Pepper Center Publications

• A SAS macro for multilevel Cosinor analysis.Doyle MM, Murphy TE, Miner B, Knauert MP. Comput Methods Programs Biomed. 2026 Feb 1; 2025 Nov 14. PMID: 41297072.
• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.Liu T, Lin Y, Luo X, Sun Y, Zhao H. Commun Biol. 2026 Jan 8; 2026 Jan 8. PMID: 41507434.
• A novel two-sample Mendelian randomization framework integrating common and rare variants: application to assess the effect of HDL-C on preeclampsia risk.Zhang Y, Li M, Haas DM, Bairey Merz CN, Workalemahu T, Ryckman K, Catov JM, Levine LD, Freedman A, Saade GR, Hu J, Zhao H, Li X, Liu N, Yan Q. Brief Bioinform. 2026 Jan 7. PMID: 41499219.
• Healing at Home: Receipt of Home Health Care and Patient-Centered Outcomes Among Older Adults After Acute Myocardial Infarction.Hajduk AM, Falvey JR, Shang J, Kern LM, Sterling M, Tsang S, Herrin J, Chaudhry SI. J Am Med Dir Assoc. 2026 Jan 3; 2026 Jan 3. PMID: 41494639.
• Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors.Doni Jayavelu N, Samaha H, Wimalasena ST, Hoch A, Gygi JP, Gabernet G, Ozonoff A, Liu S, Milliren CE, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Schaenman J, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuit NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Gen LN, Fernandez Sesma A, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Langelier CR, Guan L, Maecker HT, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Altman MC. Commun Med (Lond). 2026 Jan 3; 2026 Jan 3. PMID: 41484172.
• Response to Freedman and Schrack: drawing inferences about Medicare mortality from the National Health and Aging Trends Study.Gill TM, Liang J, Davis-Plourde K. J Gerontol A Biol Sci Med Sci. 2026 Jan 2. PMID: 41482503.
• Losses to Follow-Up in a Nationally Representative Study of Community-Living Older Americans: Two Approaches to Censoring and Implications for Mortality Outcomes.Gill TM, Liang J, Becher RD, Davis-Plourde K. J Am Geriatr Soc. 2026 Jan; 2025 Sep 10. PMID: 40928486.
• Frailty and functional decline after elective endovascular abdominal aortic aneurysm repair in octogenarians.Li J, Slade MD, Gill TM, Bader J, Guzman RJ, Tonnessen BH, Kuwayama DP, Dardik A, Cardella JA, Ochoa Chaar CI. J Vasc Surg. 2026 Jan; 2025 Aug 18. PMID: 40835162.
• Development and Feasibility of PATH: Preparation for Appropriate Transitions From Home.Fried TR, Bouranis N, Cohen AB. J Am Geriatr Soc. 2025 Dec 31; 2025 Dec 31. PMID: 41472534.
• PERADIGM: Phenotype embedding similarity-based rare disease gene mapping.Zheng W, Xie Y, Gu J, Li H, Somlo S, Besse W, Zhao H. PLoS Genet. 2025 Dec; 2025 Dec 18. PMID: 41411243.
• Unravelling the Immunological Enigma of Sickle Cell Disease: Current Understanding and Future Directions.Jamwal S, Calhoun C, Mohanty S, Montgomery RR, Krishnamurti L, Shaw AC, Yildirim I. Immunology. 2025 Dec 12; 2025 Dec 12. PMID: 41387179.
• Improving polygenic risk prediction performance by integrating electronic health records through phenotype embedding.Xu L, Zheng W, Hu J, Lin Y, Zhao J, Wang G, Liu T, Zhao H. Am J Hum Genet. 2025 Dec 4. PMID: 41349513.
• Combined and synergistic effects of heat and fine particulate matter on hospitalization among patients with Alzheimer's disease and related dementias.Spoto F, Zanobetti A, Delaney SW, Gill TM, Bell ML, Dominici F, Braun D, Mork D. Environ Epidemiol. 2025 Dec; 2025 Nov 21. PMID: 41293543.
• Evaluating COVID-19 severity prediction and immune dynamics with NULISAseq: Insights from the IMPACC study.Abe K, Holmes TH, Nguyen TT, Kim-Schulze S, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenman J, Reed EF, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Maecker HT. J Immunol. 2025 Dec 1. PMID: 41166719.
• Artificial Intelligence and Clinical Care: JAMA Internal Medicine Call for Papers.Gross CP, Richman IB, Stall NM, Kneifati-Hayek JZ, Allore HG, Rittenberg E, Katz MH, Grady D, Durant RW, Anderson TS, Tripodis Y, Wang TY, Corbie G, Mody L, Perlis RH, Ganguli I, Inouye SK. JAMA Intern Med. 2025 Dec 1. PMID: 41082189.
• Comparing Disaster-Related Surge Staffing Practices Across Rural and Non-Rural Nursing Homes.Festa N, Alexovitz K, Davis-Plourde K, Marottoli R, Cohen AB, Dosa D, Fulmer T, Gill TM. J Am Geriatr Soc. 2025 Dec; 2025 Sep 12. PMID: 40938301.
• TCPGdb: A comprehensive T cell perturbation genomics database for identification of critical T cell regulators.Dong C, Zhang F, Tang K, Verma N, Zhu X, Feng D, Cai J, Zhao H, Chen S. Cancer Immunol Res. 2025 Nov 21; 2025 Nov 21. PMID: 41270225.
• The cutaneous response to a mosquito bite is influenced by the diurnal rhythm.Raduwan H, Park J, Marín-López A, Skadow MH, Chen TY, Flavell RA, Shaw AC, Montgomery RR, Fikrig E. iScience. 2025 Nov 21; 2025 Sep 30. PMID: 41146707.
• Science for vaccine policy: Independent review of the September 2025 ACIP processes, deliberations and votes.Asturias EJ, Chen LH, Shaw AC, Moser CA, Maldonado YA, Zucker JR, Chu HY, Talbot HK, Cineas S, Lyons K, Schechter R, Kamboj M, Wiley Z, Brewer NT. Vaccine. 2025 Nov 20; 2025 Oct 23. PMID: 41135287.
• Improving newborn screening accuracy through genome sequencing, targeted metabolomics, and machine learning.Xie Y, Peng G, Tikhonova I, Enns G, Zhao H, Cowan T, Scharfe C. BMC Med Genomics. 2025 Nov 19; 2025 Nov 19. PMID: 41257776.
• A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies.Wang Z, Zeng Y, Tan Z, Chen Y, Huang X, Zhao H, Lin Z, Yang C. Proc Natl Acad Sci U S A. 2025 Nov 18; 2025 Nov 12. PMID: 41223223.
• Recessive genomic and phenotypic variation in consanguineous families with cerebral palsy.Bisarad P, Wang YC, Skidmore PT, Galaz-Montoya CI, Lewis SA, Alhaddad B, Kong N, Julian D, Magee H, Kruer TN, Xie Y, Zheng W, Li B, Rajabpour FV, Liu J, Revanur A, Bakur K, Firouzabadi SG, Sharbatkhori S, Tafakhori A, Taghiabadi E, Nezaminargabad E, Vosoogh S, Jamshidi J, Arefnia S, Hosseini SA, Khajehmirzaei A, Jamali F, Ahmadifard A, Khodadadi H, Daneshmand P, Bohlega S, Maddirevula S, Nadeef SS, Hashem MO, Salih MA, Mohmed IN, Sticht H, Morias SP, Damásio J, Santos M, Loureiro JL, Rodrigues R, Stevanin G, Benkirane M, Dauriat B, Head N, Baptista J, Shahhosseini S, Mohammad F, Zhao H, Padilla-Lopez S, Alkuraya F, Bakhtiari S, Kruer MC, Jin SC, Darvish H. medRxiv. 2025 Nov 6; 2025 Nov 6. PMID: 41282771.
• A multiomics recovery factor predicts long COVID in the IMPACC study.Gabernet G, Maciuch J, Gygi JP, Moore JF, Hoch A, Syphurs C, Chu T, Doni Jayavelu N, Corry DB, Kheradmand F, Baden LR, Sekaly RP, McComsey GA, Haddad EK, Cairns CB, Rouphael N, Fernandez-Sesma A, Simon V, Metcalf JP, Agudelo Higuita NI, Hough CL, Messer WB, Davis MM, Nadeau KC, Pulendran B, Kraft M, Bime C, Reed EF, Schaenman J, Erle DJ, Calfee CS, Atkinson MA, Brakenridge SC, Melamed E, Shaw AC, Hafler DA, Augustine AD, Becker PM, Ozonoff A, Bosinger SE, Eckalbar W, Maecker HT, Kim-Schulze S, Steen H, Krammer F, Westendorf K, Peters B, Fourati S, Altman MC, Levy O, Smolen KK, Montgomery RR, Diray-Arce J, Kleinstein SH, Guan L, Ehrlich LI. J Clin Invest. 2025 Nov 3; 2025 Sep 9. PMID: 40924481.
• Aligning Surgical Decisions With Older Adults' Outcome Goals.Naik AD, Schwarze ML, Banks J, Soni S, Arain SA, Goyal P, Matlock DD, Lampert R, Tinetti ME. J Am Geriatr Soc. 2025 Nov; 2025 Jul 24. PMID: 41288195.
• Spatial dynamics of brain development and neuroinflammation.Zhang D, Rubio Rodríguez-Kirby LA, Lin Y, Wang W, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Bao S, Wang S, Chen XL, Gao F, Wang D, Xu H, Ma C, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R. Nature. 2025 Nov; 2025 Nov 5. PMID: 41193846.
• Evaluating the Applicability of Federal Regulatory Metrics for Nursing Home Fire Safety and Emergency Preparedness.Festa N, Alexovitz K, Throgmorton KF, Davis-Plourde K, Dosa DM, Gill TM. J Am Med Dir Assoc. 2025 Nov; 2025 Sep 11. PMID: 40882948.
• Type 2 immune responses are associated with less severe COVID-19 in a hospitalized cohort.Jayavelu ND, Qi J, Milliren CE, Ozonoff A, Liu S, Levy O, Baden LR, Melamed E, McComsey GA, Cairns CB, Schaenman J, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Sesma AF, Simon V, Krammer F, Bime C, Calfee CS, Bosinger SE, Eckalbar W, Steen H, Maecker HT, Augustine AD, Diray-Arce J, Haddad EK, Sekaly RP, Kraft M, Woodruff PG, Erle DJ, Ehrlich LIR, Montgomery RR, Becker PM, Altman MC, Fourati S. J Allergy Clin Immunol Glob. 2025 Nov; 2025 Jun 12. PMID: 40709330.
• Microfluidics combined with electron microscopy for rapid and high-throughput mapping of antibody-viral glycoprotein complexes.Sewall LM, de Paiva Froes Rocha R, Gibson G, Louie M, Xie Z, Bangaru S, Tran AS, Ozorowski G, Mohanty S, Beutler N, Rogers TF, Burton DR, Shaw AC, Batista FD, Chocarro Ruiz B, Torrents de la Peña A, Ward AB. Nat Biomed Eng. 2025 Nov; 2025 Jun 3. PMID: 40461656.
• Association of Parental Income with Attrition from MD-PhD Training Programs.Nguyen M, Cavazos JE, Chaudhry SI, Mason HR, Castillo-Page L, Boatright D. J Gen Intern Med. 2025 Nov; 2025 May 12. PMID: 40353992.
• Efficacy of antiobesity medications for weight reduction in older adults: a systematic review.Chen AS, Hajduk AM, Grimshaw AA, Fried TR, Jastreboff AM, Lipska KJ. Obesity (Silver Spring). 2025 Nov; 2024 Dec 26. PMID: 39725567.
• PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.Zhang Z, Zhao H, Wang T. Nucleic Acids Res. 2025 Oct 31; 2025 Oct 31. PMID: 41171140.
• Pdgfrα deficiency in islet β-cells up-regulates apoptosis of beta-cells and disturbs glucose metabolism in B6 mice.Zhang L, Xing Y, Wang P, Gu J, Peng J, Huang J, Pearson JA, Hu Y, Zhao H, Wong FS, Wen L. Front Endocrinol (Lausanne). 2025; 2025 Oct 29. PMID: 41234234.
• UNICORN: Towards universal cellular expression prediction with a multi-task learning framework.Liu T, Huang T, Wang L, Lin Y, Ying R, Zhao H. Nat Commun. 2025 Oct 27; 2025 Oct 27. PMID: 41145510.
• Neighborhood Deprivation and Symptom Burden Among Older Adults After Hospitalization for COVID-19.Falvey JR, Acampora D, Araujo K, Geda M, Gill TM, McAvay G, Murphy TE, Hajduk A, Cohen AB, Ferrante LE. J Appl Gerontol. 2025 Oct 27; 2025 Oct 27. PMID: 41145178.
• Effect of prescribing and deprescribing oxycodone on pain and function in a mouse model of osteoarthritis: impact of polypharmacy and sex on response.Mach J, Blaker CL, Winters B, Otsu Y, Clarke EC, Allore H, Wyk BV, Winardi K, Peel R, Gregson CW, Assareh N, Kourieh M, Hilmer SN. bioRxiv. 2025 Oct 23; 2025 Oct 23. PMID: 41279379.
• Disparities in Geographic Access to Cardiac Rehabilitation Among Socially Vulnerable Communities.Chen EW, Wu WC, Han L, Gandhi PU, Bastian LA, Brandt CA, Mattocks KM, Oen-Hsiao J, Varghese MS. J Am Heart Assoc. 2025 Oct 21; 2025 Oct 9. PMID: 41065247.
• Beyond the Genotype: A Multi-Omic Analysis of APOEe4's Role in Alzheimer's Disease.Markov Y, Priyanka A, Xu L, Wang W, Thrush-Evensen K, Gonzalez J, Borrus D, Kasamoto J, Sehgal R, Zou G, Fraij J, Carlyle BC, Horvath S, Bennett DA, Zhao H, van Dyck CH, Lam TT, Levine ME, Higgins-Chen AT. bioRxiv. 2025 Oct 16; 2025 Oct 16. PMID: 41279801.
• Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS.Costa Monteiro AC, Pickering H, Sarma A, Taylor CS, Jenkins MM, Hsu FM, Nadel B, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Geng LN, Fernandez-Sesma A, Simon V, Krammer F, Kraft M, Bime C, Calfee CS, Erle DJ, Bosinger S, Eckalbar W, Maecker H, Rahman A, Guan L, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Agus M, Kulkarni H, Schaenmann JM, Salehi-Rad R, Matthay MA, Reed EF, Sapru A. Crit Care. 2025 Oct 14; 2025 Oct 14. PMID: 41088445.
• Identifying Implementation Needs and Developing Strategies to Optimize Integration of Patient Priorities Care in Primary Care: A Qualitative Formative Evaluation of Two Study Sites.Arney J, Banks J, Mecca MC, Catic A, Wydermyer S, Shanahan ML, Zenoni M, Kiefer L, Dindo L, Fried T, Naik AD. J Gen Intern Med. 2025 Oct 13; 2025 Oct 13. PMID: 41083892.
• VISTA Uncovers Missing Gene Expression and Spatial-induced Information for Spatial Transcriptomic Data Analysis.Liu T, Lin Y, Luo X, Sun Y, Zhao H. Res Sq. 2025 Oct 7; 2025 Oct 7. PMID: 41282090.
• Trends in State Palliative Care Legislation Across the US.Ouyang N, Han L, Jiang W, Sinclair S, Rusyn E, Feder SL. JAMA Health Forum. 2025 Oct 3; 2025 Oct 3. PMID: 41134560.
• Incorporating additive genetic effects and linkage disequilibrium information to discover gene-environment interactions using BV-LDER-GE.Dong Z, Jiang W, Shen J, Li H, Xie Y, DeWan AT, Zhao H. Genome Biol. 2025 Oct 3; 2025 Oct 3. PMID: 41044620.
• scGPD: single-cell informed gene panel design for targeted spatial transcriptomics.Guo Y, Zhao J, Chang RB, Zhao H. bioRxiv. 2025 Oct 2; 2025 Oct 2. PMID: 41256660.
• Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies.Zhang X, Wang L, Zhao J, Zhao H. Am J Hum Genet. 2025 Oct 2; 2025 Sep 2. PMID: 40902598.
• Student and Faculty Diversity in Medical School Selection.Nguyen M, Chaudhry SI, Hajduk AM, Ogedegbe G, Henderson D, Venkataraman S, Boatright D. JAMA Netw Open. 2025 Oct 1; 2025 Oct 1. PMID: 41118168.
• Agape Crossing a Barrier.Quagliarello V. Ann Intern Med. 2025 Oct. PMID: 41115299.
• What Matters About What Matters Most.Tinetti ME, Nettles BS. JAMA Netw Open. 2025 Oct 1; 2025 Oct 1. PMID: 41051780.
• Differential results of genetic risk scoring for multiple sclerosis in European and African American populations.Rivier CA, Xu L, Clocchiatti-Tuozzo S, Zhao H, Ohno-Machado L, Hafler DA, Falcone GJ, Longbrake EE. Mult Scler. 2025 Oct; 2025 Sep 24. PMID: 40991630.
• Patient and Caregiver Outcomes of Health System, Community-Based, and Usual Dementia Care: A Prespecified Analysis of the Dementia Care Study (D-CARE) Randomized Clinical Trial.Reuben DB, Stevens AB, Gill TM, Williamson J, Volpi E, Lichtenstein ML, Jennings LA, Galloway R, Summapund J, Araujo K, Bass D, Weitzman L, Tan ZS, Evertson LC, Yang M, Green AS, Samper-Ternent R, Borek P, Xu Y, Peduzzi P, Greene EJ. JAMA Intern Med. 2025 Oct 1. PMID: 40892399.
• Reply to: Reevaluating Functional Recovery Post-COVID-19: A Call for Broader Considerations.Ho JQ, McAvay GJ, Murphy TE, Acampora D, Araujo K, Geda M, Gill TM, Hajduk AM, Cohen AB, Ferrante LE. J Am Geriatr Soc. 2025 Oct; 2025 May 20. PMID: 40390544.
• Intervention for hospitalized people with chronic pain and elevated risk for opioid-related harm: A pilot randomized controlled trial.Weimer MB, Buonora MJ, Hajduk AM, Ackerman AL, Daggula KR, Becker WC, Chaudhry SI, Fiellin DA. J Hosp Med. 2025 Oct; 2025 Apr 24. PMID: 40271961.
• Associations between Social Determinants of Health and Post-Hospitalization Rehabilitation among Critically Ill Older Adults.Jain S, Murphy TE, Falvey JR, Leo-Summers L, Zang E, Gill TM, Krumholz HM, Ferrante LE. Ann Am Thorac Soc. 2025 Sep 30; 2025 Sep 30. PMID: 41025933.
• Underrepresentation of Filipino, Laotian, Cambodian, and Indonesians Among US Allopathic Medical Students.Yang DH, Zhang L, Li BUK, Pang J, Hu JR, Hajduk AM, Chaudhry SI, Yi SS, Đoàn LN, Kwon SC, Boatright D. J Gen Intern Med. 2025 Sep 29; 2025 Sep 29. PMID: 41023302.
• Percutaneous Disruption of Endocarditis Vegetations: The Moment Has Arrived.Quagliarello V, Mehra A, Spellberg B. J Am Coll Cardiol. 2025 Sep 23. PMID: 40962373.
• Obtaining population-based estimates for survey data using Bayesian hierarchical models with Poststratification.Zhang Y, Gill TM, Bandeen-Roche K, Becher RD, Davis-Plourde K, Zang EX. Am J Epidemiol. 2025 Sep 22; 2025 Sep 22. PMID: 40977048.
• SuperGLUE facilitates an explainable training framework for multi-modal data analysis.Liu T, Zhao J, Zhao H. Cell Rep Methods. 2025 Sep 15; 2025 Sep 5. PMID: 40914154.
• High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties.Zhang JY, Rajendran BK, Desai SS, Gibson J, DiPalermo J, LoRusso P, Kong Y, Zhao H, Cecchini M, Schalper KA. J Immunother Cancer. 2025 Sep 10; 2025 Sep 10. PMID: 40935566.
• Designing Stepped Wedge Cluster Randomized Trials With a Baseline Measurement of the Outcome.Davis-Plourde K, Goldfeld K, Allore H, Taljaard M, Li F. Stat Med. 2025 Sep. PMID: 40988307.
• Corrigendum to "Novel indices of state- and county-level social disadvantage in older Americans and disparities in mortality" [Health Place 92 (2025) 103438].Wang Y, Zang EX, Davis-Plourde K, Gill TM, Becher RD. Health Place. 2025 Sep; 2025 Jul 18. PMID: 40683782.
• Emergency Department Utilization Among Co-Residing Family Caregivers of Persons Living With Dementia.Cha PC, Rothenberg C, Chary AN, Seidenfeld J, Hwang U, Fried T, Monin JK, Venkatesh AK, Gettel CJ. J Am Geriatr Soc. 2025 Sep; 2025 May 10. PMID: 40347207.
• The Importance of Geriatric Emergency Department Assessments: Recognizing Patient Risks and Value of Data in Research-A Reply.Hwang U, Cohen I, Carpenter C, Han L, Hung W. Acad Emerg Med. 2025 Aug 28; 2025 Aug 28. PMID: 40875581.
• Advisory Committee on Immunization Practices at a Crossroads.Asturias EJ, Brewer NT, Brooks O, Chen LH, Chu HY, Cineas S, Loehr J, Jamieson DJ, Kamboj M, Kuchel GA, Lyons K, Maldonado YA, Moser CA, Schechter R, Shaw AC, Talbot K, Zucker JR. JAMA. 2025 Aug 26. PMID: 40522971.
• Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics.Liu T, Zhang X, Lin J, Pinello L, Ying R, Zhao H. bioRxiv. 2025 Aug 23; 2025 Aug 23. PMID: 40894641.
• scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis.Liu T, Chen T, Zheng W, Luo X, Chen Y, Zhao H. bioRxiv. 2025 Aug 23; 2025 Aug 23. PMID: 40894586.
• Health-related social needs before and after critical illness among Medicare beneficiaries.Kaminski TA, Murphy TE, O'Leary JR, Leo-Summers L, Ferrante LE. J Gerontol B Psychol Sci Soc Sci. 2025 Aug 23. PMID: 40587086.
• The Path Forward for Vaccine Policy in the United States.Chu HY, Brewer NT, Asturias EJ, Brooks O, Cineas S, Jamieson DJ, Kamboj M, Kuchel GA, Loehr J, Lyons K, Maldonado YA, Moser CA, Schechter R, Shaw AC, Talbot HK, Zucker JR, Chen LH. N Engl J Med. 2025 Aug 21; 2025 Jul 30. PMID: 40737616.
• Polygenic Resistance to Blood Pressure Treatment and Stroke Risk: Insights from the All of Us Research Program.Huo S, Rivier CA, Clocchiatti-Tuozzo S, Renedo D, Petersen N, de Havenon A, Meeker D, Zhao H, Ohno-Machado L, Sheth KN, Falcone GJ. Ann Neurol. 2025 Aug 19; 2025 Aug 19. PMID: 40827941.
• spVelo: RNA velocity inference for multi-batch spatial transcriptomics data.Long W, Liu T, Xue L, Zhao H. Genome Biol. 2025 Aug 11; 2025 Aug 11. PMID: 40790237.
• MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury.Pickering H, Alipanah-Lechner N, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Cotsapas C, Steen H, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, Kraft M, Bime C, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Altman MC, Bosinger S, Eckalbar W, Calfee CS, Aguilar OA, Reed EF, Greenland JR, Calabrese DR. JCI Insight. 2025 Aug 8; 2025 Jul 3. PMID: 40608426.
• Leveraging local ancestry and cross-ancestry genetic architecture to improve genetic prediction of complex traits in admixed populations.Zhou G, Yolou I, Xie Y, Zhao H. Am J Hum Genet. 2025 Aug 7; 2025 Jul 8. PMID: 40633541.
• Medical School Admissions After the Supreme Court's 2023 Affirmative Action Ruling.Nguyen M, Hajduk AM, Fancher TL, Henderson MC, Herrin J, Henderson D, Richardson J, Venkataraman S, Castillo-Page L, Shin SM, O'Connell M, Ayedun A, Boatright D, Chaudhry SI. JAMA Netw Open. 2025 Aug 1; 2025 Aug 1. PMID: 40857005.
• Agreement Between Self-Reported and Proxy-Reported Pain in Veterans With Advanced Heart Failure.Akgün KM, Han L, Zhan Y, Abel EA, Feder SL. Am J Hosp Palliat Care. 2025 Jul 31; 2025 Jul 31. PMID: 40741915.
• Symptom trajectories after COVID hospitalization and risk factors for symptom burden in older persons: a longitudinal cohort study.Pan Y, Cho G, Geda M, Gill TM, Cohen AB, Ferrante LE, Hajduk AM, Miner B. J Gerontol A Biol Sci Med Sci. 2025 Jul 24. PMID: 40512177.
• The tumor microenvironment of non-small cell lung cancer impairs immune cell function in people with HIV.Desai SS, Salahuddin S, Yusuf R, Ranjan K, Gu J, Osmani L, Lin YW, Mehta S, Talmon R, Kang I, Kluger Y, Zhao H, Schalper K, Emu B. J Clin Invest. 2025 Jul 15; 2025 Jun 3. PMID: 40459946.
• The Geriatric Emergency Care Applied Research Standardization Study (GEARSS): An Observational Study of Older Emergency Department Patients.Hwang U, Sifnugel N, Cohen I, Han L, Araujo K, Bianco LM, Brandt CA, Capelli S, Carpenter CR, Cruz DS, Dresden SM, Fishman IL, Gipson K, Hastings SN, Hung WW, Kang R, Lockhart M, Meeker D, Ohuabunwa U, Ottilie-Kovelman S, Partridge C, Platts-Mills TF, Sandoval J, Taylor Z, Tomasino DF, Vaughan CP. Acad Emerg Med. 2025 Jul 12; 2025 Jul 12. PMID: 40650481.
• Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset.Nagel CL, Chen S, Allore HG, Botoseneanu A, Newsom JT, Bishop N, Dorr DA, Kaye J, Quiñones AR. PLoS One. 2025; 2025 Jul 10. PMID: 40638618.
• High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19.Qualls AE, Tsao T, Lui I, Lim SA, Su Y, Chen E, Duchen D, Maecker HT, Kim-Schulze S, Montgomery RR, Krammer F, Langelier CR, Levy O, Baden LR, Melamed E, Ehrlich LI, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez-Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Schaenmann J, Ozonoff A, Peters B, Kleinstein SH, Augustine AD, Diray-Arce J, Becker PM, Rouphael N, Goldman JD, Calabrese DR, Heath JR, Wells JA, Reed EF, Lanier LL, Pickering H, Aguilar OA. JCI Insight. 2025 Jul 8; 2025 May 22. PMID: 40402577.
• spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model.Liu T, Huang T, Jin W, Chu T, Ying R, Zhao H. bioRxiv. 2025 Jul 7; 2025 Jul 7. PMID: 40631230.
• Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study.Hou J, Haslund-Gourley B, Diray-Arce J, Hoch A, Rouphael N, Becker PM, Augustine AD, Ozonoff A, Guan L, Kleinstein SH, Peters B, Reed E, Altman M, Langelier CR, Maecker H, Kim S, Montgomery RR, Krammer F, Wilson M, Eckalbar W, Bosinger SE, Levy O, Steen H, Rosen LB, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Schaenman J, Shaw AC, Hafler DA, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Agudelo Higuita NI, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Fernandez Sesma A, Simon V, Kraft M, Bime C, Calfee CS, Erle DJ, Impacc Network, Robinson LF, Cairns CB, Haddad EK, Comunale MA. Front Med (Lausanne). 2025; 2025 Jul 4. PMID: 40687705.
• Incorporating local ancestry information to predict genetically associated DNA methylation in admixed populations.Cheng Y, Zhou G, Li H, Zhang X, Justice A, Martinez C, Aouizerat BE, Xu K, Zhao H. Brief Bioinform. 2025 Jul 2. PMID: 40622482.
• What Matters Most: An Example of Implementing Patient Priorities Care.Mecca MC, Ouellet GM, Tinetti M, Ouellet JA. Sr Care Pharm. 2025 Jul 1. PMID: 40616225.
• Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD.Hwang A, Skarica M, Xu S, Coudriet J, Lee CY, Lin L, Terwilliger R, Sliby AN, Wang J, Nguyen T, Li H, Wu M, Dai Y, Duan Z, Srinivasan SS, Zhang X, Lin Y, Cruz D, Deans PJM, Huber BR, Levey D, Glausier JR, Lewis DA, Gelernter J, Holtzheimer PE, Friedman MJ, Gerstein M, Sestan N, Brennand KJ, Xu K, Zhao H, Krystal JH, Young KA, Williamson DE, Che A, Zhang J, Girgenti MJ. Nature. 2025 Jul; 2025 Jun 18. PMID: 40533550.
• The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour.Yoshida TM, Nguyen M, Zhang L, Lu BY, Zhu B, Murray KN, Mineur YS, Zhang C, Xu D, Lin E, Luchsinger J, Bhatta S, Waizman DA, Coden ME, Ma Y, Israni-Winger K, Russo A, Wang H, Song W, Al Souz J, Zhao H, Craft JE, Picciotto MR, Grutzendler J, Distasio M, Palm NW, Hafler DA, Wang A. Nature. 2025 Jul; 2025 May 28. PMID: 40437096.
• The Longitudinal Course of Physical Activity Behavior Poststroke and Its Variation Across Subgroups: The Norwegian Cognitive Impairment After Stroke Study.Luzum G, Allore H, Han L, Saltvedt I, Tan X, Thingstad P, Håberg A, Askim T. Phys Ther. 2025 Jul 1. PMID: 40360170.
• Upholding Our Duty to Care for Undocumented Immigrants.Gross CP, Richman IB, Ganguli I, Anderson TS, Rittenberg E, Stall NM, Kneifati-Hayek JZ, Durant RW, Grady D, Allore HG, Corbie G, Inouye SK. JAMA Intern Med. 2025 Jul 1. PMID: 40354074.
• Correction: Single-nucleus RNA sequencing reveals distinct pathophysiological trophoblast signatures in spontaneous preterm birth subtypes.Uhm C, Gu J, Ju W, Pizzella S, Oktay H, Peng JY, Guariglia S, Liu Y, Zhao H, Wang Y, Menon R, Zhong N. Cell Biosci. 2025 Jun 26; 2025 Jun 26. PMID: 40571915.
• Robust pleiotropy-decomposed polygenic scores identify distinct contributions to elevated coronary artery disease polygenic risk.Hu J, Ye Y, Zhang C, Ruan Y, Natarajan P, Zhao H. PLoS Comput Biol. 2025 Jun; 2025 Jun 26. PMID: 40570042.
• Social Support and Social Strain Sources as Predictors of Multimorbidity Changes in Middle-Aged and Older Adults.Newsom JT, Saucedo J, Kroeck MR, O'Neill AS, Allore HG, Nagel CL, Botoseneanu A, Trubits EF, Dorr DA, Quiñones AR. J Aging Health. 2025 Jun 25; 2025 Jun 25. PMID: 40557788.
• APOE ε4 and Risk of Intracranial Hemorrhage in Patients With Atrial Fibrillation Taking Apixaban.Clocchiatti-Tuozzo S, Rivier CA, Renedo D, Huo S, de Havenon A, Hawkes MA, Gilmore E, Schwamm LH, Sheth KN, Gill TM, Falcone GJ. JAMA Neurol. 2025 Jun 23; 2025 Jun 23. PMID: 40549373.
• Almost Free Enhancement of Multi-Population PRS: From Data-Fission to Pseudo-GWAS Subsampling.Xu L, Dong Y, Zeng X, Bian Z, Zhou G, Guan L, Zhao H. bioRxiv. 2025 Jun 20; 2025 Jun 20. PMID: 40611909.
• Empiric Azithromycin in COVID-19 Impacts the Respiratory Microbiome and Antimicrobial Resistome without Anti-inflammatory Benefit.Langelier C, Glascock A, Maguire C, Van Phan H, Lydon E, Calfee C, Corry D, Kheradmand F, Baden L, Sekaly RP, McComsey G, Haddad E, Cairns C, Pulendran B, Fernandez-Sesma A, Simon V, Metcalf J, Higuita N, Messer W, Davis M, Nadeau KC, Kraft M, Bime C, Schaenman J, Erle D, Atkinson M, Ehrlich LIR, Melamed E, Montgomery R, Shaw A, Hough C, Geng L, Hoch A, Hafler D, Augustine A, Becker P, Peters B, Ozonoff A, Kim-Schulze S, Krammer F, Bosinger S, Eckalbar W, Altman M, Wilson M, Guan L, Maecker H, Steen H, Diray-Arce J, Rouphael N, Kleinstein S, Reed E, Levy O, Chu V. Res Sq. 2025 Jun 20; 2025 Jun 20. PMID: 40585204.
• Effects of ambient temperature on hospital admissions and mortality among older adults with and without dementia in South Korea.Byun G, Kim S, Festa N, Choi Y, Lee WW, Lee JT, Gill TM, Bell ML. Int J Epidemiol. 2025 Jun 11. PMID: 40795076.
• Incomplete Ascertainment of Mortality in a Nationally Representative Longitudinal Study of Community-Living Older Americans.Gill TM, Liang J, Vander Wyk B, Leo-Summers L, Wang Y, Becher RD, Davis-Plourde K. J Gerontol A Biol Sci Med Sci. 2025 Jun 10. PMID: 39823281.
• Glis3 is a modifier of cyst progression in autosomal dominant polycystic kidney disease.Wei Z, Gu J, Tian X, Zhang C, Zhao H, Somlo S. bioRxiv. 2025 Jun 9; 2025 Jun 9. PMID: 40661540.
• Development and Validation of Models to Estimate the Incident Risk of Cognitive Impairment and Atherosclerotic Cardiovascular Disease in Older Adults.Nanna MG, Wojdyla D, Peterson ED, Navar AM, Williamson JD, Colantonio LD, Wang SY, Jamil Y, Bertoni AG, Nahid M, Damluji AA, Goyal P, Chaudhry SI, Gill TM, Alexander KP. J Am Heart Assoc. 2025 Jun 3; 2025 May 22. PMID: 40401627.
• The COVID-19 Pandemic and Goals-of-Care Conversations in Veterans Health Administration Clinics.Linsky AM, Canter BE, Glickman M, Qian S, Ryan SK, Still M, Fried TR, Wiener RS. JAMA Netw Open. 2025 Jun 2; 2025 Jun 2. PMID: 40522660.
• Intersectionality of Sexual Orientation, Race, and Ethnicity in Medical School Attrition.Nguyen M, Boatright D, Sánchez JP, Hajduk AM, Venkataraman S, O'Connell M, Aviles A, Rajbhandari P, Chaudhry SI. JAMA Netw Open. 2025 Jun 2; 2025 Jun 2. PMID: 40493371.
• Contribution of chronic conditions to mortality: Differences by race and ethnicity.Elman MR, Quiñones AR, McAvay GJ, Vander Wyk B, Nagel CL, Allore HG. Aging Health Res. 2025 Jun; 2025 Apr 23. PMID: 40575585.
• Detection of emergency department patients at risk of dementia through artificial intelligence.Cohen I, Taylor RA, Xue H, Faustino IV, Festa N, Brandt C, Gao E, Han L, Khasnavis S, Lai JM, Mecca AP, Sapre AV, Young J, Zanchelli M, Hwang U. Alzheimers Dement. 2025 Jun. PMID: 40457744.
• Incidence of Frailty, Dementia, and Disability Among Community-Living Older Americans According to County-Level Disadvantage.Wang Y, Zang EX, Davis-Plourde K, Vander Wyk B, Gill TM, Becher RD. J Am Geriatr Soc. 2025 Jun; 2025 Apr 8. PMID: 40196885.