Biomedical Informatics

Publications

Aetesam, H; Maji, SK; Prasath, VB S. Hyperspectral image restoration using noise gradient and dual priors under mixed noise conditions. CAAI Transactions on Intelligence Technology. 2025; 10:72-93.

Aetesam, H; Prasath, VB S. Variational Weighted ℓp−ℓq$\ell _p-\ell _q$ Regularization for Hyperspectral Image Restoration Under Mixed Noise. IET Image Processing. 2025; 19.

Alarcon, PC; Ulanowicz, CJ; Damen, MS M A; Eom, J; Sawada, K; Chung, H; Alahakoon, T; Oates, JR; Wayland, JL; Stankiewicz, TE; Moreno-Fernandez, ME; Zacharias, WJ; Salomonis, N; Divanovic, S. Obesity Uncovers the Presence of Inflammatory Lung Macrophage Subsets With an Adipose Tissue Transcriptomic Signature in Influenza Virus Infection. The Journal of Infectious Diseases. 2025; 231:e317-e327.

Alcântara, RB; Scalabrini Neto, A; Almeida, AM; Gonçalves, IM; Almeida, MV L D; Brandão, CF S; Cavalcanti, LC; Generoso Junior, JR. Comparação entre alta e baixa fidelidade na aprendizagem das emergências cardiovasculares. 2025; 25:e20639.

Allen, AJ; Nguyen, N; Lorman, V; Maltenfort, M; Mosa, AS M; Sekar, A; Mejias, A; Taylor, E; Mendonca, EA; Nabower, AM; Downs, SM; Ostasiewski, B; Kaushal, R; Campion, T. Respiratory and Other Infections Following COVID. Pediatrics. 2025; 156:e2024068280.

Bell, MB; Kane, MS; Ouyang, X; Young, ME; Jegga, AG; Chatham, JC; Darley-Usmar, V; Zhang, J. Brain Transcriptome Changes Associated With an Acute Increase of Protein O-GlcNAcylation and Implications for Neurodegenerative Disease. Journal of Neurochemistry. 2025; 169:e16302.

Börner, K; Blood, PD; Silverstein, JC; Ruffalo, M; Satija, R; Teichmann, SA; Pryhuber, GJ; Misra, RS; Purkerson, JM; Fan, J; Longacre, TA; Lindsay, SA; Lin, Y; Lin, S. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods. 2025; 22:845-860.

Boudissa, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Surya Prasath, VB. Vision Transformers for Histopathological Image Classification with Efficient Head Pruning. Procedia Computer Science. 2025; 270:2274-2283.

Bowen, C; Morton, S; Avillach, P; Brueckner, M; Chung, W; Cnota, J; Gelb, B; Lewis, M; Liu, C; Roberts, A; Wagner, M; Seidman, C; Newburger, J; Geva, T. Abstract 4363833: Impact of Damaging Genetic Variants on Right Ventricular Function in Tetralogy of Fallot. Circulation. 2025; 152:a4363833.

Brailsford, J; Labilloy, G; Menze, N; Henson, M; Fishe, J. Updated analysis of the pharmacogenomics of pediatric bronchodilator response. Pharmacogenetics and Genomics. 2025; 35:116-118.

Bunnell, HT; Reedy, C; Lorman, V; Jhaveri, R; Rivera-Sepulveda, A; Salamon, KS; Patel, PB; Morse, KE; Davenport, MA; Cowell, LG; Cummins, MR; Gouripeddi, R; Cowell, LG; Reeder, P. A natural language processing pipeline for identifying pediatric long COVID symptoms and functional impacts in freeform clinical notes: a RECOVER study. JAMIA Open. 2025; 8:ooaf089.

Chandrashekar, M; Tschida, J; Strawn, JR; Hanson, HA; Santel, D; Goethert, I; Kapadia, AJ; Glauser, T; Pestian, J; Agasthya, GA. Comparison of Expert Vocabulary Usage Patterns Between Mental Health and Nonmental Health Clinicians When Diagnosing Pediatric Anxiety Disorders. The Journal of Pediatrics. 2025; 286:114735.

Chung, E; Nosrati, F; Adam, M; Potter, A; Sayed, M; Ahn, C; Humphreys, BD; Lim, HW; Hu, YC; Potter, SS; Park, JS. Proximal Tubule Cells Contribute to the Thin Descending Limb of the Loop of Henle during Mouse Kidney Development. Journal of the American Society of Nephrology : JASN. 2025; 36:1928-1938.

Cotia, AL F; Scorsato, AP; da Silva Victor, E; Prado, M; Gagliardi, G; de Barros, JE V; Generoso, JR; de Menezes, FG; Hsieh, MK; Lopes, GO V; Edmond, MB; Perencevich, EN; Goto, M; Wey, SB; Marra, AR. Integration of an electronic hand hygiene auditing system with electronic health records using machine learning to predict hospital-acquired infection in a health care setting. American Journal of Infection Control. 2025; 53:58-64.

Cowell, LG; Christley, S; Breden, F; Burns, KA; Corrie, BD; Lees, WD; Overton, JA; Peters, B; Richardson, E; Roskin, KM; Scheffer, L; Vita, R; Watson, CT; Yaari, G. The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community. Cell Systems. 2025; 16:101401.

Debsarkar, SS; Aronow, B; Prasath, VB S. Advancements in automated nuclei segmentation for histopathology using you only look once-driven approaches: A systematic review. Computers in Biology and Medicine. 2025; 190:110072.

Dong, W; Jin, SC; Sierant, MC; Lu, Z; Li, B; Lu, Q; Morton, SU; Zhang, J; López-Giráldez, F; Nelson-Williams, C; Gelb, BD; Seidman, CE; Lifton, RP; Brueckner, M. Recessive genetic contribution to congenital heart disease in 5,424 probands. Proceedings of the National Academy of Sciences of USA. 2025; 122:e2419992122.

Ediga, HH; Vemulapalli, CP; Sontake, V; Patel, PK; Miyazaki, H; Popov, D; Jensen, MB; Jegga, AG; Huang, SK; Englert, C; Schedl, A; Gupta, N; McCormack, FX; Madala, SK. Wilms tumor 1 impairs apoptotic clearance of fibroblasts in distal fibrotic lung lesions. The Journal of Clinical Investigation. 2025; 135:e188819.

Farris, RW D; Shah, SS; Bennett, TD; Brown, SR; Cornell, TT; Dziorny, AC; Flynn, A; Grunwell, J; Heneghan, JA; Kennedy, CE; Rogerson, C; Tawfik, DS; Wetzel, RC; Sanchez-Pinto, LN. The PICU Data Collaborative: A Novel, Multi-Institutional, Pediatric Critical Care Dataset. Pediatric Critical Care Medicine. 2025; 26:e941-e951.

Feldman, ER; Li, Y; Cutler, DJ; Rosser, TC; Wechsler, SB; Sanclemente, L; Rachubinski, AL; Elliott, N; Vyas, P; Roberts, I; Lupo, PJ; de Smith, AJ; Sherman, SL; Leslie-Clarkson, EJ. Genome-Wide Association Studies of Down Syndrome Associated Congenital Heart Defects Suggests a Genetically Heterogeneous Risk for CHD in DS. Genetic Epidemiology. 2025; 49:e70010.

Ferchen, K; Zhang, X; Thakkar, K; Li, G; Bernardicius, D; Sen, S; Rawat, P; Olsson, A; Bennett, SN; Potter, C; Morris, S; Singh, H; Salomonis, N; Grimes, HL. A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice. Nature Immunology. 2025; 26:2086-2099.

Garibaldi, BT; Hollon, M; Knopp, MI; Winkel, AF; Burk-Rafel, J; Caretta-Weyer, HA. How Data Analytics Can Be Leveraged to Enhance Graduate Clinical Skills Education. Journal of Graduate Medical Education. 2025; 17:37-41.

Ghandikota, S; Jegga, AG. From Gene Networks to Therapeutics: A Causal Inference and Deep Learning Approach for Drug Discovery. Pharmaceuticals. 2025; 18:1304.

Greve, K; Bailes, AF; Zhang, N; Long, J; Aronow, B; Mitelpunkt, A. Physical Therapy Dose After Orthopedic Multilevel Surgery Varies by Ambulatory Status in Children With Cerebral Palsy: A Pilot Study. Pediatric Physical Therapy. 2025; 37:37-44.

Halurkar, MS; Inoue, O; Singh, A; Mukherjee, R; Ginugu, M; Ahn, C; Bonatto Paese, CL; Duszynski, M; Brugmann, SA; Lim, HW; Sanchez-Gurmaches, J. The widely used Ucp1-Cre transgene elicits complex developmental and metabolic phenotypes. Nature Communications. 2025; 16:770.

Hand, SM; Zhao, Y; Li, D; Burke, S; Lim, HW; Yester, J; Garg, V; Accornero, F; Li, X; Li, D; Jang, J. Loss of Methyltransferase and Hypomethylated m6A Sarcomere Transcripts Leading to Early-Onset Dilated Cardiomyopathy. Circulation. 2025; 151:1692-1695.

Idnay, B; Xu, Z; Adams, WG; Adibuzzaman, M; Anderson, NR; Bahroos, N; Bell, DS; Bumgardner, C; Campion, T; Castro, M; Xu, H; Bian, J; Weng, C; Peng, Y. Environment scan of generative AI infrastructure for clinical and translational science. 2025; 2:4.

Iyer, B; Deoghare, S; Ranjan, K; Aronow, BJ; Prasath, VB S. Benchmarking HEp-2 cell segmentation methods in indirect immunofluorescence images - standard models to deep learning. Computers in Biology and Medicine. 2025; 192:110150.

Jennings, KM; Knopp, MI; Kinnear, B; Warm, EJ; Powers-Fletcher, MV; Santen, SA; Schauer, DP. Association Between Electronic Health Record Use Metrics and Clinical Performance in an Outpatient Primary Care Resident Clinic. Academic Medicine. 2025; 100:968-974.

Jin, K; Zhang, Z; Zhang, K; Viggiani, F; Callahan, C; Tang, J; Aronow, BJ; Shu, J. Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings. Nature Communications. 2025; 16:6618.

Johnstone, ME; Leck, AL; Lange, TE; Wilcher, KE; Shephard, MS; Paranjpe, A; Schutte, S; Wells, SI; Kappes, F; Salomonis, N; Privette Vinnedge, LM. DEK promotes mammary hyperplasia and is associated with H3K27me3 epigenetic modifications. Life Science Alliance. 2025; 8:e202503230.

Kanbar, LJ; Dexheimer, JW; Benscoter, DT; Amin, RS; Schuler, CL; Pajor, N. Timeline of Weaning in Pediatric Long-Term Mechanical Ventilator Dependent Children: A Longitudinal Cohort Study. Pediatric Pulmonology. 2025; 60:e27405.

Kanbar, LJ; Osborn, A; Cifuentes, A; Combs, J; Sorter, M; Barzman, D; Dexheimer, JW. Forecasting school violence risk with incomplete interview data: an automated assessment approach. JAMIA Open. 2025; 8:ooaf084.

Kantor, P; Ware, S; Hamza, T; Shi, L; Colan, S; Rossano, J; Towbin, J; LEE, T; Lal, A; Webber, S; Dexheimer, P; Schubert, J; Wilkinson, J; Lipshultz, S. Abstract 4346181: The Impact of Genotype on Phenotypic Severity and Survival in Pediatric Dilated Cardiomyopathy: a report from the Pediatric Cardiomyopathy Registry. Circulation. 2025; 152:a4346181.

Khan, I; Rodriguez-Brotons, A; Bhattacharjee, A; Bezrookove, V; Dar, A; De Semir, D; Nosrati, M; Ice, R; Soroceanu, L; Leong, SP; Bosenberg, M; Salomonis, N; McAllister, S; Kashani-Sabet, M. Combinatorial therapy regimens targeting preclinical models of melanoma resistant to immune checkpoint blockade. The Journal of Clinical Investigation. 2025; 135:e185220.

Kolli, V; Gomez-Arroyo, J; Gu, M; Elwing, JM; Jegga, A; Sarangdhar, M. Evaluating Antidiabetic Modulatory Effects on Drug-induced Pulmonary Arterial Hypertension Using Real-world Data. American Journal of Respiratory and Critical Care Medicine. 2025; 211:a4977.

Krishnan, JM; Kong, L; Meeds, HL; Roskin, KM; Medvedovic, M; Sherman, KE; Blackard, JT. The synthetic opioid fentanyl increases HIV replication in macrophages. Editor, Banoub J. PloS one. 2025; 20:e0298341.

Kudira, R; Yang, ZF; Osuji, I; Damen, MS M A; Yang vom Hofe, A; Singh, M; Karns, R; Bariya, P; Pfuhler, L; Mullen, M; Subramanian, S; Salomonis, N; Miraldi, ER; Miethke, AG. Bile acids engage the SIPR-STAT3 signaling axis to modulate regulatory T cell responses in fibrosing cholangiopathies. Journal of Hepatology. 2025; 83:1128-1141.

Labilloy, G; Tanaka, S; Black, LP; Augustin, B; Hopson, C; Bethencourt, J; Wu, D; Sulaiman, D; Bertrand, A; Salomão, R; Graim, K; Datta, S; Reddy, S; Guirgis, FW; Hofmaenner, DA. IDENTIFYING A SEPSIS SUBPHENOTYPE CHARACTERIZED BY DYSREGULATED LIPOPROTEIN METABOLISM USING A SIMPLIFIED CLINICAL DATA ALGORITHM. Shock. 2025; 64:218-225.

Ladha, F; Vanderpluym, C; Avillach, P; Brueckner, M; Chung, W; Cnota, J; Gelb, B; Lewis, M; Liu, C; Roberts, A; Seidman, C; Tristani-Firouzi, M; Wagner, M; Morton, S; Newburger, J. Abstract 4359742: Thrombophilia Variants Do Not Predict Thrombotic Events in Congenital Heart Disease: Insights from the Pediatric Cardiac Genomics Consortium. Circulation. 2025; 152:a4359742.

Lambourne, L; Mattioli, K; Santoso, C; Sheynkman, G; Inukai, S; Kaundal, B; Berenson, A; Spirohn-Fitzgerald, K; Bhattacharjee, A; Rothman, E; Sahni, N; Vidal, M; Bulyk, ML; Fuxman Bass, JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. Molecular Cell. 2025; 85:1445-1466.e13.

Lape, M; Schnell, D; Parameswaran, S; Ernst, K; O’Connor, S; Salomonis, N; Martin, LJ; Harnett, BM; Kottyan, LC; Weirauch, MT. A survey of pathogenic involvement in non-communicable human diseases. Communications Medicine. 2025; 5:242.

Li, Y; Huang, B; Andorf, S; Yue, X; Lovell, DJ; Brunner, HI. Comparative Effectiveness and Safety of the JAK Inhibitors and Biologic Disease-Modifying Antirheumatic Drugs in Treating Children With Nonsystemic Juvenile Idiopathic Arthritis: A Bayesian Meta-Analysis of Randomized Controlled Trials. ACR Open Rheumatology. 2025; 7:e11788.

Lorman, V; Bailey, LC; Song, X; Rao, S; Hornig, M; Utidjian, L; Razzaghi, H; Mejias, A; Leikauf, JE; Brill, SB; Cummins, MR; Jhaveri, R; Blecker, S; Forrest, CB. Pediatric Long COVID Subphenotypes: An EHR-based study from the RECOVER program. Editor, Sbaffi L. PLOS Digital Health. 2025; 4:e0000747.

McGrady, ME; Hommel, KA; Mara, CA; Breen, G; Kouril, M. Engaging end-users to develop a novel algorithm to process electronic medication adherence monitoring device data. JAMIA Open. 2025; 8:ooaf135.

Mihalas, AB; Arora, S; O’Connor, SA; Feldman, HM; Cucinotta, CE; Mitchell, K; Bassett, J; Kim, D; Jin, K; Hoellerbauer, P; Aronow, B; Plaisier, CL; Patel, AP; Paddison, PJ. KAT5 regulates neurodevelopmental states associated with G0-like populations in glioblastoma. Nature Communications. 2025; 16:4327.

Miller, RL; Schuh, H; Chandran, A; Habre, R; Angal, J; Aris, IM; Aschner, JL; Bendixsen, CG; Blossom, J; Bosquet-Enlow, M; Wright, RJ; Zanobetti, A; Zoratti, EM; Johnson, CC. Child Opportunity Index at birth and asthma with recurrent exacerbations in the US ECHO program. Journal of Allergy and Clinical Immunology. 2025; 156:627-639.

Minja, NW; Pulle, J; Rwebembera, J; Ollberding, NJ; Fall, N; Atala, J; Kamarembo, J; Oyella, L; Odong, F; De Loizaga, SR; Okello, E; Beaton, AZ; Watkins, DA; Danforth, KM. Integrating secondary prevention of rheumatic heart disease into the primary healthcare system in Northern Uganda. BMJ Global Health. 2025; 10:e018835.

Molloy, E; Loeb, D; Generoso Junior, J; Zackoff, M. 1582: VERBALIZATION VERSUS RECOGNITION OF SEPSIS BY RESIDENTS IN A VIRTUAL REALITY SIMULATION. Critical Care Medicine. 2025; 53.

Norte, G; Sá-Couto, C; Brandão, CF S; Generoso Junior, JR; Matos, FM. Tradução e adaptação para a Língua Portuguesa da Declaração de Consenso Global sobre a Prática Baseada em Simulação na Saúde. 2025; 25:e20508.

Oluwafemi, R; Ajayi, B; Mendonca, E; Biondich, P; Ekhaguere, O. Looped Audiovisual Health Education Talk Reduces Vaccine Clinic Wait Time in Nigeria. Child: Care, Health and Development. 2025; 51:e70152.

Opipari-Arrigan, L; Kouril, M; Connor, J; Ford, C; McWilliams, E; Green, A; Siracusa, C; Milla, C; Muther, E; Nasr, SZ; Sathe, M; Sawicki, GS; Schechter, MS; Snell, C; Stark, LJ. Evaluating Feasibility, Acceptability, and Effectiveness of a Digital Behavioral Nutrition Intervention in Cystic Fibrosis Care. Clinical Practice in Pediatric Psychology. 2025; 13:269-279.

Peters, AL; DePasquale, EA K; Begum, G; Roskin, KM; Kotliar, M; Barski, A; Salomonis, N; Shi, T; Ranganathan, S; Woodle, ES; Hildeman, DA. Single-cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells. American Journal of Transplantation. 2025; 25:2345-2360.

Peters, M; Teodorescu, P; Pasca, S; Zhang, X; Wang, R; Yegnasubramanian, S; Grimes, LH; Salomonis, N; Gondek, LP; Ghiaur, G. Comprehensive characterization of human bone marrow microenvironment shows age-related changes. Haematologica: the hematology journal. 2025; 110:2844-2848.

Phelan, KJ; Roskin, KM; Burkle, JW; Chang, WC; Martin, LJ; Biagini, JM; Satish, L; Haslam, DB; Spagna, D; Jenkins, S; Visness, CM; Altman, MC; Gern, JE; Khurana Hershey, GK. Early-life wheeze trajectories are associated with distinct asthma transcriptomes later in life. Journal of Allergy and Clinical Immunology. 2025; 156:640-650.

Qiao, J; Wang, Q; Zhao, Y; Chang, M; Sun, S; Zhang, P; Yao, K; Chen, M; Zheng, L; Xing, X; Pauklin, S; Zou, R; Yang, Y; Feng, Y. Contribution of leukocyte telomere length to cardiovascular disease onset from genome-wide cross-trait analysis. Nature Communications. 2025; 16:8677.

Rao, S; Allen, AJ; Maltenfort, M; Mejias, A; Mendonca, E; Horne, B; Taylor, E; Mosa, A; Sekar, A; Lorman, V. P-727. Is there increased risk of RSV infection following SARS-CoV-2 infection in children? An EHR-based cohort study from the RECOVER Program. Open Forum Infectious Diseases. 2025; 12:ofae631.923.

Renugadevi, M; Ramkumar, K; Raju, N; Adalarasu, K; Prasath, S; Narasimhan, K. Self‐Supervised DRL With Twin Critics: A Novel Framework for Glioblastoma Survival Prognostication. International Journal of Imaging Systems and Technology. 2025; 35.

Riggins, DP; Mendonca, EA; Bulgarelli, L; Tachinardi, P; Tu, W; Rogerson, C. Estimating the Effects of Continuous Albuterol Dosage on Clinical Outcomes for Pediatric Critical Asthma Exacerbation: A Retrospective Cohort Study. Pediatric Pulmonology. 2025; 60:e71293.

Rogerson, C; Abu-Sultaneh, S; Nelson Sanchez-Pinto, L; Gaston, B; Wiehe, S; Schleyer, T; Tu, W; Mendonca, E. 1203: A MATCHED ANALYSIS OF THE USE OF HIGH-FLOW NASAL CANNULA FOR PEDIATRIC SEVERE ACUTE ASTHMA. Critical Care Medicine. 2025; 53.

Rogerson, C; Nelson Sanchez-Pinto, L; Gaston, B; Wiehe, S; Schleyer, T; Tu, W; Mendonca, E. 1208: IDENTIFICATION OF SEVERE ACUTE PEDIATRIC ASTHMA PHENOTYPES USING UNSUPERVISED MACHINE LEARNING. Critical Care Medicine. 2025; 53.

Roskin, KM; Meeds, HL; Madhuravasal Krishnan, J; Juhascik, M; Cafardi, JM; Brown, JL; Freiermuth, C; Lyons, MS; Sherman, KE; Blackard, JT. Single cell RNA transcriptome response to fentanyl use in persons with hepatitis C virus infection. Frontiers in Virology. 2025; 5:1585217.

S, P; K, R; K, N; Prasath, VB S; S, V. Web based AI-driven framework combining multi-modal data with CNN and LLM for Parkinson's disease diagnosis. Scientific Reports. 2025; 15:38556.

Sarangdhar, M; Ghandikota, S; Kolli, V; Jegga, A. Network Propagation Analysis to Uncover the Mechanisms of Antidiabetics as Therapeutic Candidates in Pulmonary Arterial Hypertension. American Journal of Respiratory and Critical Care Medicine. 2025; 211:a4976.

Sayed, M; Wang, YJ; Lim, HW. Systematic benchmark of single-cell hashtag demultiplexing approaches reveals robust performance of a clustering-based method. Briefings in Functional Genomics. 2025; 24:elae039.

Schmidt, SK; Dexheimer, JW; Zorc, JJ; Palmer, CA; Casper, TC; Stukus, KS; Pickett, ML; Mollen, CJ; Elsholz, CL; Cruz, AT; Augustine, EM; Goyal, MK; Reed, JL. Multisite Implementation of a Sexual Health Survey and Clinical Decision Support to Promote Adolescent Sexually Transmitted Infection Screening. Applied Clinical Informatics - ACI. 2025; 16:283-294.

Schoettler, N; Gebretsadik, T; Singh, S; Gress, L; Mendonça, EA; Snyder, BM; Eapen, AA; LeBeau, P; Gangnon, R; Seroogy, CM; Pierce, M; Polacek, DA; Poleon, K; Rajamanickam, V. Genotypes in the 17q12-q21 asthma risk locus and early-life viral wheezing illnesses. Pediatric Allergy and Immunology. 2025; 36:e70165.

Schwendeman, E; Kaminski, HJ; Vanderver, A; Wagner, M; King, E; Benatar, M; Crosby, LE; King, E; Kretzler, M; Lumsden, J; Ruediger, S; Urv, T; Vanderver, A; Macaluso, M. Data Sharing Experience, Guidance, and Resources From the Rare Diseases Clinical Research Network (RDCRN). Clinical and Translational Science. 2025; 18:e70340.

Seetharaman, A; Galagali, H; Linarte, E; Liu, MH X; Cohen, JD; Chetal, K; Sadreyev, R; Tate, AJ; Montgomery, TA; Ruvkun, G. Decreased SynMuv B gene activity in response to viral infection leads to activation of the antiviral RNAi pathway in C. elegans. Editor, Mehle A. PLoS Biology. 2025; 23:e3002748.

Shao, H; Thorpe, LE; Islam, S; Bian, J; Guo, Y; Li, P; Bost, S; Dabelea, D; Conway, R; Crume, T; Rolka, D; Imperatore, G; Pavkov, ME; Divers, J. Developing a Computable Phenotype for Identifying Children, Adolescents, and Young Adults With Diabetes Using Electronic Health Records in the DiCAYA Network. Diabetes Care. 2025; 48:914-921.

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Prasath, VB S; Surya Prasath, VB. Multimodal Ensemble Fusion Deep Learning Using Histopathological Images and Clinical Data for Glioma Subtype Classification. IEEE Access. 2025; 13:57780-57797.

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, B; Surya Prasath, VB. Multiple Instance Learning Using Reduced Deep Learning Model For Glioma Subtype Classification. Procedia Computer Science. 2025; 270:2434-2442.

Sierant, MC; Jin, SC; Bilguvar, K; Morton, SU; Dong, W; Jiang, W; Lu, Z; Li, B; López-Giráldez, F; Tikhonova, I; Gelb, BD; Seidman, CE; Brueckner, M; Lifton, RP. Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes. Proceedings of the National Academy of Sciences of USA. 2025; 122:e2420343122.

Solano, AF; Preusse, K; Cain, B; Hotz, R; Gavini, P; Yuan, Z; Bowen, B; Maco, G; Neal, H; Gagliani, EK; Southgate, L; Kovall, RA; Kopan, R; Gebelein, B. Defective Notch1 signaling in endothelial cells drives pathogenesis in a mouse model of Adams-Oliver Syndrome. The Journal of Clinical Investigation. 2025; 135:e187532.

Srivastava, AK; Juodakis, J; Sole-Navais, P; Chen, J; Bacelis, J; Teramo, K; Hallman, M; Njølstad, PR; Evans, DM; Jacobsson, B; Muglia, LJ; Zhang, G. Haplotype-based analysis distinguishes maternal-fetal genetic contribution to pregnancy-related outcomes. Editor, Cordell HJ. PLoS Genetics. 2025; 21:e1011575.

Tan, JM E; Cheng, L; Calhoun, RP; Weller, AH; Drareni, K; Fong, S; Barbara, E; Lim, HW; Xue, C; Winter, H; Reilly, MP; Maegdefessel, L; Lutgens, E; Seale, P. PRDM16 regulates smooth muscle cell identity and atherosclerotic plaque composition. Nature Cardiovascular Research. 2025; 4:1573-1588.

Tran, YH; Park, S; Coven, SL; Mendonca, EA. Area-Level Indices and Health Care Use in a Pediatric Brain and Central Nervous System Tumor Cohort: Observational Study. JMIR Public Health and Surveillance. 2025; 11:e66834.

Turner, L; Knopp, MI; Mendonca, EA; Desai, S. Bridging Artificial Intelligence and Medical Education: Navigating the Alignment Paradox. ATS Scholar. 2025; 6:135-148.

Tursi, AR; Lages, CS; Quayle, K; Koenig, ZT; Loni, R; Eswar, S; Cobeña-Reyes, J; Thornton, S; Tilburgs, T; Andorf, S. Automated descriptive cell type naming in flow and mass cytometry with CytoPheno. Scientific Reports. 2025; 15:26750.

Venkatasubramanian, M; Schwartz, L; Ramachandra, N; Bennett, J; Subramanian, KR; Chen, X; Gordon-Mitchell, S; Fromowitz, A; Pradhan, K; Shechter, D; Grimes, HL; Starczynowski, DT; Verma, A; Salomonis, N. Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias. Science Translational Medicine. 2025; 17:eadr1471.

Vest, JR; Mendonca, EA. Presence of Children in Household Is Associated With Increased Health-Related Social Need Burden. 2025; 1:1-8.

Vest, JR; Wu, W; Gregory, ME; Kasturi, SN; Mendonca, EA; Bian, J; Magoc, T; Grannis, S; McNamee, C; Harle, CA. Performance of 4 Methods to Assess Health-Related Social Needs. JAMA Network Open. 2025; 8:e2527426.

Vidović, D; Shamsaei, B; Schürer, SC; Kogan, P; Chojnacki, S; Kouril, M; Medvedovic, M; Niu, W; Azeloglu, EU; Birtwistle, MR; Sharma, V; Pillai, A; Meller, J; MacCoss, MJ. Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data. Molecular and Cellular Proteomics. 2025; 24:100947.

Wang, X; Zhang, Y; Li, Z; Liu, B; Sakabe, M; Yang, T; Pan, M; Chen, J; Huang, W; Xin, M; Fan, G. Abstract 4355964: Probiotic Extracellular Vesicles Stimulate Macrophage Efferocytosis to Limit Ischemia/Reperfusion-Induced Damage by Delivering 5s-rRNA-Derived Short RNA. Circulation. 2025; 152:a4355964.

Watkins, WS; Hernandez, EJ; Miller, TA; Blue, NR; Zimmerman, RM; Griffiths, ER; Frise, E; Bernstein, D; Boskovski, MT; Brueckner, M; Wagner, M; Yost, HJ; Yandell, M; Tristani-Firouzi, M. Genome sequencing is critical for forecasting outcomes following congenital cardiac surgery. Nature Communications. 2025; 16:6365.

Yacu, GS; Sayed, M; Zhou, Y; Ward, SE; Gomez, RA; Sequeira Lopez, ML S; Park, J; Lim, HW; Quaggin, SE; Winter, DR; Finer, G. Tcf21 Preserves Stromal Cell Identity and Restrains Profibrotic Fate Adoption During Kidney Development. Journal of the American Society of Nephrology : JASN. 2025; 36:10.1681/asn.2025mrv8hbra.

Yang, Z; Shikany, A; Husami, A; Wang, X; Mendonca, E; Nicole Weaver, K; Chen, J. Sequencing validates deep learning models for EHR-based detection of Noonan syndrome in pediatric patients. npj Genomic Medicine. 2025; 10:56.

Zackoff, M; Graciela, A; Collins, K; Loeb, D; Meisman, A; James, K; Generoso, J; Ortega, K; Butcher, B; Cifra, C; Badke, C; Dewan, M. Understanding Clinical Decision Support Failures in Pediatric Intensive Care Units via Applied Systems Safety Engineering and Human Factors Problem Analysis: Insights From the DISCOVER Learning Lab. Journal of Patient Safety. 2025; 21:S21-S28.

Zarate, YA; Abdelmoti, L; Oh, S; White, A; Starks, C; Au, MG; Chen, J; Weaver, NK; Korotkov, KV; Galperin, E. ACTC1 Variants Result in Isolated and Syndromic Cardiac Phenotypes. Clinical Genetics: an international journal of genetics and molecular medicine. 2025; 108:713-719.

Zaslavsky, ME; Craig, E; Michuda, JK; Sehgal, N; Ram-Mohan, N; Lee, JY; Nguyen, KD; Hoh, RA; Pham, TD; Röltgen, K; Yang, S; Tibshirani, R; Kundaje, A; Boyd, SD. Disease diagnostics using machine learning of B cell and T cell receptor sequences. Science. 2025; 387:eadp2407.