Biomedical Informatics

Publications

Bartram, J; Treichel, S; Song, BA; Xu, J; Sharma, D; Nasr, W; Frangiosa, M; Harley, A; Nemkov, T; D'alessandro, A; Salomonis, N; Grimes, HL; Filippi, M-D. Activation of a branched-chain amino acid rheostat restores replication-dependent hematopoietic stem cell fitness. Cell Stem Cell. 2026; 33(2):289-305.e6.

Bian, J; Peng, Y; Mendonca, E; Banerjee, I; Xu, H. Biomedical multimodal large language models: From model-centric development to clinically grounded evaluation and integration. Journal of Biomedical Informatics. 2026; 177:105023.

Boudissa, S; Kawanaka, H; Aronow, B; Prasath, VBS. Cross-Architecture Knowledge Distillation for Histopathological Image Analysis. IEEE Access. 2026; 14:58187-58209.

Brandão, CFS; Fernandes, GCVR; Neto, FC; Generoso Júnior, JR. Structured Clinical Reasoning Through a Formative Web-OSCE Model: A Scalable Innovation Within a Simulation-Based Undergraduate Curriculum. Journal of General Internal Medicine. 2026.

Chinnachinnanagari, AR; Debsarkar, SS; Prasath, VBS. Pathology Public Datasets for Artificial Intelligence: A Systematic Review. J Imaging Inform Med. 2026.

Cobeña-Reyes, J; Wanjalla, CN; Feria, MG; Simmons, J; Temu, T; Nochowicz, C; Arafat, SY; Kityo, C; Erem, G; Longenecker, CT; Andorf, S; Huaman, MA. Characterization of Distinct Monocyte Subtypes and Immune Features Associated with HIV, Tuberculosis, and Coronary Artery Disease in a Ugandan Cohort Using Mass Cytometry. Pathogens and Immunity. 2026; 11(1):14-38.

Colom Díaz, PA; Mistry, JJ; Young, KA; Chou, C-H; Boyer, N; Levine, RL; Salomonis, N; Grimes, HL; Trowbridge, JJ. Metallothionein 1 mediates growth and survival of Dnmt3a;Npm1-mutant acute myeloid leukemia. Haematologica. 2026; 111(1):373-378.

Conderino, S; Kirchner, HL; Thorpe, LE; Divers, J; Hirsch, AG; Nordberg, CM; Schwartz, BS; Zhang, L; Cai, B; Rudisill, C; Zaganjor, I; Pavkov, ME; Rosenman, M; Titus, AR. Multi-site analysis of COVID-19 and new-onset diabetes reveals need for improved sensitivity of EHR-based COVID-19 phenotypes-a DiCAYA Network analysis. Journal of the American Medical Informatics Association : JAMIA. 2026; 33(3):710-718.

Debsarkar, SS; Prasath, VBS. A multi-expert deep learning framework with LLM-guided arbitration for multimodal histopathology prediction. Computerized Medical Imaging and Graphics. 2026; 128:102704.

Debsarkar, SS; Aronow, B; Prasath, VBS. Unsupervised biomarker discovery leveraging foundation models: a multimodal approach to clinical data integration. Neural Computing and Applications. 2026; 38(5):93.

Deliberato, RO; Tachinardi, U; Mendonça, EA. Why do intensive care units in countries without board-certified clinical informatics specialists risk falling behind in the Artificial Intelligence era? Revista Brasileira de Terapia Intensiva. 2026; 38:e20260314.

Devonshire, AL; Magier, AZ; Wilson, BE; Rosenberg, C; Winslow, A; Risma, KA; Abonia, JP; Sherenian, MG; Assa'ad, AH; Andorf, S; Schwartz, JT. Peanut oral immunotherapy at a single academic medical center using a volume-based approach with store-purchased peanut products. Journal of Allergy and Clinical Immunology: Global. 2026; 5(3):100652.

Drucker, M; Lee, D; Bowman, M; Zhang, X; Kain, BN; Nicolet, D; Bandopadhyay, R; Singh, V; Wang, Z; Stone, RM; Grimes, HL; Eisfeld, A-K; Bowman, RL; Miles, LA. Genotype-immunophenotype relationships in NPM1-mutated AML clonal evolution uncovered by single-cell multiomic analysis. Blood. 2026; 147(26):3209-3216.

Eshleman, EM; Rice, T; Waddell, A; Kumar, S; Didriksen, BJ; Engleman, L; Vidyant, S; Sayed, M; Karns, R; Lim, H-W; Denson, LA; Alenghat, T. Tuft cells protect against intestinal inflammation through histone deacetylase 3. Mucosal Immunology. 2026; 100356.

Eswar, S; Koenig, ZT; Tursi, AR; Cobeña-Reyes, J; Tilburgs, T; Andorf, S. CytoBatchFlagR: A Comprehensive Framework to Objectively Assess High-Parameter Cytometry Data for Batch Effects. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2026; 109(4):241-256.

Farrow, E; Rao, S; Han, SJY; Chang, X; Huynh, C; Brugmann, SA; Lim, H-W; Tchieu, J; Campbell, K; Gebelein, B. An inducible system to study the regulatory functions of GSX2 in human lateral ganglionic eminence-like progenitors. Developmental Biology. 2026; 532:35-51.

Ferreira, JMG; Marra, VS; Generoso, JR; Tudino, CH; Hsieh, MK; Pardo, I; Campagnoli, PS; Ceccon, LE; Celeghini, PD; Zancopé, BB; Perencevich, EN; Goto, M; Edmond, MB; Marra, AR. Quality of hand hygiene performance: A systematic literature review. American Journal of Infection Control. 2026; 54(2):192-209.

Finer, G; Yacu, GS; Khan, MD; Zhou, Y; Gadhvi, G; Ward, SE; Sayed, M; Gomez, RA; Sequeira-Lopez, MLS; Park, J-S; Lim, H-W; Quaggin, SE; Winter, DR. The transcription factor Tcf21 is necessary for adoption of cell fates by Foxd1+ stromal progenitors during kidney development. American Journal of Physiology - Renal Physiology. 2026; 330(4):F347-F364.

Fisher, EG; Glass, SE; Sievers, CK; Cao, Z; Bechard, ME; Ellis, ST; Aramnadla, R; Zhao, P; Smith, RT; Wang, Y; Liu, Q; Lau, KS; Aronow, B; Coffey, RJ. Abstract 4760: Uncovering a highly transforming, Myc-stabilizing isoform of dipeptidase-1 in colorectal cancer. Cancer Research. 2026; 86(7_Supplement):4760-4760.

Gill, KK; Moore, C; Nwogu, O; Kroner, JW; Chang, W-C; Burkle, J; Virolainen, SJ; Stevens, ML; Baatyrbek, A; Miraldi, ER; Martin, LJ; Andorf, S; Khurana Hershey, GK; Roskin, KM. B-Cell Repertoire of Children With Atopic Dermatitis Exhibits Altered IgE Maturation Associated With Allergic Food Sensitization. Allergy. European Journal of Allergy and Clinical Immunology. 2026; 81(2):513-523.

Glaser, K; Depasquale, EAK; Berklite, L; Hickner, BT; Rao, P; Patel, RH; Badachhape, AA; Roy, S; Schepers, E; Timchenko, NA; Takebe, T; Woodfield, SE; Vasudevan, SA; Bondoc, AJ. Investigating the oncogenic role of aberrant EZH2 in hepatoblastoma. Scientific Reports. 2026; 16(1).

Groenendijk, A; Aronow, BJ; Cost, N; Cajaiba, M; Renfro, LA; Perlman, EJ; Dyer, L; Smolarek, TA; Mullen, EA; Pervaiz, S; Ehrlich, PF; Van Den Heuvel-Eibrink, MM; Dome, JS; Geller, JI. Integrated Molecular, Genomic, and Clinical Characterization of Pediatric and Adolescent Translocation Renal Cell Carcinoma: A Report from the Children's Oncology Group. Biomedicines. 2026; 14(5).

Gutfreund, MC; Callado, GY; Pardo, I; Hsieh, MK; Celeghini, PD; Lopes, GOV; Marra, PS; Cheng, YR; Kobayashi, T; Pinho, JRR; Amgarten, DE; Malta, FDM; Edmond, MB; Marra, AR. Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis. Diagnostic Microbiology and Infectious Disease. 2026; 114(4):117248.

Hartlage, CS; Duan, Q; Manning, ER; Dexheimer, JW; Beck, AF; Brokamp, C. Precision risk assessment for pediatric hospitalization using address-level data in Cincinnati, Ohio. Journal of Clinical and Translational Science. 2026; 10(1):e75.

Ive, J; Bondaronek, P; Yadav, V; Santel, D; Glauser, T; Strawn, JR; Agasthya, G; Tschida, J; Choo, S; Chandrashekar, M; Kapadia, AJ; Pestian, J. A data-centric approach to detecting and mitigating demographic bias in pediatric mental health text. Communications Medicine. 2026; 6(1).

Kahn, J; Luttmann-Gibson, H; Blossom, J; Ryan, PH; Coull, BA; Datta, S; Hartert, T; Zanobetti, A; Ramratnam, SK; Mendonça, EA; Shiroshita, A; Zoratti, EM; Gern, JE; Gold, DR. Redlining, Community Wealth, and Air Pollution: A Tale of Three Cities-Boston, Nashville, and Detroit. Journal of Urban Health. 2026; 103(1):120-134.

Kamsheh, AM; Ware, SM; Bhatnagar, S; Martin, LJ; Lee, TM; Towbin, JA; Kantor, PF; Lal, AK; Bansal, N; Ballweg, JA; Colan, SD; Aronow, BJ; Canter, CE; Lipshultz, SE. Cardiomyopathy-Associated Pathogenic Variants in Pediatric Myocarditis: A Study From the Pediatric Cardiomyopathy Registry. Circulation: Heart Failure. 2026; 19(1):e013104.

King, C; Jankowski, M; Coghill, R; Chidambaran, V; Brunner, H; Schulert, G; Ogbu, E; Zwolski, C; Wagner, M; Andorf, S; Huang, B; Kashikar-Zuck, S. 399 Biopsychosocial Risk Influences on Development and Generation of Early-onset Pain: The BRIDGE Pain Study Protocol. Journal of Pain. 2026; 41:106046.

Knopp, MI; Leonard, R; Geers, W; Tellez, S; Vidonish, B; Muthuvel, G; Magella, B; Yayah Jones, N-H; Espinoza, J; Corathers, SD. Multivendor Continuous Glucose Monitor Integration into the Electronic Health Record: Real-World Experience of an Academic Pediatric Endocrinology Clinic. Diabetes Technology and Therapeutics. 2026; 28(5):472-482.

Koenig, ZT; Eswar, S; Tsuda, S; Schuldt, N; Chougnet, CA; Forde, B; Andorf, S; Tilburgs, T. Decidual CD4 Effector Memory and Resident Memory T Cells Respond to Cord Blood Allo-Antigens. American Journal of Reproductive Immunology. 2026; 95(2):e70213.

Kottyan, LC; Richards, S; Tracy, ME; Lawson, LP; Kottyan, IC; Curwin, A; Cobb, B; Esslinger, S; Gerwe, M; Morgan, J; Muglia, L; Harley, JB; Chepelev, I; Kaufman, KM. Sequencing and health data resource of children of African ancestry. Genetics in Medicine. 2026; 28(3):101660.

Kumar, A; Ghandikota, S; Walzer, J; Ruban, M; Alcorn, JF; Anathy, V; Jegga, A. A74-08 Gene Expression Network Analysis Reveals PDIA3-linked UPR-fibrosis Crosstalk Driving Lung Pathophysiology in Influenza-infected Mice. American Journal of Respiratory and Critical Care Medicine. 2026; 212(Supplement_1):aamag162.4216.

Kumar, A; Ghandikota, S; Walzer, J; Ruban, M; Schwartz, DA; Evans, CM; Janssen-Heininger, YM; Jegga, A; Anathy, V. C71-05 Role of Protein Disulfide Isomerase A3 in Muc5b Production and Pathology of Pulmonary Fibrosis. American Journal of Respiratory and Critical Care Medicine. 2026; 212(Supplement_1):aamag162.2775.

Ladha, FA; Avillach, P; Opotowsky, AR; Nael, A; Brueckner, M; Chung, WK; Cnota, JF; Gelb, BD; Lewis, M; Liu, C; Wagner, M; Newburger, JW; Kim, Y; Morton, SU. Rare KDR Variants Define a Distinct Genetic Contribution to Congenital Heart Disease. Circulation. Genomic and precision medicine. 2026; e005659.

Ladha, FA; Vanderpluym, C; Mondragon-Estrada, E; Avillach, P; Brueckner, M; Chung, WK; Cnota, JF; Gelb, BD; Lewis, M; Liu, C; Tristani-Firouzi, M; Wagner, M; Morton, SU; Newburger, JW. Prothrombin G20210A and Factor V Leiden Variants Are Not Associated With Thrombotic Events in Congenital Heart Disease: An Observational Trial. Journal of the American Heart Association. 2026; 15(6):e046959.

Lee, EW; Choo, S; Maguire, D; Shivanna, A; Santel, D; Bhatnagar, S; Goethert, I; Patterson, K; Gholap, J; Hanson, HA; Brokamp, C; Strawn, JR; Kapadia, AJ; Agasthya, G. Comparing machine and deep learning models for pediatric anxiety classification using structured EHRs and area-based measures of health data. PLoS ONE. 2026; 21(5):e0324673.

Manakkat Vijay, GK; Ramaswami, B; Gierlack, S; Pease, NA; Gerges, P; Chen, D; Thakkar, K; Mena Hernandez, L; Keshari, S; Xu, H; Salomonis, N; Das, J; Rothstein, DM; Singh, H. BLIMP1 shapes germinal center B cell clonal diversity by gating chromatin accessibility during light-to-dark zone transition. Nature Immunology. 2026; 27(6):1294-1305.

Martin, KE; Fernandes, AT; Sayed, M; Hanlon, MA; Fallon, S; Lim, H-W; Waxman, JS. Nr2f1a and Isl1 repress acquisition of epicardial identity in venous atrial cardiomyocytes. Development. 2026; 153(11).

Mckinney, CM; Howard, W; Bijlani, K; Kinter, S; Crerand, C; Dang, R; Jackson, O; Discolo, C; Rosenman, M; Mendonca, E; Ormanidou, I; Dickinson, K; Heike, CL. Growth in Children with a Cleft Lip and/or Palate in 8 US Hospitals: A Retrospective Cohort Study. JDR Clinical and Translational Research. 2026; 23800844261423910.

Myers, KC; Skala, EJ; Ghandikota, S; Jegga, AG; Mousa, N; Siefert, ME; Lane, A; Reffatto, V; Towe, C; Luebbering, N; Bridgeland, A; Goldfarb, S; Davies, SM; Ziady, AG. Blood proteomics of paediatric bronchiolitis obliterans syndrome after haematopoietic cell transplant. ERJ Open Research. 2026; 12(3).

Nguyen, V; Harper, A; Azuero, M; Castellanos, I; He, S; Hochman, ML; Wenceslau, CF; Chen, D-B; Jegga, AG; Wang, Y; Fan, D; Nelson, JS; Tan, W. Vascular Organoids Derived from Capillary malformation-induced Pluripotent Stem Cells Exhibit Disease-Relevant Phenotypes. Stem Cell Reviews and Reports. 2026; 22(1):668-675.

Park, S; Coven, SL; Tran, YH; Mendonca, EA. Examining the Impact of Social Determinants of Health on Pediatric Central Nervous System Tumor Outcomes Through Medical Record Linkage. American Journal of Clinical Oncology: Cancer Clinical Trials. 2026; 49(2):82-88.

Reigle, J; Liu, X; Lopez-Nunez, O; Drysdale, E; Qtaish, D; Walters, TD; Mack, D; Boyle, BM; Kugathasan, S; Denson, N; Denson, LA; Griffiths, AM; Siddiqui, I; Dhaliwal, J. Automated Eosinophil Quantification Using Deep Learning to Predict Therapy Escalation in Pediatric Ulcerative Colitis. Clinical and Translational Gastroenterology. 2026.

Rogerson, C; Severns, D; Stemple, J; Monroig, V; Hanson, AE; Mendonca, E. A computational phenotype for pediatric asthma exacerbations requiring hospitalization using electronic health record data. JAMIA Open. 2026; 9(3):ooag113.

Rogerson, C; Riggins, D; Bulgarelli, L; Tachinardi, P; Tu, W; Mendonca, E. 1297: MATCHED ANALYSIS OF 10 MG/HR OF CONTINUOUS ALBUTEROL VS 15 MG/HR FOR PEDIATRIC CRITICAL ASTHMA. Critical Care Medicine. 2026; 54(3S).

Rogerson, CM; Bartlett, CW; Price, J; Li, L; Mendonca, EA; Grannis, S. Derivation and validation of an algorithm for maternal-child linkage in electronic health records. Journal of the American Medical Informatics Association : JAMIA. 2026; 33(2):451-456.

Roskin, KM; Meeds, HL; Krishnan, JM; 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 HIV infection. Scientific Reports. 2026; 16(1).

Santos, JO; Do Bú, E; Hara, T; Mendonça, C; Hagá, S; Pogacar, R; Kouril, M. Implicit association tests for all: Using iatgen for non-English and offline samples. PLoS ONE. 2026; 21(4):e0342742.

Sawada, K; Eom, J; Mahoney-Sutherland, BA; Stankiewicz, TE; Oates, JR; Giles, DA; Alarcon, PC; Damen, MSMA; Cannata, A; Hargis, J; Hogan, SP; Salomonis, N; Moreno-Fernandez, ME; Divanovic, S. Ambient temperature regulates CD4+ T cell tonic T cell receptor signaling and responsiveness. iScience. 2026; 29(5):115801.

Shirae, S; Debsarkar, SS; Kawanaka, H; Aronow, BJ; Prasath, VBS. End-to-End Multimodal Multiple Instance Learning for Cancer Histopathology Classification with Dual-Attention Fusion. Journal of Medical Systems. 2026; 50(1).

Shiroshita, A; Zanobetti, A; Coull, BA; Ryan, PH; Datta, S; Blossom, J; Oken, E; Gern, JE; Luttmann-Gibson, H; Mendonça, EA; Rivera-Spoljaric, K; Zoratti, EM; Hartert, TV; Gold, DR. Individual and combined effects of indoor home exposures and ambient PM2.5 during early life on childhood asthma in us birth cohort studies. Environmental Epidemiology. 2026; 10(1):e443.

Singh, P; Patel, PK; Kasam, RK; Lawson, R; Ediga, HH; Jegga, AG; Madala, SK. PLK1 inhibition by volasertib suppresses key transcriptional regulators underlying fibroblast activation and pulmonary fibrosis. American Journal of Physiology - Lung Cellular and Molecular Physiology. 2026; 330(2):L132-L144.

Tachinardi, P; Callado, GY; Ferreira, JMG; Gutfreund, MC; Pardo, I; Lopes, ECD; Bulgarelli, L; Rogerson, CM; Deliberato, RO; Marra, AR; Mendonça, EA. Association between nocturnal asthma, symptom severity, and clinical outcomes: a systematic review. Journal of Asthma. 2026; 1-8.

Thakkar, K; Yarlagadda, S; Alkhudairy, L; Potter, A; Thorner, K; Chaturvedi, P; Cebrian, C; Mccracken, KW; Salomonis, N; Kopan, R; Schuh, MP. Single cell RNA sequencing reveals transitional states and signaling shifts in nephron progenitor cells of the late-gestation rhesus macaque kidney. BMC Genomics. 2026; 27(1).

Tsai, C-Y; Bo, N; Tran, TH; Abu-El-Haija, M; Swaminathan, G; Lee, B; Ghandikota, S; Wen, L; Théorêt, Y; Mittelman, SD; Ladas, EJ; Jegga, AG; Silverman, LB; Ding, Y; Husain, SZ. A lipid-immune network signature defines susceptibility to asparaginase-associated pancreatitis. JCI Insight. 2026; 11(12).

Tschida, J; Chandrashekar, M; Hanson, HA; Goethert, I; Santel, D; Pestian, J; Strawn, JR; Glauser, T; Kapadia, AJ; Agasthya, GA. Evolving language of pediatric anxiety in electronic health records. JAMIA Open. 2026; 9(2):ooag041.

Ulanowicz, CJ; Alarcon, PC; Damen, MSMA; Wayland, JL; Sawada, K; Eom, J; Stankiewicz, TE; Chung, H; Lampe, K; Szabo, S; Moreno-Fernandez, ME; Salomonis, N; Divanovic, S. Distinct inflammatory programming of thoracic cavity white adipose immune cells regulates influenza pathogenesis. Journal of Infectious Diseases. 2026.

Walzer, J; Kumar, A; Ruban, M; Blasius, A; Song, X; Jegga, A; Alcorn, JF; Anathy, V. D18-07 IRE1 Signaling as a Regulator of Sialic Acid Production: Impacts on Influenza Infection in Asthma. American Journal of Respiratory and Critical Care Medicine. 2026; 212(Supplement_1):aamag162.4541.

Wang, G-Y; Xia, S; Sarangdhar, M; Noguchi, Y; Zhou, J-F. Prioritization of adverse events related to integrase inhibitors and NNRTIs: a disproportionality analysis using data from the FAERS database. Journal of Antimicrobial Chemotherapy. 2026; 81(4).

Ware, K; Peter, J; Yazell, J; Thapa, C; Taranov, A; Bedolla, A; Distel, C; Lammich, S; Feederle, R; Sülzen, A; Liddelow, S; Roskin, K; Luo, Y. Inhibition of TGF-β signaling in microglia stimulates hippocampal adult neurogenesis and reduces anxiety-like behavior in adult mice. Nature Communications. 2026; 17(1):1440.

Wissel, BD; Percy, Z; Zachem, TJ; Beaulieu-Jones, B; Kohane, IS; Goldstein, SL; Gecili, E; Dexheimer, JW. Heterogenous effect of automated alerts on mortality. Journal of the American Medical Informatics Association : JAMIA. 2026; 33(3):653-662.

Yu, X; Lu, P; Varney, A; Thiemann, C; Wu, G; Dawson, B; Mendonca, E; Weaver, KN; Chen, J. P521: A systematic evaluation of structured electric health record for rare genetic disease detection. Genetics in Medicine Open. 2026; 4:104013.

Yung, E; Liu, X; Aundhia, M; Chen, C; Wagner, M; Huang, B; Brunner, HI. Differences in time to drug initiation and inactive disease achievement by insurance type in patients with nonsystemic juvenile idiopathic arthritis. Drugs and Therapy Perspectives. 2026; 42(1):203-210.

Zhang, L; Hirsch, AG; Crume, T; Liese, AD; Anthopolos, R; Shao, H; Guo, Y; Dixon, BE; Dabelea, D; Conderino, S; Knight, L; Divers, J; Thorpe, L; Rosenman, M. 2344-P: Electronic Health Record (EHR)-Based Estimates of Diabetes Prevalence by Type in Children: The Diabetes in Children, Adolescents, and Young Adults Network (DICAYA), 2018 and 2022. Diabetes. 2026; 75(Supplement_1).