of print. PMID: 40020669
Cai CX, Hribar M, Baxter S, Goetz K, Swaminathan SS, Flowers A, Brown EN, Toy B, Xu B, Chen J, Chen A, Wang S, Lee C, Leng T, Ehrlich JR, Barkmeier A, Armbrust KR, Boland MV, Dorr D, Boyce D, Alshammari T, Swerdel J, Suchard MA, Schuemie M, Bu F, Sena AG, Hripcsak G, Nishimura A, Nagy P, Falconer T, DuVall SL, Matheny M, Viernes B, O'Brien W, Zhang L, Martin B, Westlund E, Mathioudakis N, Fan R, Wilcox A, Lai A, Stocking JC, Takkouche S, Lee LH, Xie Y, Humes I, McCoy DB, Adibuzzaman M, Areaux RG Jr, Rojas-Carabali W, Brash J, Lee DA, Weiskopf NG, Mawn L, Agrawal R, Morgan-Cooper H, Desai P, Ryan PB. Semaglutide and Nonarteritic Anterior Ischemic Optic Neuropathy.JAMA Ophthalmol. 2025 Feb 20. doi: 10.1001/jamaophthalmol.2024.6555. Online ahead of print. PMID: 39976940

Arthur TD, Nguyen JP, Henson BA, D'Antonio-Chronowska A, Jaureguy J, Silva N; iPSCORE Consortium; Panopoulos AD, Izpisua Belmonte JC, D'Antonio M, McVicker G, Frazer KA. Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants. Cell Genom. 2025 Feb 16:100775. doi: 10.1016/j.xgen.2025.100775. Online ahead of print. PMID: 39986281

Ford JS, Morrison JC, Kyaw M, Hewlett M, Tahir P, Jain S, Nemati S, Malhotra A, Wardi G. The Effect of Severe Sepsis and Septic Shock Management Bundle (SEP-1) Compliance and Implementation on Mortality Among Patients With Sepsis : A Systematic Review. Ann Intern Med. 2025 Feb 18. doi: 10.7326/ANNALS-24-02426. Online ahead of print. PMID: 39961104 Review.
Rountree L, Lin YT, Liu C, Salvatore M, Admon A, Nallamothu BK, Singh K, Basu A, Bu F, Mukherjee B. Reporting of Fairness Metrics in Clinical Risk Prediction Models: A Call for Change to Ensure Equitable Precision Health Benefits for All. Online J Public Health Inform. 2025 Feb 17. doi: 10.2196/66598. Online ahead of print. PMID: 39962044
Syal G, Barnes E, Raffals L, Al Kazzi E, Haydek J, Agrawal M, Singh S. Correction to: Medical Therapies for Prevention and Treatment of Inflammatory Pouch Disorders-A Systematic Review and Meta-Analysis. Am J Gastroenterol. 2025 Feb 17. doi: 10.14309/ajg.0000000000003285. Online ahead of print. PMID: 39950961 No abstract available.
Alina Arseniev-Koehler, Ming Tai-Seale, Crystal W. Cené, Eduardo Grunvald, Amy Sitapati,
Leveraging diagnosis and biometric data from the All of Us Research Program to uncover disparities in obesity diagnosis, Obesity Pillars, Volume 13, 2025, 100165, ISSN 2667-3681,
D'Antonio M, Arthur TD, Gonzalez Rivera WG, Wu X, Nguyen JP, Gymrek M, Woo-Yeong P, Frazer KA. Genetic analysis of elevated levels of creatinine and cystatin C biomarkers reveals novel genetic loci associated with kidney function. Hum Mol Genet. 2025 Feb 10:ddaf018. doi: 10.1093/hmg/ddaf018. Online ahead of print. PMID: 39927731
Owsley C, Matthies DS, McGwin G, Edberg JC, Baxter SL, Zangwill LM, Owen JP, Lee CS; AI-READI Consortium. Cross-sectional design and protocol for Artificial Intelligence Ready and Equitable Atlas for Diabetes Insights (AI-READI). BMJ Open. 2025 Feb 6;15(2):e097449. doi: 10.1136/bmjopen-2024-097449. PMID: 39915016
Kuo TT, Gabriel RA, Koola J, Schooley RT, Ohno-Machado L. Distributed cross-learning for equitable federated models - privacy-preserving prediction on data from five California hospitals. Nat Commun. 2025 Feb 5;16(1):1371. doi: 10.1038/s41467-025-56510-9. PMID: 39910076 Free PMC article.
Baxter SL. Precision Population-Based Screening for Glaucoma. JAMA Netw Open. 2025 Feb 3;8(2):e2457849. doi: 10.1001/jamanetworkopen.2024.57849. PMID: 39913142 No abstract available.
Luke JJ, Sweis RF, Hecht JR, Schneider R, Stein MN, Golan T, Yap TA, Khilnani A, Huang M, Zhao R, Jemielita T, Patel SP. Intratumoral or Subcutaneous MK-2118, a Non-Cyclic Dinucleotide STING Agonist, With or Without Pembrolizumab for Advanced or Metastatic Solid Tumors or Lymphomas. Clin Cancer Res. 2025 Jan 23. doi: 10.1158/1078-0432.CCR-24-2824. Online ahead of print.PMID: 39846804
Gabriel RA, Park BH, Hsu CN, Macias AA. A Review of Leveraging Artificial Intelligence to Predict Persistent Postoperative Opioid Use and Opioid Use Disorder and its Ethical Considerations. Curr Pain Headache Rep. 2025 Jan 23;29(1):30. doi: 10.1007/s11916-024-01319-2. PMID: 39847176 Review.
Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R. Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data. Nat Commun. 2025 Jan 18;16(1):825. doi: 10.1038/s41467-025-56077-5. PMID: 39827261
Pham A, El-Kareh R, Myers F, Ohno-Machado L, Kuo TT. Predicting positive Clostridioides difficile test results using large-scale longitudinal data of demographics and medication history. Heliyon. 2024 Dec 18;11(1):e41350. doi: 10.1016/j.heliyon.2024.e41350. eCollection 2025 Jan 15. PMID: 39958729 Free PMC article.

Tully JL, Litake O, Meineke MN, Simpson S, Waterman RS, Gabriel RA. Classification of Surgical Patients Needing Preoperative Cardiac Evaluations: A Comparison of General-Purpose and Domain-Specific Large Language Models. Anesth Analg. 2025 Jan 14. doi: 10.1213/ANE.0000000000007408. Online ahead of print. PMID: 39808709 No abstract available.
Faraji F, Ramirez SI, Clubb LM, Sato K, Burghi V, Hoang TS, Officer A, Anguiano Quiroz PY, Galloway WMG, Mikulski Z, Medetgul-Ernar K, Marangoni P, Jones KB, Cao Y, Molinolo AA, Kim K, Sakaguchi K, Califano JA 3rd, Smith Q, Goren A, Klein OD, Tamayo P, Gutkind JS. YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution. Nat Commun. 2025 Jan 8;16(1):498. doi: 10.1038/s41467-024-55660-6. PMID: 39779672 Free PMC article.
McCradden MD, London AJ, Gichoya JW, Sendak M, Erdman L, Stedman I, Oakden-Rayner L, Akrout I, Anderson JA, Farmer LA, Greer R, Goldenberg A, Ho Y, Joshi S, Louise J, Mamdani M, Mazwi ML, Mohamud A, Palmer LJ, Peperidis A, Pfohl SR, Rickard M, Semmler C, Singh K, Singh D, Soremekun S, Tikhomirov L, van der Vegt AH, Verspoor K, Liu X. CANAIRI: the Collaboration for Translational Artificial Intelligence Trials in healthcare. Nat Med. 2025 Jan 6. doi: 10.1038/s41591-024-03364-1. Online ahead of print. PMID: 39762426 No abstract available.
Begzati A, Godinez-Macias KP, Long T, Watrous JD, Moranchel R, Kantz ED, Tuomilehto J, Havulinna AS, Niiranen TJ, Jousilahti P, Salomaa V, Yu B, Norby F, Rebholz CM, Selvin E, Winzeler EA, Cheng S, Alotaibi M, Goyal R, Ideker T, Jain M, Majithia AR. Plasma Lipid Metabolites, Clinical Glycemic Predictors, and Incident Type 2 Diabetes. Diabetes Care. 2025 Jan 6:dc242266. doi: 10.2337/dc24-2266. Online ahead of print. PMID: 39761415
Kiraly J, Berzi A, El-Kareh R, Sebestyen E, Ujvarosy D, Emri M, Bhattoa HP, Kappelmayer J, Miller KE, Toth G. Breaking the guidelines: how financial unawareness fuels guideline deviations and inefficient DVT diagnostics. Diagnosis (Berl). 2025 Jan 6. doi: 10.1515/dx-2024-0165. Online ahead of print. PMID: 39752665
Chen JS, Esko JD, Walker E, Gordts PLSM, Baxter SL, Toomey CB. High Density Lipoproteins Associate with Age-Related Macular Degeneration in the All of Us Research Program. Ophthalmology. 2025 Jan 3:S0161-6420(25)00002-8. doi: 10.1016/j.ophtha.2024.12.039. Online ahead of print. PMID: 39756691
Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. Nat Genet. 2025 Jan 2. doi: 10.1038/s41588-024-01994-2. Online ahead of print. PMID: 39747598
Lo JE, Schmickl CN, Vaida F, Nemati S, Singh K, Sands SA, Owens RL, Malhotra A, Orr JE. The combination of physiology and machine learning for prediction of CPAP pressure and residual AHI in OSA. J Clin Sleep Med. 2025 Jan 2. doi: 10.5664/jcsm.11498. Online ahead of print. PMID: 39745438
Car J, Ong QC, Erlikh Fox T, Leightley D, Kemp SJ, Švab I, Tsoi KKF, Sam AH, Kent FM, Hertelendy AJ, Longhurst CA, Powell J, Hamdy H, Nguyen HVQ, Aoun Bahous S, Wang M, Baumgartner M, Mahendradhata Y, Popovic N, Khong AWH, Prober CG, Atun R; Digital Health Systems Collaborative; Bekele Zerihun A, Poncette AS, Molina AJR, Ferreira AVL, Fajkic A, Kaushal A, Farmer AJ, Lane AS, Kononowicz AA, Bhongir AV, Alayande BT, Bene BA, Dameff CJ, Hallensleben C, Back DA, Hawezy DJ, Tulantched DSM, Kldiashvili E, Achampong EK, Ramachandran G, Hauser G, Grove J, Cheung JPY, Imaralu JO, Sotunsa JO, Bulnes Vides JP, Lawrence KS, Agha-Mir-Salim L, Saba L, Zhang L, Elfiky MMA, Hesseling MW, Guppy MP, Phatak MS, Al Saadoon MAA, Lai NM, Chavannes NH, Kimberger O, Povoa P, Goh PS, Grainger R, Nannan Panday RS, Forsyth R, Vento S, Lee SY, Yadav SK, Syed-Abdul S, Appenzeller S, Denaxas S, Garba SE, Flügge T, Bokun T, Dissanayake VHW, Ho V, Obadiel YA. The Digital Health Competencies in Medical Education Framework: An International Consensus Statement Based on a Delphi Study. JAMA Netw Open. 2025 Jan 2;8(1):e2453131. doi: 10.1001/jamanetworkopen.2024.53131. PMID: 39888625
Mandeville R, Sedghamiz H, Mansfield P, Sheean G, Studer C, Cordice D, Ghanbari G, Malhotra A, Nemati S, Koola J. Deep learning enhanced transmembranous electromyography in the diagnosis of sleep apnea. BMC Neurosci. 2024 Dec 31;25(1):80. doi: 10.1186/s12868-024-00913-9. PMID: 39741274 Free PMC article.
Yuan Y, Biswas P, Zemke NR, Dang K, Wu Y, D'Antonio M, Xie Y, Yang Q, Dong K, Lau PK, Li D, Seng C, Bartosik W, Buchanan J, Lin L, Lancione R, Wang K, Lee S, Gibbs Z, Ecker J, Frazer K, Wang T, Preissl S, Wang A, Ayyagari R, Ren B. Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. bioRxiv [Preprint]. 2024 Dec 29:2024.12.28.630634. doi: 10.1101/2024.12.28.630634. PMID: 39764062 Free PMC article.
Bendik J, Castro A, Califano J, Carter H, Guo T. Identifying Strong Neoantigen MHC-I/II Binding Candidates for Targeted Immunotherapy with SINE. Int J Mol Sci. 2024 Dec 29;26(1):205. doi: 10.3390/ijms26010205. PMID: 39796063 Free PMC article.
Rojo Domingo M, Conlin CC, Karunamuni R, Ollison C, Baxter MT, Kallis K, Do DD, Song Y, Kuperman J, Shabaik AS, Hahn ME, Murphy PM, Rakow-Penner R, Dale AM, Seibert TM. Utility of quantitative measurement of T₂ using restriction spectrum imaging for detection of clinically significant prostate cancer. Sci Rep. 2024 Dec 28;14(1):31318. doi: 10.1038/s41598-024-82742-8. PMID: 39732834 Free PMC article.
Lee HH, Solitano V, Singh S, Ananthakrishnan AN, Jairath V, Syal G, Boland BS, Ghosh P, Chang JT, Singh S. Differential Efficacy of Advanced Therapies in Inducing Remission in Ulcerative Colitis Based on Prior Exposure to TNF Antagonists. Clin Gastroenterol Hepatol. 2024 Dec 26:S1542-3565(24)01132-7. doi: 10.1016/j.cgh.2024.12.007. Online ahead of print. PMID: 39732355 Review.
Do VM, Simpson S, Fisch KM, Gabriel RA. Associations Between Social Determinants of Health and Opioid-Use Disorder Among Chronic Pain Patients From a Multi-Institutional Dataset. Anesth Analg. 2024 Dec 23. doi: 10.1213/ANE.0000000000007247. Online ahead of print. PMID: 39715077
Shiller M, Johnson M, Auber R, Patel SP. Clinical perspectives on the value of testing for STK11 and KEAP1 mutations in advanced NSCLC. Front Oncol. 2024 Dec 5;14:1459737. doi: 10.3389/fonc.2024.1459737. eCollection 2024. PMID: 39703851 Free PMC article.
Boussina A, Krishnamoorthy R, Quintero K, Joshi S, Wardi G, Pour H, Hilbert N, Malhotra A, Hogarth M, Sitapati AM, VanDenBerg C, Singh K, Longhurst CA, Nemati S. Large Language Models for More Efficient Reporting of Hospital Quality Measures. NEJM AI. 2024 Oct 24;1(11):10.1056/aics2400420. doi: 10.1056/aics2400420. Epub 2024 Oct 21. PMID: 39703686 Free PMC article.
Reeves JJ, Goldhaber N, Hollandsworth H, Cox K, Dumitru AM, Zhao B, Longhurst CA, Berumen J, Berndtson AE, Jacobsen G, Clary B. Leveraging Lean Methodology to Improve Compliance With Work-Hour Restrictions. JAMA Surg. 2024 Dec 18. doi: 10.1001/jamasurg.2024.5518. Online ahead of print.PMID: 39693087
Shashikumar SP, Nemati S. A Prospective Comparison of Large Language Models for Early Prediction of Sepsis. Pac Symp Biocomput. 2025;30:109-120.PMID: 39670365

Lam JY, Lu X, Shashikumar SP, Lee YS, Miller M, Pour H, Boussina AE, Pearce AK, Malhotra A, Nemati S. Development, deployment, and continuous monitoring of a machine learning model to predict respiratory failure in critically ill patients. JAMIA Open. 2024 Dec 11;7(4):ooae141. doi: 10.1093/jamiaopen/ooae141. eCollection 2024 Dec. PMID: 39664647 Free PMC article.
Park BH, Macias AA, Fisch KM, Simpson S, Chen J, Gabriel RA. The Association of Social Determinants of Health With Reported Daily Pain Scores Among Patients With a History of Chronic Pain Using the "All of Us" Research Program. Anesth Analg. 2024 Dec 11. doi: 10.1213/ANE.0000000000007211. Online ahead of print. PMID: 39661558 No abstract available.
Haynesworth A, Yeh KH, Lee HH, Kirkpatrick M, Boland BS, Syal G, Xu R, Singh S. Long-Term Outcomes of an Infliximab-First Versus Vedolizumab-First Treatment Strategy in Biologic-Naïve Patients With Ulcerative Colitis. Aliment Pharmacol Ther. 2024 Dec 11. doi: 10.1111/apt.18441. Online ahead of print. PMID: 39660680
Sears T, Carter H. MHC-Hammer decodes HLA disruption in tumors. Cancer Res. 2024 Dec 5. doi: 10.1158/0008-5472.CAN-24-4553. Online ahead of print. PMID: 39636736
Luo Y, Huang CC, Howard NC, Wang X, Liu Q, Li X, Zhu J, Amariuta T, Asgari S, Ishigaki K, Calderon R, Raman S, Ramnarine AK, Mayfield JA, Moody DB, Lecca L, Fortune SM, Murray MB, Raychaudhuri S. Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis. Nat Commun. 2024 Nov 29;15(1):10393. doi: 10.1038/s41467-024-54741-w. PMID: 39613754 Free PMC article.
Quon JC, Long CP, Halfpenny W, Chuang A, Cai CX, Baxter SL, Daketi V, Schmitz A, Bahroos N, Xu BY, Toy BC. Implementing a Common Data Model in Ophthalmology: Mapping Structured Electronic Health Record Ophthalmic Examination Data to Standard Vocabularies. Ophthalmol Sci. 2024 Nov 28;5(2):100666. doi: 10.1016/j.xops.2024.100666. eCollection 2025 Mar-Apr. PMID: 39896425 Free PMC article.
Rule A, El-Kareh R. Employing EHR usage data to improve care requires clinician engagement and trust. J Hosp Med. 2024 Nov 28. doi: 10.1002/jhm.13565. Online ahead of print. PMID: 39609937 No abstract available.
Yu Y, Edelson M, Pham A, Pekar JE, Johnson B, Post K, Kuo TT. Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network. J Am Med Inform Assoc. 2024 Nov 21:ocae288. doi: 10.1093/jamia/ocae288. Online ahead of print. PMID: 39569448
Arseniev-Koehler A. Theoretical foundations and limits of word embeddings: What types of meaning can they capture? Sociol Methods Res. 2024 Nov;53(4):1753-1793. doi: 10.1177/00491241221140142. Epub 2022 Dec 7. PMID: 39554804 Free PMC article.
Heinke A, Zhang H, Broniarek K, Michalska-Małecka K, Elsner W, Galang CMB, Deussen DN, Warter A, Kalaw F, Nagel I, Agnihotri A, Mehta NN, Klaas JE, Schmelter V, Kozak I, Baxter SL, Bartsch DU, Cheng L, An C, Nguyen T, Freeman WR. Cross-instrument optical coherence tomography-angiography (OCTA)-based prediction of age-related macular degeneration (AMD) disease activity using artificial intelligence. Sci Rep. 2024 Nov 7;14(1):27085. doi: 10.1038/s41598-024-78327-0. PMID: 39511248
Chuang EG, Richardson AC, Boulil Z, Kuelbs CL, Huang JS. Disparities in Patient Portal Activation and Usage at a Large Pediatric Academic Institution. J Racial Ethn Health Disparities. 2024 Nov 4. doi: 10.1007/s40615-024-02009-w. Online ahead of print. PMID: 39497018
Murphy PM, An JY, Wojdyla LM, Searleman AC, Khurana A, Loehfelm TW, Fowler KJ, Longhurst CA. Diagnostic Performance of a Next-Generation Virtual/Augmented Reality Headset: A Pilot Study of Diverticulitis on CT.J Imaging Inform Med. 2024 Nov 4. doi: 10.1007/s10278-024-01292-7. Online ahead of print. PMID: 39495441
Hallaj S, Halfpenny W, Chuter BG, Weinreb RN, Baxter SL, Cui QN. Response to: "Comment on: Association between Glucagon-Like Peptide 1 (GLP-1) Receptor Agonists Exposure and Intraocular Pressure Change". Am J Ophthalmol. 2024 Oct 30:S0002-9394(24)00493-8. doi: 10.1016/j.ajo.2024.10.021. Online ahead of print. PMID: 39486630 No abstract available.
Murphy PM, An JY, Wojdyla LM, Searleman AC, Khurana A, Loehfelm TW, Fowler KJ, Longhurst CA. Diagnostic Performance of a Next-Generation Virtual/Augmented Reality Headset: A Pilot Study of Diverticulitis on CT. J Imaging Inform Med. 2024 Nov 4. doi: 10.1007/s10278-024-01292-7. Online ahead of print. PMID: 39495441
Hallaj S, Halfpenny W, Chuter BG, Weinreb RN, Baxter SL, Cui QN. Response to: "Comment on: Association between Glucagon-Like Peptide 1 (GLP-1) Receptor Agonists Exposure and Intraocular Pressure Change". Am J Ophthalmol. 2024 Oct 30:S0002-9394(24)00493-8. doi: 10.1016/j.ajo.2024.10.021. Online ahead of print. PMID: 39486630
Sanz Vidorreta FJ, Dudley MT, Walling AM, Tseng CH, Hogarth M, Wenger NS. Patient characteristics and health system encounters of decedents not marked deceased in the electronic health record. JAMIA Open. 2024 Oct 29;7(4):ooae121. doi: 10.1093/jamiaopen/ooae121. eCollection 2024 Dec. PMID: 39473881
Koola JD, Ramesh K, Mao J, Ahn M, Davis SE, Govindarajulu U, Perkins AM, Westerman D, Ssemaganda H, Speroff T, Ohno-Machado L, Ramsay CR, Sedrakyan A, Resnic FS, Matheny ME. A machine learning framework to adjust for learning effects in medical device safety evaluation. J Am Med Inform Assoc. 2024 Oct 29:ocae273. doi: 10.1093/jamia/ocae273. Online ahead of print.
PMID: 39471493
Tahir MW, Rosli Y, Leung C, Wysham KD, Lee J, Stovall R, Goulabchand R, Makris UE, Singh S, Singh N. Frailty and its association with readmissions in patients with rheumatoid arthritis: A national readmissions database study.Clin Rheumatol. 2024 Oct 19. doi: 10.1007/s10067-024-07200-2. Online ahead of print. PMID: 39425849
Ananthakrishnan AN, Murad MH, Scott FI, Agrawal M, Haydek JP, Limketkai BN, Loftus EV Jr, Singh S. Comparative Efficacy of Advanced Therapies for Management of Moderate-to-Severe Ulcerative Colitis: 2024 American Gastroenterological Association Evidence Synthesis. Gastroenterology. 2024 Oct 18:S0016-5085(24)05480-5. doi: 10.1053/j.gastro.2024.07.046. Online ahead of print. PMID: 39425738
Stadnick NA, Aarons GA, Edwards HN, Bryl AW, Kuelbs CL, Helm JL, Brookman-Frazee L. Cluster randomized trial of a team communication training implementation strategy for depression screening in a pediatric healthcare system: a study protocol. Implement Sci Commun. 2024 Oct 18;5(1):117. doi: 10.1186/s43058-024-00641-5.PMID: 39425229
Chae YK, Othus M, Patel SP, Wilkinson KJ, Whitman-Purves EM, Lea J, Schallenkamp JM, Adra N, Appleman LJ, Alden M, Thomes Pepin J, Ellerton JA, Poklepovic A, Walter A, Rampurwala MM, Robinson WR, Kim HS, Chung LI, McLeod CM, Lopez G, Chen HX, Sharon E, Streicher H, Ryan CW, Blanke CD, Kurzrock R. SWOG/NCI Phase II Dual Anti-CTLA-4/PD-1 Blockade in Rare Tumors (DART): Non-Epithelial Ovarian Cancer. Clin Cancer Res. 2024 Oct 17. doi: 10.1158/1078-0432.CCR-24-0606. Online ahead of print. PMID: 39417692
Chae YK, Othus M, Bedi S, Liu Y, Orr-Ewing L, Dash D, Koyejo S, Callahan A, Fries JA, Wornow M, Swaminathan A, Lehmann LS, Hong HJ, Kashyap M, Chaurasia AR, Shah NR, Singh K, Tazbaz T, Milstein A, Pfeffer MA, Shah NH. Testing and Evaluation of Health Care Applications of Large Language Models: A Systematic Review. JAMA. 2024 Oct 15:e2421700. doi: 10.1001/jama.2024.21700. Online ahead of print. PMID: 39405325
Solitano V, Hogan M, Singh S, Danese S, Peyrin-Biroulet L, Zou G, Yuan Y, Sands BE, Feagan BG, Dulai PS, Narula N, Ma C, Jairath V. Placebo rates in Crohn's disease randomized clinical trials: An individual patient data meta-analysis. Gastroenterology. 2024 Oct 14:S0016-5085(24)05571-9. doi: 10.1053/j.gastro.2024.10.009. Online ahead of print. PMID: 39414161
Jansen CS, Pagadala MS, Cardenas MA, Prabhu RS, Goyal S, Zhou C, Chappa P, Vo BT, Ye C, Hopkins B, Zhong J, Klie A, Daniels T, Admassu M, Green I, Pfister NT, Neill SG, Switchenko JM, Prokhnevska N, Hoang KB, Torres MA, Logan S, Olson JJ, Nduom EK, Del Balzo L, Patel K, Burri SH, Asher AL, Wilkinson S, Lake R, Kesarwala AH, Higgins KA, Patel P, Dhere V, Sowalsky AG, Carter H, Khan MK, Kissick H, Buchwald ZS. Pre-operative stereotactic radiosurgery and peri-operative dexamethasone for resectable brain metastases: a two-arm pilot study evaluating clinical outcomes and immunological correlates. Nat Commun. 2024 Oct 14;15(1):8854. doi: 10.1038/s41467-024-53034-6.PMID: 39402027
Ahuja D, Zou G, Solitano V, Syal G, Lee HH, Ma C, Jairath V, Singh S. No Impact of Concomitant Medications on Efficacy and Safety of Biologics and Small Molecules for Ulcerative Colitis.Clin Gastroenterol Hepatol. 2024 Oct 10:S1542-3565(24)00877-2. doi: 10.1016/j.cgh.2024.08.040. Online ahead of print. PMID: 39395572
Johnson B, Curtius K. Digital twins are integral to personalizing medicine and improving public health. Nat Rev Gastroenterol Hepatol. 2024 Oct 9. doi: 10.1038/s41575-024-00992-3. Online ahead of print. PMID: 39384936 No abstract available.
Zumsteg ZS, Sheth S, Jabbour SK, Patel KR, Kimple RJ, Williams TM, Xu-Welliver M, Torres-Saavedra PA, Monjazeb AM, Mayadev J, Finkelstein SE, Buatti JM, Patel SP, Lin SH. Challenges and opportunities for early phase clinical trials of novel drug-radiotherapy combinations: recommendations from NRG Oncology, the American Society for Radiation Oncology (ASTRO), the American College of Radiology (ACR), the Sarah Cannon Research Institute, and the American College of Radiation Oncology (ACRO). Lancet Oncol. 2024 Oct;25(10):e489-e500. doi: 10.1016/S1470-2045(24)00264-X.PMID: 39362260 Review.
Bongbong DN, Abdou W, Said ET, Gabriel RA. National trends in perioperative epidural analgesia use for surgical patients. J Clin Anesth. 2024 Oct 1;99:111642. doi: 10.1016/j.jclinane.2024.111642. Online ahead of print. PMID: 39357395

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2024 (selected publications)

Chae YK, Othus M, Patel S, Powers B, Hsueh CT, Govindarajan R, Bucur S, Kim HS, Chung LI, McLeod C, Chen HX, Sharon E, Streicher H, Ryan CW, Blanke C, Kurzrock R. Phase II basket trial of dual anti-CTLA-4 and anti-PD-1 blockade in rare tumors (DART) SWOG S1609: the desmoid tumors. J Immunother Cancer. 2024 Sep 28;12(9):e009128. doi: 10.1136/jitc-2024-009128. PMID: 39343510 Free PMC article. Clinical Trial.
Chen JS, Reddy AJ, Al-Sharif E, Shoji MK, Kalaw FGP, Eslani M, Lang PZ, Arya M, Koretz ZA, Bolo KA, Arnett JJ, Roginiel AC, Do JL, Robbins SL, Camp AS, Scott NL, Rudell JC, Weinreb RN, Baxter SL, Granet DB. Analysis of ChatGPT Responses to Ophthalmic Cases: Can ChatGPT Think like an Ophthalmologist? Ophthalmol Sci. 2024 Aug 23;5(1):100600. doi: 10.1016/j.xops.2024.100600. eCollection 2025 Jan-Feb. PMID: 39346575 Free PMC article.
Goldhaber NH, Ramesh K, Horton LE, Longhurst CA, Huang E, Horgan S, Jacobsen GR, Sandler BJ, Broderick RC. The Long Haul to Surgery: Long COVID Has Minimal Burden on Surgical Departments. Int J Environ Res Public Health. 2024 Sep 12;21(9):1205. doi: 10.3390/ijerph21091205. PMID: 39338088
Chen JS, Reddy AJ, Al-Sharif E, Shoji MK, Kalaw FGP, Eslani M, Lang PZ, Arya M, Koretz ZA, Bolo KA, Arnett JJ, Roginiel AC, Do JL, Robbins SL, Camp AS, Scott NL, Rudell JC, Weinreb RN, Baxter SL, Granet DB. Analysis of ChatGPT Responses to Ophthalmic Cases: Can ChatGPT Think like an Ophthalmologist? Ophthalmol Sci. 2024 Aug 23;5(1):100600. doi: 10.1016/j.xops.2024.100600. eCollection 2025 Jan-Feb. PMID: 39346575
Bongbong DN, Abdou W, Said ET, Gabriel RA. National trends in perioperative epidural analgesia use for surgical patients. J Clin Anesth. 2024 Oct 1;99:111642. doi: 10.1016/j.jclinane.2024.111642. Online ahead of print.
Gabriel RA, Litake O, Simpson S, Burton BN, Waterman RS, Macias AA. On the development and validation of large language model-based classifiers for identifying social determinants of health. Proc Natl Acad Sci U S A. 2024 Sep 24;121(39):e2320716121. doi: 10.1073/pnas.2320716121. Epub 2024 Sep 16. PMID: 39284061
DeForest N, Wang Y, Zhu Z, Dron JS, Koesterer R, Natarajan P, Flannick J, Amariuta T, Peloso GM, Majithia AR. Genome-wide discovery and integrative genomic characterization of insulin resistance loci using serum triglycerides to HDL-cholesterol ratio as a proxy. Nat Commun. 2024 Sep 14;15(1):8068. doi: 10.1038/s41467-024-52105-y. PMID: 39277575
Yoo K, Lee C, Baxter SL, Xu BY. Relationship Between Glaucoma and Chronic Stress Quantified by Allostatic Load Score in the All of Us Research Program. Am J Ophthalmol. 2024 Sep 11:S0002-9394(24)00429-X. doi: 10.1016/j.ajo.2024.09.009. Online ahead of print.PMID: 39271092
Simpson S, Zhong W, Mehdipour S, Armaneous M, Sathish V, Walker N, Said ET, Gabriel RA. Classifying High-Risk Patients for Persistent Opioid Use After Major Spine Surgery: A Machine-Learning Approach. Anesth Analg. 2024 Oct 1;139(4):690-699. doi: 10.1213/ANE.0000000000006832. Epub 2024 Sep 4.PMID: 39284134
Sears TJ, Pagadala MS, Castro A, Lee KH, Kong J, Tanaka K, Lippman SM, Zanetti M, Carter H. Integrated germline and somatic features reveal divergent immune pathways driving response to immune checkpoint blockade. Cancer Immunol Res. 2024 Sep 10. doi: 10.1158/2326-6066.CIR-24-0164. Online ahead of print. PMID: 39255339
Neprash HT, Dameff C, Tully J. Cybersecurity Lessons From the Change Healthcare Attack. JAMA Intern Med. 2024 Sep 9. doi: 10.1001/jamainternmed.2024.3162. Online ahead of print. PMID: 39250110
Shashikumar SP, Le JP, Yung N, Ford J, Singh K, Malhotra A, Nemati S, Wardi G. Development and Validation of a Deep Learning Model for Prediction of Adult Physiological Deterioration. Crit Care Explor. 2024 Sep 11;6(9):e1151. doi: 10.1097/CCE.0000000000001151. eCollection 2024 Sep 1. PMID: 39258951
Kalaw FGP, Baxter SL. Ethical considerations for large language models in ophthalmology. Curr Opin Ophthalmol. 2024 Aug 27. doi: 10.1097/ICU.0000000000001083. Online ahead of print. PMID: 39259616
Graber ML, Castro GM, Danforth M, Tilly JL, Croskerry P, El-Kareh R, Hemmalgarn C, Ryan R, Tozier MP, Trowbridge B, Wright J, Zwaan L. Root cause analysis of cases involving diagnosis. Diagnosis (Berl). 2024 Sep 3. doi: 10.1515/dx-2024-0102. Online ahead of print. PMID: 39238228
Radgoudarzi N, Dallalzadeh L, Saseendrakumar BR, Guo J, Halfpenny W, Kikkawa DO, Baxter S. Medical, Environmental, and Social Determinants Associated With Periocular Cutaneous Malignancies in the United States Using the All of Us National Database. Cureus. 2024 Jul 31;16(7):e65831. doi: 10.7759/cureus.65831. eCollection 2024 Jul. PMID: 39219888 Free PMC article.
Florez N, Patel SP, Wakelee H, Bazhenova L, Massarelli E, Salgia R, Stiles B, Peters S, Malhotra J, Gadgeel SM, Nieva JJ, Afkhami M, Hirsch FR, Gubens M, Cascone T, Levy B, Sabari J, Husain H, Ma PC, Backhus LM, Iyengar P, Lee P, Miller R, Sands J, Kim E. Proceedings of the 1st biannual bridging the gaps in lung cancer conference. Oncologist. 2024 Sep 5:oyae228. doi: 10.1093/oncolo/oyae228. Online ahead of print. PMID: 39237103
Graber ML, Castro GM, Danforth M, Tilly JL, Croskerry P, El-Kareh R, Hemmalgarn C, Ryan R, Tozier MP, Trowbridge B, Wright J, Zwaan L. Root cause analysis of cases involving diagnosis. Diagnosis (Berl). 2024 Sep 3. doi: 10.1515/dx-2024-0102. Online ahead of print. PMID: 39238228
Hallaj S, Halfpenny W, Chuter BG, Weinreb RN, Baxter SL, Cui QN. Association between Glucagon-Like Peptide 1 (GLP-1) Receptor Agonists Exposure and Intraocular Pressure Change: GLP-1 Receptor Agonists and Intraocular Pressure Change. Am J Ophthalmol. 2024 Sep 3:S0002-9394(24)00392-1. doi: 10.1016/j.ajo.2024.08.030. Online ahead of print. PMID: 39237049
Tyack Z, McPhail S, Aarons GA, McGrath K, Barron A, Carter H, Larkins S, Barnett A, Hummell E, Tulleners R, Fisher O, Harvey G, Jones L, Murray K, Abell B. Evaluating the tailored implementation of a multisite care navigation service for mental health in rural and remote Australia (The Bridging Study): protocol for a community-engaged hybrid effectiveness-implementation study. Implement Sci. 2024 Sep 4;19(1):62. doi: 10.1186/s13012-024-01391-7. PMID: 39232820
Radgoudarzi N, Dallalzadeh L, Saseendrakumar BR, Guo J, Halfpenny W, Kikkawa DO, Baxter S. Medical, Environmental, and Social Determinants Associated With Periocular Cutaneous Malignancies in the United States Using the All of Us National Database. Cureus. 2024 Jul 31;16(7):e65831. doi: 10.7759/cureus.65831. eCollection 2024 Jul. PMID: 39219888 Free PMC article.
Hallaj S, Chuter BG, Lieu AC, Singh P, Kalpathy-Cramer J, Xu BY, Christopher M, Zangwill LM, Weinreb RN, Baxter SL. Federated Learning in Glaucoma: A Comprehensive Review and Future Perspectives. Ophthalmol Glaucoma. 2024 Aug 28:S2589-4196(24)00143-1. doi: 10.1016/j.ogla.2024.08.004. Online ahead of print. PMID: 39214457 Review.
Zamani M, Alizadeh-Tabari S, Ajmera V, Singh S, Murad MH, Loomba R. Global prevalence of advanced liver fibrosis and cirrhosis in the general population: a systematic review and meta-analysis. Clin Gastroenterol Hepatol. 2024 Aug 27:S1542-3565(24)00790-0. doi: 10.1016/j.cgh.2024.08.020. Online ahead of print. PMID: 39209202 Review.
Singh S, Poulsen GJ, Bisgaard TH, Bonfils L, Jess T. Epidemiology of Elderly-Onset IBD: A Nationwide Population-based Cohort Study. Clin Gastroenterol Hepatol. 2024 Aug 27:S1542-3565(24)00779-1. doi: 10.1016/j.cgh.2024.08.011. Online ahead of print. PMID: 39209204
Gastrointestinal Malignancy: Genetic Implications to Clinical Applications.Trembath HE, Yeh JJ, Lopez NE. Gastrointestinal Malignancy: Genetic Implications to Clinical Applications. Cancer Treat Res. 2024;192:305-418. doi: 10.1007/978-3-031-61238-1_15. PMID: 39212927 Review.
Lyons PG, Dorr DA, Melton GB, Singh K, Payne PRO. Meeting the Artificial Intelligence Needs of U.S. Health Systems. Ann Intern Med. 2024 Aug 27. doi: 10.7326/ANNALS-24-00396. Online ahead of print. PMID: 39186786 No abstract available.
Malka S, Biswas P, Berry AM, Sangermano R, Ullah M, Lin S, D'Antonio M, Jestin A, Jiao X, Quinodoz M, Sullivan L, Gardner JC, Place EM, Michaelides M, Kaminska K, Mahroo OA, Schiff E, Wright G, Cancellieri F, Vaclavik V, Santos C, Rehman AU, Mehrotra S, Azhar Baig HM, Iqbal M, Ansar M, Santos LC, Sousa AB, Tran VH, Matsui H, Bhatia A, Naeem MA, Akram SJ, Akram J, Riazuddin S, Ayuso C, Pierce EA, Hardcastle AJ, Riazuddin SA, Frazer KA, Hejtmancik JF, Rivolta C, Bujakowska KM, Arno G, Webster AR, Ayyagari R. Substitution of a single non-coding nucleotide upstream of TMEM216 causes non-syndromic retinitis pigmentosa and is associated with reduced TMEM216 expression. Am J Hum Genet. 2024 Aug 20:S0002-9297(24)00281-7. doi: 10.1016/j.ajhg.2024.07.020. Online ahead of print. PMID: 39191256
Lyons PG, Dorr DA, Melton GB, Singh K, Payne PRO. Meeting the Artificial Intelligence Needs of U.S. Health Systems. Ann Intern Med. 2024 Aug 27. doi: 10.7326/ANNALS-24-00396. Online ahead of print. PMID: 39186786 No abstract available.
Gabriel RA, Curran BP, Swisher MW, Sztain JF, Tsuda PS, Said ET, Alexander B, Finneran JJ 4th, Abramson WB, Black JR, Wallace AM, Blair S, Donohue MC, Abdullah B, Xu NY, Cha BJ, Ilfeld BM. Paravertebral versus Pectoralis-II (Interpectoral and Pectoserratus) Nerve Blocks for Postoperative Analgesia after Non-Mastectomy Breast Surgery: A Randomized, Controlled, Observer-Masked Noninferiority Trial. Anesthesiology. 2024 Aug 26. doi: 10.1097/ALN.0000000000005207. Online ahead of print. PMID: 39186671
Shehab M, Alrashed F, Alsayegh A, Aldallal U, Ma C, Narula N, Jairath V, Singh S, Bessissow T. Comparative Efficacy of Biologics and Small Molecule in Ulcerative Colitis: A Systematic Review and Network Meta-analysis. Clin Gastroenterol Hepatol. 2024 Aug 23:S1542-3565(24)00767-5. doi: 10.1016/j.cgh.2024.07.033. Online ahead of print. PMID: 39182898
Satybaldiyeva N, Gamst A, Oren E, Park JY, Zhu SH. Secondhand smoke exposure and asthma status among adolescents: Findings from the 2019-2020 California Student Tobacco Survey. Prev Med Rep. 2024 Jul 27;45:102842. doi: 10.1016/j.pmedr.2024.102842. eCollection 2024 Sep. PMID: 39185324 Free PMC article.
Malka S, Biswas P, Berry AM, Sangermano R, Ullah M, Lin S, D'Antonio M, Jestin A, Jiao X, Quinodoz M, Sullivan L, Gardner JC, Place EM, Michaelides M, Kaminska K, Mahroo OA, Schiff E, Wright G, Cancellieri F, Vaclavik V, Santos C, Rehman AU, Mehrotra S, Azhar Baig HM, Iqbal M, Ansar M, Santos LC, Sousa AB, Tran VH, Matsui H, Bhatia A, Naeem MA, Akram SJ, Akram J, Riazuddin S, Ayuso C, Pierce EA, Hardcastle AJ, Riazuddin SA, Frazer KA, Hejtmancik JF, Rivolta C, Bujakowska KM, Arno G, Webster AR, Ayyagari R. Substitution of a single non-coding nucleotide upstream of TMEM216 causes non-syndromic retinitis pigmentosa and is associated with reduced TMEM216 expression. Am J Hum Genet. 2024 Aug 20:S0002-9297(24)00281-7. doi: 10.1016/j.ajhg.2024.07.020. Online ahead of print. PMID: 39191256
Talcott KE, Baxter SL, Chen DK, Korot E, Lee A, Kim JE, Modi Y, Moshfeghi DM, Singh RP. American Society of Retina Specialists Artificial Intelligence Task Force Report. J Vitreoretin Dis. 2024 Apr 20;8(4):373-380. doi: 10.1177/24741264241247602. eCollection 2024 Jul-Aug. PMID: 39148579
Mathews IT, Saminathan P, Henglin M, Liu M, Nadig N, Fang C, Mercader K, Chee SJ, Campbell AM, Patel AA, Tiwari S, Watrous JD, Ramesh K, Dicker M, Dao K, Meyer MA, Jousilahti P, Havulinna AS, Niiranen T, Salomaa V, Joosten LAB, Netea MG, Zheng P, Kronenberg M, Patel SP, Gutkind JS, Ottensmeier C, Long T, Kaech SM, Hedrick CC, Cheng S, Jain M, Sharma S. Linoleoyl-lysophosphatidylcholine suppresses immune-related adverse events due to immune checkpoint blockade. medRxiv [Preprint]. 2024 Aug 8:2024.08.07.24310974. doi: 10.1101/2024.08.07.24310974. PMID: 39148854 Free PMC article. Preprint.
Pham D, Lomeli A, Goldhaber NH, Valentine HD, Knight R, Longhurst CA, Laurent LC, Jacobs MB. Longitudinal assessment of the impact of COVID-19 infection on mask-wearing behaviors. BMC Public Health. 2024 Aug 16;24(1):2230. doi: 10.1186/s12889-024-19776-0. PMID: 39152377 Free PMC article.
Haldeman PB, Harfouche C, Rosales R, Trimm C, Chun L, Reid C, Flint JH, Chiarappa F. Immediate and delayed flap reconstruction have equivalent outcomes and associated costs following soft tissue sarcoma surgery. J Surg Oncol. 2024 Aug 19. doi: 10.1002/jso.27770. Online ahead of print. PMID: 39155702
Kalaw FGP, Most J, Kako RN, Sharma P, Arias JD, Chen JS, Lin AC, Walker E, Bartsch DG, Baxter SL, Ferreyra H, Freeman WR, Borooah S. Retinal structural changes after cessation of pentosan polysulfate sodium. Retina. 2024 Jul 3. doi: 10.1097/IAE.0000000000004197. Online ahead of print. PMID: 39174300
Radgoudarzi N, Gregg C, Quackenbush Q, Yiu G, Freeby M, Su G, Baxter S, Thorne C, Willard-Grace R. Implementation Mapping of the Collaborative University of California Teleophthalmology Initiative (CUTI): A Qualitative Study Using the Exploration, Preparation, Implementation, and Sustainment (EPIS) Framework. Cureus. 2024 Jul 9;16(7):e64179. doi: 10.7759/cureus.64179. eCollection 2024 Jul. PMID: 39119397 Free PMC article.
Pham A, Edelson M, Nouri A, Kuo TT. Distributed management of patient data-sharing informed consents for clinical research. Comput Biol Med. 2024 Aug 8;180:108956. doi: 10.1016/j.compbiomed.2024.108956. Online ahead of print. PMID: 39121682
Acuff KN, Radha Saseendrakumar B, Weinreb RN, Baxter SL. Assessment of Missing Data on Glaucoma Severity among Participants in the NIH All of Us Research Program of the United States. J Glaucoma. 2024 Aug 13. doi: 10.1097/IJG.0000000000002480. Online ahead of print. PMID: 39133059
Heinke A, Radgoudarzi N, Huang BB, Baxter SL. A Review of Ophthalmology Education in the Era of Generative Artificial Intelligence. Asia Pac J Ophthalmol (Phila). 2024 Aug 10:100089. doi: 10.1016/j.apjo.2024.100089. Online ahead of print. PMID: 39134176 Review.
Shehab M, Hassan A, Alrashed F, Abbas A, Ma C, Narula N, Jairath V, Singh S, Bessissow T. Comparative Efficacy of Biologics and Small Molecule Therapies in Improving Patient-Reported Outcomes in Ulcerative Colitis: Systematic Review and Network Meta-Analysis. Inflamm Bowel Dis. 2024 Aug 13:izae163. doi: 10.1093/ibd/izae163. Online ahead of print. PMID: 39137239
Smith HS, Rubanovich CK, Robinson JO, Levchenko AN, Classen SA, Malek J, Buchanan AH, Biesecker B, Brothers KB, Wilfond BS, Rini C, Bloss CS, McGuire AL, Knight SJ. Measuring perceived utility of genomic sequencing: Development and validation of the GENEtic Utility (GENE-U) scale for adult screening. Genet Med. 2024 Aug 10:101240. doi: 10.1016/j.gim.2024.101240. Online ahead of print. PMID: 39140259
Fudman D, McConnell RA, Ha C, Singh S. Modern Advanced Therapies for Inflammatory Bowel Diseases: Practical Considerations and Positioning. Clin Gastroenterol Hepatol. 2024 Aug 13:S1542-3565(24)00728-6. doi: 10.1016/j.cgh.2024.06.050. Online ahead of print. PMID: 39147217 Review.
Hallaj S, Khawaja AP, Rodrigues IAS, Boland MV, Brown EN, Chen A, Stagg BC, Stein JD, Sun CQ, Mahe-Cook AL, Swaminathan SS, Wang SY, Xu BY, Weinreb RN, Baxter SL. Gap Analysis of Glaucoma Examination Concept Representations within Standard SNOMED Clinical Terms.Ophthalmol Glaucoma. 2024 Aug 13:S2589-4196(24)00140-6. doi: 10.1016/j.ogla.2024.08.001. Online ahead of print. PMID: 39147325
Ratwani RM, Classen D, Longhurst C. The Compelling Need for Shared Responsibility of AI Oversight: Lessons From Health IT Certification.JAMA. 2024 Aug 12. doi: 10.1001/jama.2024.12630. Online ahead of print. PMID: 39133493
McDaniels-Davidson C, Parada H Jr, Kasiri N, Patel SP, Strong D, Doran N. The association of perceived cannabis risks and benefits with cannabis use since cancer diagnosis.J Natl Cancer Inst Monogr. 2024 Aug 15;2024(66):244-251. doi: 10.1093/jncimonographs/lgad024. PMID: 39108239
Mohammadzadeh V, Liang Y, Moghimi S, Xie P, Nishida T, Mahmoudinezhad G, Eslani M, Walker E, Kamalipour A, Micheletti E, Wu JH, Christopher M, Zangwill LM, Javidi T, Weinreb RN. Detection of glaucoma progression on longitudinal series of en-face macular optical coherence tomography angiography images with a deep learning model. Br J Ophthalmol. 2024 Aug 7:bjo-2023-324528. doi: 10.1136/bjo-2023-324528. Online ahead of print. PMID: 39117359
Rojas-Carabali W, Agrawal R, Gutierrez-Sinisterra L, Baxter SL, Cifuentes-González C, Wei YC, Abisheganaden J, Kannapiran P, Wong S, Lee B, de-la-Torre A, Agrawal R. Natural Language Processing in medicine and ophthalmology: A review for the 21st-century clinician. Asia Pac J Ophthalmol (Phila). 2024 Jul 25:100084. doi: 10.1016/j.apjo.2024.100084. Online ahead of print. PMID: 39059557 Review.
Patel SP, Othus M, Chae YK, Huynh T, Tan B, Kuzel T, McLeod C, Lopez G, Chen HX, Sharon E, Streicher H, Ryan CW, Blanke C, Kurzrock R. Phase II basket trial of Dual Anti-CTLA-4 and Anti-PD-1 blockade in Rare Tumors (DART) SWOG S1609: adrenocortical carcinoma cohort. J Immunother Cancer. 2024 Jul 27;12(7):e009074. doi: 10.1136/jitc-2024-009074. PMID: 39067873 Free PMC article. Clinical Trial.
Leung C, Tahir W, Rosli Y, Lieber SB, Makris UE, Lee J, Ali H, Goulabchand R, Singh S, Singh N.Association Between Frailty Status and Readmissions in Hospitalized Patients With Systemic Lupus Erythematosus. ACR Open Rheumatol. 2024 Jul 29. doi: 10.1002/acr2.11722. Online ahead of print. PMID: 39074031
Sehgal A, Ziaei-Jam H, Shen A, Gymrek M. Genome-wide detection of somatic mosaicism at short tandem repeats. Bioinformatics. 2024 Jul 30:btae485. doi: 10.1093/bioinformatics/btae485. Online ahead of print. PMID: 39078205
Talwar JV, Klie A, Pagadala MS, Carter H. GRIEVOUS: Your command-line general for resolving cross-dataset genotype inconsistencies.Bioinformatics. 2024 Jul 30:btae489. doi:10.1093/bioinformatics/btae489. Online ahead of print. PMID: 39078222
Acuff KN, Villatoro GA, Baxter SL. Acute Bilateral Periorbital Edema in a Psychiatric Patient.JAMA Ophthalmol. 2024 Aug 1. doi: 10.1001/jamaophthalmol.2024.2815. Online ahead of print. PMID: 39088236
Pham D, Lomeli A, Goldhaber NH, Valentine HD, Knight R, Longhurst CA, Laurent LC, Jacobs MB.
Longitudinal assessment of the impact of COVID-19 infection on mask-wearing behaviors. BMC Public Health. 2024 Aug 16;24(1):2230. doi: 10.1186/s12889-024-19776-0. PMID: 39152377 Free PMC article.
Acuff KN, Radha Saseendrakumar B, Weinreb RN, Baxter SL. Assessment of Missing Data on Glaucoma Severity among Participants in the NIH All of Us Research Program of the United States. J Glaucoma. 2024 Aug 13. doi: 10.1097/IJG.0000000000002480. Online ahead of print. PMID: 39133059
Pham A, Edelson M, Nouri A, Kuo TT. Distributed management of patient data-sharing informed consents for clinical research. Comput Biol Med. 2024 Aug 8;180:108956. doi: 10.1016/j.compbiomed.2024.108956. Online ahead of print. PMID: 39121682
Ratwani RM, Classen D, Longhurst C. The Compelling Need for Shared Responsibility of AI Oversight: Lessons From Health IT Certification. JAMA. 2024 Aug 12. doi: 10.1001/jama.2024.12630. Online ahead of print. PMID: 39133493
Sadiq KO, Dobke MK, Boland BS, Lopez N, Eisenstein S. Autologous Fat Grafting For Perianal Fistula in Behçet's Disease: A Case Report.Inflamm Bowel Dis. 2024 Jul 20:izae157. doi: 10.1093/ibd/izae157. Online ahead of print. PMID: 39031965
Patel SH, Rudolf F, Schwartz K, Gabriel RA, Hastings RH, Daniel M, Suresh PJ. Enhancing Laryngoscopy Mastery: The Impact of Autonomous Practice with Feedback-Providing Simulators.A A Pract. 2024 Jul 22;18(7):e01825. doi: 10.1213/XAA.0000000000001825. eCollection 2024 Jul 1. PMID: 39037074
Jin Q, Chen F, Zhou Y, Xu Z, Cheung JM, Chen R, Summers RM, Rousseau JF, Ni P, Landsman MJ, Baxter SL, Al'Aref SJ, Li Y, Chen A, Brejt JA, Chiang MF, Peng Y, Lu Z. Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine. NPJ Digit Med. 2024 Jul 23;7(1):190. doi: 10.1038/s41746-024-01185-7. PMID: 39043988
Systrom HK, Rai V, Singh S, Baidoo L, Cheifetz AS, Devlin SM, Gecse KB, Irving PM, Kaplan GG, Kozuch PL, Ullman T, Sparrow MP, Melmed GY, Siegel CA. When Perfect Is the Enemy of Good: Results of a RAND Appropriateness Panel on Treat to Target in Asymptomatic IBD. Am J Gastroenterol. 2024 Jul 15. doi: 10.14309/ajg.0000000000002964. Online ahead of print. PMID: 39008539
Rudolf F, Oyama LC, El-Kareh R. Impact of an automated patient outcome feedback system on emergency medicine resident patient follow-up: An interrupted time series analysis. AEM Educ Train. 2024 Jul 4;8(4):e11011. doi: 10.1002/aet2.11011. eCollection 2024 Aug. PMID: 38974783
Gabriel RA, Seng EC, Curran BP, Winston P, Trescot AM, Filipovski I. A Narrative Review of Ultrasound-Guided and Landmark-based Percutaneous Cryoneurolysis for the Management of Acute and Chronic Pain.Curr Pain Headache Rep. 2024 Jul 4. doi: 10.1007/s11916-024-01281-z. Online ahead of print. PMID: 38963513 Review.
Shepard RM, Ghebremedhin A, Pratumchai I, Robinson SR, Betts C, Hu J, Sasik R, Fisch KM, Zak J, Chen H, Paradise M, Rivera J, Amjad M, Uchiyama S, Seo H, Campos AD, Dayao DA, Tzipori S, Piedra-Mora C, Das S, Hasteh F, Russo H, Sun X, Xu L, E Alexander LC, Duran JM, Odish M, Pretorius V, Kirchberger NC, Chin SM, Von Schalscha T, Cheresh D, Morrey JD, Alargova R, O'Connell B, Martinot TA, Patel SP, Nizet V, Martinot AJ, Coussens LM, Teijaro JR, Varner JA.PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections.Sci Transl Med. 2024 Jul 3;16(754):eadi6887. doi: 10.1126/scitranslmed.adi6887. Epub 2024 Jul 3. PMID: 38959328
Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Rep. 2024 Jul 4;43(7):114436. doi: 10.1016/j.celrep.2024.114436. Online ahead of print. PMID: 38968069
Ziaei Jam H, Zook JM, Javadzadeh S, Park J, Sehgal A, Gymrek M. LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads. Genome Biol. 2024 Jul 4;25(1):176. doi: 10.1186/s13059-024-03319-2. PMID: 38965568 Free PMC article.
Yaseen F, Taj M, Ravindran R, Zaffar F, Luciw PA, Ikram A, Zafar SI, Gill T, Hogarth M, Khan IH. An exploratory deep learning approach to investigate tuberculosis pathogenesis in nonhuman primate model: Combining automated radiological analysis with clinical and biomarkers data. J Med Primatol. 2024 Aug;53(4):e12722. doi: 10.1111/jmp.12722. PMID: 38949157
Wu JH, Halfpenny W, Bu J, Brar M, Weinreb RN, Baxter SL. Social factors associated with the risk of glaucoma suspect conversion to glaucoma: analysis of the nationwide All of Us Program.
Ophthalmol Glaucoma. 2024 Jul 1:S2589-4196(24)00102-9. doi: 10.1016/j.ogla.2024.06.007. Online ahead of print. PMID: 38959998
Study: AI Surveillance Tool Successfully Helps to Predict Sepsis, Saves Lives, UC San Diego Today, 2024, Jan 23.
Ayers JW, Poliak A, Beros NT, Paul M, Dredze M, Hogarth M, Smith DM. A Digital Cohort Approach for Social Media Monitoring: A Cohort Study of People Who Vape E-Cigarettes. Am J Prev Med. 2024 Mar 16:S0749-3797(24)00028-X. doi:10.1016/j.amepre.2024.01.016. Online ahead of print. PMID: 38904592
Nodora JN, Martinez ME, McDaniels-Davidson C, Shen J, Sitapati AM, Torriani F, Mandel J, Hill L. Distribution of COVID-19 Home Testing Through Community Health Centers: Results of the COVID CoNOce MÁS Study. J Prim Care Community Health. 2024 Jan-Dec;15:21501319241259684. doi: 10.1177/21501319241259684. PMID: 38864213
Krishnamoorthy R, Nagarajan V, Pour H, Shashikumar SP, Boussina A, Farcas E, Nemati S, Josef CS. Voice-Enabled Response Analysis Agent (VERAA): Leveraging Large Language Models to Map Voice Responses in SDoH Survey. AMIA Jt Summits Transl Sci Proc. 2024 May 31;2024:258-265. eCollection 2024. PMID: 38827075
Smith S, Goldhaber N, Maysent K, Lang U, Daniel M, Longhurst C Impact of a virtual coaching program for women physicians on burnout, fulfillment, and self-valuation. BMC Psychol. 2024 Jun 5;12(1):331. doi: 10.1186/s40359-024-01763-0. PMID: 38840137
Amrollahi F, Kennis BD, Shashikumar SP, Malhotra A, Taylor SP, Ford J, Rodriguez A, Weston J, Maheshwary R, Nemati S, Wardi G, Meier A. Prediction of Readmission Following Sepsis Using Social Determinants of Health. Crit Care Explor. 2024 May 24;6(6):e1099. doi: 10.1097/CCE.0000000000001099. eCollection 2024 Jun 1. PMID: 38787299
Lacson R, Yu Y, Kuo TT, Ohno-Machado L Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review. J Am Med Inform Assoc. 2024 May 10:ocae084. doi: 10.1093/jamia/ocae084. Online ahead of print. PMID: 38726710
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
Kalaw FGP, Chen JS, Baxter SL. Variations in Using Diagnosis Codes for Defining Age-Related Macular Degeneration Cohorts.Informatics (MDPI). 2024 Jun;11(2):28. doi: 10.3390/informatics11020028. Epub 2024 May 1. PMID: 40012991 Free PMC article.
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
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

2023 (selected publications)

Montazid S, Bandyopadhyay S, Hart DW, Gao N, Johnson B, Thrumurthy SG, Penn DJ, Wernisch B, Bansal M, Altrock PM, Rost F, Gazinska P, Ziolkowski P, Hayee B, Liu Y, Han J, Tessitore A, Koth J, Bodmer WF, East JE, Bennett NC, Tomlinson I, Irshad S. Adult stem cell activity in naked mole rats for long-term tissue maintenance. Nat Commun. 2023 Dec 20;14(1):8484. doi: 10.1038/s41467-023-44138-6. PMID: 38123565
Wenger NS, Sanz Vidorreta FJ, Dudley MT, Walling AM, Hogarth M. Consequences of a Health System Not Knowing Which Patients Are Deceased - PubMed (nih.gov) JAMA Intern Med. 2023 Dec 4:e236428. doi: 10.1001/jamainternmed.2023.6428. PMID: 38048124
Boyle EA, Goldberg G, Schmok JC, Burgado J, Izidro Layng F, Grunwald HA, Balotin KM, Cuoco MS, Chang KC, Ecklu-Mensah G, Arakaki AKS, Ahmed N, Garcia Arceo X, Jagannatha P, Pekar J, Iyer M; DASL Alliance; Yeo GW. Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM. PLoS One. 2023 Nov 2;18(11):e0293322. doi: 10.1371/journal.pone.0293322. eCollection 2023. PMID: 37917746
Bruce LK, Kasl P, Soltani S, Viswanath VK, Hartogensis W, Dilchert S, Hecht FM, Chowdhary A, Anglo C, Pandya L, Dasgupta S, Altintas I, Gupta A, Mason AE, Smarr BL. Variability of temperature measurements recorded by a wearable device by biological sex. Biol Sex Differ. 2023 Nov 1;14(1):76. doi: 10.1186/s13293-023-00558-z. PMID: 37915069
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
Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR; iPSCORE Consortium; Matsui H, Kim JH, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nat Commun. 2023 Oct 30;14(1):6928. doi: 10.1038/s41467-023-42560-4. PMID: 37903777
Chen C, Lifset ET, Han Y, Roy A, Hogarth M, Moore AA, Farcas E, Weibel N. Screen or No Screen? Lessons Learnt from a Real-World Deployment Study of Using Voice Assistants With and Without Touchscreen for Older Adults ASSETS. 2023 Oct;2023:52. doi: 10.1145/3597638.3608378. Epub 2023 Oct 22. PMID: 39086515.
Lifset ET, Charles K, Farcas E, Weibel N, Hogarth M, Chen C, Johnson JG, Draper M, Nguyen AL, Moore AA Ascertaining Whether an Intelligent Voice Assistant Can Meet Older Adults' Health-Related Needs in the Context of a Geriatrics 5Ms Framework. Gerontol Geriatr Med. 2023 Sep 30;9:23337214231201138. doi: 10.1177/23337214231201138. eCollection 2023 Jan-Dec. PMID: 37790195
Johnson B, Shuai Y, Schweinsberg J, Curtius K. cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory. Bioinformatics. 2023 Sep 12:btad561. doi: 10.1093/bioinformatics/btad561. Online ahead of print. PMID: 37699006
Classen DC, Longhurst CA, Davis T, Milstein JA, Bates DW. Inpatient EHR User Experience and Hospital EHR Safety Performance. JAMA Netw Open. 2023 Sep 5;6(9):e2333152. doi: 10.1001/jamanetworkopen.2023.33152. PMID: 37695581
Leggat-Barr K, Ryu R, Hogarth M, Stover-Fiscalini A, Veer LV', Park HL, Lewis T, Thompson C, Borowsky A, Hiatt RA, LaCroix A, Parker B, Madlensky L, Naeim A, Esserman L. Early Ascertainment of Breast Cancer Diagnoses Comparing Self-Reported Questionnaires and Electronic Health Record Data Warehouse: The WISDOM Study. JCO Clin Cancer Inform. 2023 Aug;7:e2300019. doi: 10.1200/CCI.23.00019. PMID: 37607323
Wu JH, Varkhedi V, Radha Saseendrakumar B, Acuff K, Weinreb RN, Baxter SL. Social and Healthcare Utilization Factors Associated With Ophthalmic Visit Non-adherence in Glaucoma: an All of Us study. J Glaucoma. 2023 Aug 29. doi: 10.1097/IJG.0000000000002300. PMID: 37671531
Aronoff-Spencer E, Mazrouee S, Graham R, Handcock MS, Nguyen K, Nebeker C, Malekinejad M, Longhurst CA. Exposure notification system activity as a leading indicator for SARS-COV-2 caseload forecasting. PLoS One. 2023 Aug 18;18(8):e0287368. doi: 10.1371/journal.pone.0287368. eCollection 2023. PMID: 37594936
Aruljothy A, Singh S, Narula N, Moran GW, Vuyyuru SK, Hogan M, Zayadi A, MacDonald JK, Caron B, Danese S, Peyrin Biroulet L, Ma C, Jairath V. Systematic review with meta-analysis: Medical therapies for treatment of ulcerative proctitis. Aliment Pharmacol Ther. 2023 Aug 17. doi: 10.1111/apt.17666. Online ahead of print. PMID: 37589498 Review.
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 Epub 2023 Aug 14.
Yousif ZK, Koola JD, Macedo E, Cerda J, Goldstein SL, Chakravarthi R, Lewington A, Selewski D, Zappitelli M, Cruz D, Tolwani A, Joy MS, Jha V, Ramachandran R, Ostermann M, Pandya B, Acharya A, Brophy P, Ponce D, Steinke J, Bouchard J, Irarrazabal CE, Irarrazabal R, Boltansky A, Askenazi D, Kolhe N, Claure-Del Granado R, Benador N, Castledine C, Davenport A, Barratt J, Bhandari S, Riley AA, Davis TK, Farmer C, Hogarth M, Thomas M, Murray PT, Robinson-Cohen C, Nicoletti P, Vaingankar S, Mehta R, Awdishu L. Clinical Characteristics and Outcomes of Drug-Induced Acute Kidney Injury Cases. Kidney Int Rep. 2023 Aug 14;8(11):2333-2344. doi: 10.1016/j.ekir.2023.07.037. eCollection 2023 Nov. PMID: 38025217
Kashani KB, Awdishu L, Bagshaw SM, Barreto EF, Claure-Del Granado R, Evans BJ, Forni LG, Ghosh E, Goldstein SL, Kane-Gill SL, Koola J, Koyner JL, Liu M, Murugan R, Nadkarni GN, Neyra JA, Ninan J, Ostermann M, Pannu N, Rashidi P, Ronco C, Rosner MH, Selby NM, Shickel B, Singh K, Soranno DE, Sutherland SM, Bihorac A, Mehta RL. Digital health and acute kidney injury: consensus report of the 27th Acute Disease Quality Initiative workgroup. Nat Rev Nephrol. 2023 Aug 14. doi: 10.1038/s41581-023-00744-7. Online ahead of print. PMID: 37580570 Review.
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
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
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
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
Boussina A, Wardi G, Shashikumar SP, Malhotra A, Zheng K, Nemati S. Representation Learning and Spectral Clustering for the Development and External Validation of Dynamic Sepsis Phenotypes: Observational Cohort Study - PubMed (nih.gov) J Med Internet Res. 2023 Jun 23;25:e45614. doi: 10.2196/45614. PMID: 37351927
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
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.
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
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, 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
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
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
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
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
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.
Le JP, Shashikumar SP, Malhotra A, Nemati S, Wardi G. Making the Improbable Possible: Generalizing Models Designed for a Syndrome-Based, Heterogeneous Patient Landscape. Crit Care Clin. 2023 Oct;39(4):751-768. doi: 10.1016/j.ccc.2023.02.003. Epub 2023 Apr 26. PMID: 37704338 Review.
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.
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
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
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. 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

2022 (selected publications)

Baxter, SL., Representation Matters - Diversity in Retina Clinical Trails. PMID: 36201217, DOI: 10.1001/jamaophthalmol. doi: 10.1001/jamaophthalmol.2022.3930. 2022 Nov 1;140(11):1103-1104.
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
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
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), ebook 978-1-64368-238-9 (print) | 978-1-64368-239-6 (online) 2022.