Biomedical Informatics

Publications

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 hematopoietic cell transplant. ERJ Open Research. 2025; 00745-02025.

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(1):8677.

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. 2025.

Ghandikota, S; Jegga, AG. From Gene Networks to Therapeutics: A Causal Inference and Deep Learning Approach for Drug Discovery. Pharmaceuticals. 2025; 18(9).

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. Journal of Clinical Investigation. 2025; 135(15).

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(Abstracts):a4977-a4977.

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(Abstracts):a4976-a4976.

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(1):e16302.

Kumar, A; Mark, ZF; Carbajal, MP; Delima, DS; Chamberlain, N; Walzer, J; Ruban, M; Chandrasekaran, R; Daphtary, N; Aliyeva, M; Britto, CJ; Dela Cruz, CS; Jegga, AG; Anathy, V. The protein disulfide isomerase A3 and osteopontin axis promotes influenza-induced lung remodelling. British Journal of Pharmacology. 2024; 181(22):4610-4627.

Temple, H; Donnelly, B; Mohanty, SK; Mowery, S; Poling, HM; Pasula, R; Hartman, S; Singh, A; Mourya, R; Bondoc, A; Oyama, K; Mcneal, M; Spearman, P; Tiao, G. Specific binding sites on Rhesus rotavirus capsid protein dictate the method of endocytosis inducing the murine model of biliary atresia. American Journal of Physiology - Gastrointestinal and Liver Physiology. 2024; 327(2):G267-G283.

Desai, DA; Baby, A; Ananthamohan, K; Green, LC; Arif, M; Duncan, BC; Kumar, M; Singh, RR; Koch, SE; Natesan, S; Rubinstein, J; Jegga, AG; Sadayappan, S. Roles of cMyBP-C phosphorylation on cardiac contractile dysfunction in db/db mice. Journal of Molecular and Cellular Cardiology Plus. 2024; 8.

Yombo, DJK; Ghandikota, S; Vemulapalli, CP; Singh, P; Jegga, AG; Hardie, WD; Madala, SK. SEMA3B inhibits TGFβ-induced extracellular matrix protein production and its reduced levels are associated with a decline in lung function in IPF. American Journal of Physiology - Cell Physiology. 2024; 326(6):C1659-C1668.

Feng, Y; Cai, L; Pook, M; Liu, F; Chang, C-H; Mouti, MA; Nibhani, R; Militi, S; Dunford, J; Philpott, M; Wang, Y; Huang, W; Jiang, L; Pauklin, S. BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma. Gastroenterology. 2024; 166(1):139-154.

Ghandikota, SK; Jegga, AG. Application of artificial intelligence and machine learning in drug repurposing. 2024:171-211.

Kurowski, BG; Treble-Barna, A; Pilipenko, V; Martin, LJ; Jegga, AG; Miley, AE; Zhang, N; Fabio, A; Chima, RS; Adlam, A-LR; Kaufman, K; Bell, MJ; Beers, SR; Wisniewski, SR; Wade, SL. Elucidating a genomic signature associated with behavioral and executive function after moderate to severe pediatric TBI: a systems biology informed approach. Frontiers in Systems Biology. 2024; 4:1293265.

Deveaux, SA; Vyshnya, S; Propsom, K; Gbotosho, OT; Singh, AS; Horning, RZ; Sharma, M; Jegga, AG; Niu, L; Botchwey, EA; Hyacinth, HI. Neuroinflammation underlies the development of social stress induced cognitive deficit in male sickle cell mice. Experimental Biology and Medicine. 2024; 249:10361.

Nguyen, V; Gao, C; Hochman, ML; Kravitz, J; Chen, EH; Friedman, HI; Wenceslau, CF; Chen, D; Wang, Y; Nelson, JS; Jegga, AG; Tan, W. Endothelial cells differentiated from patient dermal fibroblast-derived induced pluripotent stem cells resemble vascular malformations of port-wine birthmark. British Journal of Dermatology. 2023; 189(6):780-783.

Nguyen, V; Gao, C; Hochman, ML; Friedman, HI; Chen, EH; Wang, Y; Jegga, A; Nelson, JS; Tan, W. Abstract 14173: Generation and Characterization of Clinically Relevant Disease Models for Port Wine Birthmark Using Induced Pluripotent Stem Cells. Circulation. 2023; 148(Suppl_1):a14173-a14173.

Nguyen, V; Kravitz, J; Gao, C; Hochman, ML; Meng, D; Chen, D; Wang, Y; Jegga, AG; Nelson, JS; Tan, W. Perturbations of Glutathione and Sphingosine Metabolites in Port Wine Birthmark Patient-Derived Induced Pluripotent Stem Cells. Metabolites. 2023; 13(9).

Ananthamohan, K; Baby, A; Jegga, A; Sadayappan, S. Abstract P3038: Novel MicroRNAs Targeting Myosin Binding Protein-C3 Gene In Hypertrophic Cardiomyopathy. Circulation Research. 2023; 133(Suppl_1).

Braun, T; Sosnovski, KE; Amir, A; Benshoshan, M; Vandussen, KL; Karns, R; Levhar, N; Abbas-Egbariya, H; Hadar, R; Efroni, G; Ferrer, J; Hyams, JS; Denson, LA; Haberman, Y. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease. JCI Insight. 2023; 8(14).

Khandelwal, P; Lounder, DT; Bartlett, A; Haberman, Y; Jegga, AG; Ghandikota, S; Koo, J; Luebbering, N; Leino, D; Abdullah, S; Karns, R; Nelson, AS; Denson, LA; Davies, SM. Transcriptome analysis in acute gastrointestinal graft-versus host disease reveals a unique signature in children and shared biology with pediatric inflammatory bowel disease. Haematologica. 2023; 108(7):1803-1816.

Bell, MB; Ouyang, X; Shelton, AK; Huynh, NV; Mueller, T; Chacko, BK; Jegga, AG; Chatham, JC; Miller, CR; Darley-Usmar, V; Zhang, J. Relationships between gene expression and behavior in mice in response to systemic modulation of the O-GlcNAcylation pathway. Journal of Neurochemistry. 2023; 165(5):682-700.

Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, TD; Collins, MH; Hyams, JS; Siddiqui, I; Denson, LA; Jegga, A; Prasath, S; Dhaliwal, J. 783 DEVELOPMENT OF AN OPTIMAL MACHINE LEARNING MODEL USING TREATMENT NAÏVE DIAGNOSTIC PATHOLOGY IMAGES TO PREDICT STEROID-FREE CLINICAL REMISSION AT ONE YEAR IN PEDIATRIC ULCERATIVE COLITIS. Gastroenterology. 2023; 164(6):s-170.

Dhaliwal, J; Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, T; Collins, M; Hyams, J; Siddiqui, I; Denson, L; Jegga, A; Prasath, S. DEVELOPMENT OF AN OPTIMAL MACHINE LEARNING MODEL USING TREATMENT NAÏVE DIAGNOSTIC PATHOLOGY IMAGES TO PREDICT STEROID-FREE CLINICAL REMISSION AT ONE YEAR IN PEDIATRIC ULCERATIVE COLITIS. Gastroenterology. 2023; 164(4):s72-s73.

Zeighami, Y; Bakken, TE; Nickl-Jockschat, T; Peterson, Z; Jegga, AG; Miller, JA; Schulkin, J; Evans, AC; Lein, ES; Hawrylycz, M. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. PLoS Biology. 2023; 21(4):e3002058.

Tsai, C-Y; Saito, T; Sarangdhar, M; Abu-El-Haija, M; Wen, L; Lee, B; Yu, M; Lipata, DA; Manohar, M; Barakat, MT; Quadro, L; Anthony, TG; Jegga, AG; Husain, SZ. A systems approach points to a therapeutic role for retinoids in asparaginase-associated pancreatitis. Science Translational Medicine. 2023; 15(687):eabn2110.

Dhaliwal, J; Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, T; Collins, M; Hyams, J; Siddiqui, I; Denson, L; Jegga, A; Prasath, S. DEVELOPMENT OF AN OPTIMAL MACHINE LEARNING MODEL USING TREATMENT NAÏVE DIAGNOSTIC PATHOLOGY IMAGES TO PREDICT STEROID-FREE CLINICAL REMISSION AT ONE YEAR IN PEDIATRIC ULCERATIVE COLITIS. Inflammatory Bowel Diseases. 2023; 29(Supplement_1):s56-s57.

Ebrahimpour, A; Ahir, M; Wang, M; Jegga, AG; Bonnen, MD; Eissa, NT; Montesi, SB; Raghu, G; Ghebre, YT. Combination of esomeprazole and pirfenidone enhances antifibrotic efficacy in vitro and in a mouse model of TGFβ-induced lung fibrosis. Scientific Reports. 2022; 12(1):20668.

Clarkston, K; Karns, R; Jegga, AG; Sharma, M; Fox, S; Ojo, BA; Minar, P; Walters, TD; Griffiths, AM; Mack, DR; Haberman, Y; Hyams, JS; Denson, LA; Rosen, MJ. Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis. Journal of Crohn's and Colitis. 2022; 16(11):1735-1750.

Kalim, KW; Yang, J-Q; Wunderlich, M; Modur, V; Nguyen, P; Li, Y; Wen, T; Davis, AK; Verma, R; Lu, QR; Jegga, AG; Zheng, Y; Guo, F. Targeting of Cdc42 GTPase in regulatory T cells unleashes antitumor T-cell immunity. Journal for ImmunoTherapy of Cancer. 2022; 10(11).

Yella, JK; Ghandikota, SK; Jegga, AG. GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. bioRxiv. 2022; 2022.08.30.505168.

Zhu, C; Wu, C; Jegga, AG. Network Biology Methods for Drug Repositioning. In: Post-genomic Approaches in Drug and Vaccine Development. Taylor & Francis; 2022:115-131.

Kumar, A; Elko, E; Bruno, SR; Mark, ZF; Chamberlain, N; Mihavics, BK; Chandrasekaran, R; Walzer, J; Ruban, M; Gold, C; Jegga, AG; Gomez, JL; Janssen-Heininger, YM; Anathy, V. Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis. Thorax. 2022; 77(7):669-678.

Jurickova, I; Bonkowski, E; Angerman, E; Novak, E; Huron, A; Akers, G; Iwasawa, K; Braun, T; Hadar, R; Hooker, M; Takebe, T; Mollen, KP; Haberman, Y; Denson, LA. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflammatory Bowel Diseases. 2022; 28(7):988-1003.

Feng, Y; Cai, L; Hong, W; Zhang, C; Tan, N; Wang, M; Wang, C; Liu, F; Wang, X; Ma, J; Pauklin, S; Huang, F; Huang, W; Jiang, L. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation. 2022; 145(22):1663-1683.

Ghandikota, S; Sharma, M; Ediga, HH; Madala, SK; Jegga, AG. Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. International Journal of Molecular Sciences. 2022; 23(10).

Mun, KS; Nathan, JD; Lin, TK; Elder, DA; Jegga, AG; Naren, AP; Abu-El-Haija, M. Is There a Benefit From Islet Autotransplantation in Patients With Type 1 Diabetes Mellitus Undergoing Total Pancreatectomy? Pancreas. 2022; 51(4):399-403.

Jurickova, I; Huron, A; Angerman, E; Bonkowski, E; Jegga, A; Haberman, Y; Denson, L. EICOSATETRAYNOIC ACID REGULATES MITOCHONDRIAL AND EXTRA-CELLULAR MATRIX GENE EXPRESSION AND TISSUE STIFFNESS IN A HUMAN INTESTINAL ORGANOID MODEL OF ILEAL CROHN’S DISEASE. Gastroenterology. 2022; 162(3):s62-s63.

Jurickova, I; Huron, A; Angerman, E; Bonkowski, E; Jegga, A; Haberman, Y; Denson, L. EICOSATETRAYNOIC ACID REGULATES MITOCHONDRIAL AND EXTRA-CELLULAR MATRIX GENE EXPRESSION AND TISSUE STIFFNESS IN A HUMAN INTESTINAL ORGANOID MODEL OF ILEAL CROHN’S DISEASE. Inflammatory Bowel Diseases. 2022; 28(Supplement_1):s62-s63.

Yella, JK; Jegga, AG. MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2022; 19(5):2596-2604.

Bradford, L; Ross, MK; Minso, J; Cernelc-Kohan, M; Shayan, K; Wong, SS; Li, X; Rivier, L; Jegga, AG; Deutsch, GH; Hurley, C; Furman, W; Stokes, D; Hagood, JS. Interstitial lung disease in children with Rubinstein-Taybi syndrome. Pediatric Pulmonology. 2022; 57(1):264-272.

Yella, JK; Jegga, AG. 2.32 Magic bullets: Drug repositioning and drug combinations. In: Comprehensive Pharmacology. Elsevier; 2022:770-788.

Desai, DA; Rao, VJ; Jegga, AG; Dhandapany, PS; Sadayappan, S. Heterogeneous Distribution of Genetic Mutations in Myosin Binding Protein-C Paralogs. Frontiers in Genetics. 2022; 13:896117.

Ghandikota, S; Jegga, AG. gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks. AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science. 2022; 2022:206-215.

Mun, KS; Nathan, JD; Jegga, AG; Wikenheiser-Brokamp, KA; Abu-El-Haija, M; Naren, AP. Personalized medicine approaches in cystic fibrosis related pancreatitis. AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH. 2022; 14(10):7612-7620.

Yella, JK; Jegga, AG. Magic bullets: Drug repositioning and drug combinations. In: Comprehensive Pharmacology Seven Volume Set. 2022:V2-788.