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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.