Jegga Lab

Publications

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; 23:5448.

Ghandikota, S; Sharma, M; Jegga, AG. Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. Patterns. 2021; 2:100247.

Kasam, RK; Ghandikota, S; Soundararajan, D; Reddy, GB; Huang, SK; Jegga, AG; Madala, SK. Inhibition of Aurora Kinase B attenuates fibroblast activation and pulmonary fibrosis. EMBO Molecular Medicine. 2020; 12:e12131.

Yella, JK; Yaddanapudi, S; Wang, Y; Jegga, AG. Changing Trends in Computational Drug Repositioning. Pharmaceuticals. 2018; 11:E57.

Wang, Y; Yella, J; Chen, J; McCormack, FX; Madala, SK; Jegga, AG. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulmonary Medicine. 2017; 17:133.

Sontake, V; Wang, Y; Kasam, RK; Sinner, D; Reddy, GB; Naren, AP; McCormack, FX; White, ES; Jegga, AG; Madala, SK. Hsp90 regulation of fibroblast activation in pulmonary fibrosis. JCI insight. 2017; 2:e91454.

Sarangdhar, M; Tabar, S; Schmidt, C; Kushwaha, A; Shah, K; Dahlquist, JE; Jegga, AG; Aronow, BJ. Data mining differential clinical outcomes associated with drug regimens using adverse event reporting data. Nature Biotechnology. 2016; 34:697-700.

Wu, C; Gudivada, RC; Aronow, BJ; Jegga, AG. Computational drug repositioning through heterogeneous network clustering. BMC Systems Biology. 2013; 7 Suppl 5:S6.

Sardana, D; Zhu, C; Zhang, M; Gudivada, RC; Yang, L; Jegga, AG. Drug repositioning for orphan diseases. Briefings in Bioinformatics. 2011; 12:346-356.

Zhang, M; Zhu, C; Jacomy, A; Lu, LJ; Jegga, AG. The orphan disease networks. The American Journal of Human Genetics. 2011; 88:755-766.

Chen, J; Bardes, EE; Aronow, BJ; Jegga, AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Research. 2009; 37:W305-W311.

Feng, Y; Cai, L; Pook, M; Liu, F; Chang, CH; Mouti, MA; Nibhani, R; Militi, S; Dunford, J; Philpott, M; et al. BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma. Gastroenterology. 2024; 166:139-154.

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

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.

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; 13:983.

Braun, T; Sosnovski, KE; Amir, A; BenShoshan, M; VanDussen, KL; Karns, R; Levhar, N; Abbas-Egbariya, H; Hadar, R; Efroni, G; et al. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease. JCI insight. 2023; 8:e170181.

Khandelwal, P; Lounder, DT; Bartlett, A; Haberman, Y; Jegga, AG; Ghandikota, S; Koo, J; Luebbering, N; Leino, D; Abdullah, S; et al. Transcriptome analysis in acute gastrointestinal graft-versus host disease reveals a unique signature in children and shared biology with pediatric inflammatory bowel disease. Haematologica: the hematology journal. 2023; 108:1803-1816.

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

Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, TD; Collins, MH; Hyams, JS; Siddiqui, I; Denson, LA; Jegga, A; et al. 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:s-170.

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. Editor, Soranzo N. PLoS biology. 2023; 21:e3002058.

Dhaliwal, J; Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, T; Collins, M; Hyams, J; Siddiqui, I; Denson, L; et al. 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:s72-s73.

Tsai, CY; Saito, T; Sarangdhar, M; Abu-El-Haija, M; Wen, L; Lee, B; Yu, M; Lipata, DA; Manohar, M; Barakat, MT; et al. A systems approach points to a therapeutic role for retinoids in asparaginase-associated pancreatitis. Science Translational Medicine. 2023; 15:eabn2110.

Dhaliwal, J; Liu, X; Reigle, J; Sharma, M; Lopez-Nunez, O; Walters, T; Collins, M; Hyams, J; Siddiqui, I; Denson, L; et al. 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:s56-s57.

Ghandikota, S; Yella, JK; Jegga, AG. (2022) Multimodal feature learning framework for disease biomarker discovery. Institute of Electrical and Electronics Engineers (IEEE). 00:3252-3259.

Yella, JK; Ghandikota, SK; Jegga, AG. (2022) GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. Institute of Electrical and Electronics Engineers (IEEE). 00:1957-1965.

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; 12:20668.

Kalim, KW; Yang, JQ; Wunderlich, M; Modur, V; Nguyen, P; Li, Y; Wen, T; Davis, AK; Verma, R; Lu, QR; et al. Targeting of Cdc42 GTPase in regulatory T cells unleashes antitumor T-cell immunity. Journal for ImmunoTherapy of Cancer. 2022; 10:e004806.

Clarkston, K; Karns, R; Jegga, AG; Sharma, M; Fox, S; Ojo, BA; Minar, P; Walters, TD; Griffiths, AM; Mack, DR; et al. Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis. Journal of Crohn's and Colitis. 2022; 16:1735-1750.

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; 14:7612-7620.

Yella, J; Ghandikota, S; Jegga, A. GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. 2022; 2022.08.30.505168.

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

Zhu, C; Wu, C; Jegga, AG; Sakharkar, KR; Sakharkar, MK; Chandra, R. Network Biology Methods for Drug Repositioning. Post-genomic Approaches in Drug and Vaccine Development. : Taylor & Francis; Taylor & Francis; 2022.

Kumar, A; Elko, E; Bruno, SR; Mark, ZF; Chamberlain, N; Mihavics, BK; Chandrasekaran, R; Walzer, J; Ruban, M; Gold, C; et al. Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis. Thorax. 2022; 77:669-678.

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

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.

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

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.

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; 23:5448.

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; 51:399-403.

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: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:s62-s63.

Bradford, L; Ross, MK; Minso, J; Cernelc-Kohan, M; Shayan, K; Wong, SS; Li, X; Rivier, L; Jegga, AG; Deutsch, GH; et al. Interstitial lung disease in children with Rubinstein-Taybi syndrome. Pediatric Pulmonology. 2022; 57:264-272.

Yella, JK; Jegga, AG. 2.32 Magic bullets: Drug repositioning and drug combinations. In: Mitchell R; Bradshaw R; McManus L, Ed. Comprehensive Pharmacology. New York: Elsevier; 2022.

Ghandikota, S; Sharma, M; Jegga, AG. Computational workflow for functional characterization of COVID-19 through secondary data analysis. STAR Protocols. 2021; 2:100873.

Ebrahimpour, A; Wang, M; Li, L; Jegga, AG; Bonnen, MD; Eissa, NT; Raghu, G; Jyothula, S; Kheradmand, F; Hanania, NA; et al. Esomeprazole attenuates inflammatory and fibrotic response in lung cells through the MAPK/Nrf2/HO1 pathway. Journal of Inflammation. 2021; 18:17.

Ta, AD; Ollberding, NJ; Karns, R; Haberman, Y; Alazraki, AL; Hercules, D; Baldassano, R; Markowitz, J; Heyman, MB; Kim, S; et al. Association of Baseline Luminal Narrowing With Ileal Microbial Shifts and Gene Expression Programs and Subsequent Transmural Healing in Pediatric Crohn Disease. Inflammatory Bowel Diseases. 2021; 27:1707-1718.

Gajjala, PR; Kasam, RK; Soundararajan, D; Sinner, D; Huang, SK; Jegga, AG; Madala, SK. Dysregulated overexpression of Sox9 induces fibroblast activation in pulmonary fibrosis. JCI insight. 2021; 6:e152503.

Huynh, VN; Wang, S; Ouyang, X; Wani, WY; Johnson, MS; Chacko, BK; Jegga, AG; Qian, WJ; Chatham, JC; Darley-Usmar, VM; et al. Defining the Dynamic Regulation of O-GlcNAc Proteome in the Mouse Cortex---the O-GlcNAcylation of Synaptic and Trafficking Proteins Related to Neurodegenerative Diseases. Frontiers in Aging. 2021; 2:757801.

Tsai, C; Saito, T; Sarangdhar, M; Abu-El-Haija, M; Quadro, L; Anthony, TG; Jegga, A; Husain, SZ. 713b A Multi-Systems Approach with Big Data from Adverse Event Reporting and Health Records, Clinical Biospecimens, and Experimental Animal Data Reveal That Retinoids Impact Asparaginase-Associated Pancreatitis Outcomes in Leukemic Patients. Gastroenterology. 2021; 161:e24-e25.

Ghandikota, S; Sharma, M; Jegga, AG. Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. Patterns. 2021; 2:100247.

Zeighami, Y; Bakken, T; Nickl-Jockschat, T; Peterson, Z; Jegga, A; Miller, J; Evans, A; Lein, E; Hawrylycz, M. Structural and cellular transcriptome foundations of human brain disease. 2021; 2021.05.12.443911.

Haberman, Y; Iqbal, NT; Ghandikota, S; Mallawaarachchi, I; Tzipi Braun, ; Dexheimer, PJ; Rahman, N; Hadar, R; Sadiq, K; Ahmad, Z; et al. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology. 2021; 160:2055-2071.e0.

Haberman, Y; Iqbal, NT; Ghandikota, S; Mallawaarachchi, I; Braun, T; Dexheimer, PJ; Rehman, NU; Hadar, R; Sadiq, K; Ahmad, Z; et al. Su094 IMMUNE AND METABOLIC PATHOGENESIS OF ENVIRONMENTAL ENTERIC DYSFUNCTION IN CHILDHOOD UNDERNUTRITION: A BIRTH INCEPTION COHORT. Gastroenterology. 2021; 160:s-615.

Minar, PP; Jegga, A; Ghandikota, S; Karns, R; Hyams, JS; Noe, JD; Boyle, BM; Rosen, MJ; Denson, LA. 728 PLASMA PROTEOMIC RESPONSE SIGNATURE FOR CHILDREN RECEIVING INFLIXIMAB FOR CROHN'S DISEASE. Gastroenterology. 2021; 160:s-145-s-146.

Chidambaran, V; Pilipenko, V; Jegga, AG; Geisler, K; Martin, LJ. Systems Biology Guided Gene Enrichment Approaches Improve Prediction of Chronic Post-surgical Pain After Spine Fusion. Frontiers in Genetics. 2021; 12:594250.

Yombo, DJ K; Odayar, V; Gupta, N; Jegga, AG; Madala, SK. The Protective Effects of IL-31RA Deficiency During Bleomycin-Induced Pulmonary Fibrosis. Frontiers in Immunology. 2021; 12:645717.

Li, Y; Deng, S; Wang, X; Huang, W; Chen, J; Robbins, N; Mu, X; Essandoh, K; Peng, T; Jegga, AG; et al. Sectm1a deficiency aggravates inflammation-triggered cardiac dysfunction through disruption of LXRα signalling in macrophages. Cardiovascular Research. 2021; 117:890-902.

Haberman, Y; Minar, P; Karns, R; Dexheimer, PJ; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; et al. Mucosal Inflammatory and Wound Healing Gene Programs Reveal Targets for Stricturing Behavior in Pediatric Crohn's Disease. Journal of Crohn's and Colitis. 2021; 15:273-286.

Niklinska-Schirtz, BJ; Venkateswaran, S; Anbazhagan, M; Kolachala, VL; Prince, J; Dodd, A; Chinnadurai, R; Gibson, G; Denson, LA; Cutler, DJ; et al. Ileal Derived Organoids From Crohn's Disease Patients Show Unique Transcriptomic and Secretomic Signatures. CMGH Cellular and Molecular Gastroenterology and Hepatology. 2021; 12:1267-1280.

Cheng, Y; Yella, JK; Jegga, AG. Triangle-Based Tripartite Graph Clustering. 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2020; 00:1769-1776.

Ghandikota, S; Jegga, AG. A multi-context feature learning approach to identify disease-specific gene neighborhoods. . : Association for Computing Machinery (ACM); Association for Computing Machinery (ACM); 2020.

Kasam, RK; Ghandikota, S; Soundararajan, D; Reddy, GB; Huang, SK; Jegga, AG; Madala, SK. Inhibition of Aurora Kinase B attenuates fibroblast activation and pulmonary fibrosis. EMBO Molecular Medicine. 2020; 12:e12131.

Ouyang, X; Ahmad, I; Johnson, MS; Redmann, M; Craver, J; Wani, WY; Benavides, GA; Chacko, B; Li, P; Young, M; et al. Nuclear receptor binding factor 2 (NRBF2) is required for learning and memory. Laboratory Investigation. 2020; 100:1238-1251.

Kasam, RK; Gajjala, PR; Jegga, AG; Courtney, JA; Randell, SH; Kramer, EL; Clancy, JP; Madala, SK. Fibrocyte accumulation in the lungs of cystic fibrosis patients. Journal of Cystic Fibrosis. 2020; 19:815-822.

Treble-Barna, A; Pilipenko, V; Wade, SL; Jegga, AG; Yeates, KO; Taylor, HG; Martin, LJ; Kurowski, BG. Cumulative Influence of Inflammatory Response Genetic Variation on Long-Term Neurobehavioral Outcomes after Pediatric Traumatic Brain Injury Relative to Orthopedic Injury: An Exploratory Polygenic Risk Score. Journal of Neurotrauma. 2020; 37:1491-1503.

Chidambaran, V; Ashton, M; Martin, LJ; Jegga, AG. Systems biology-based approaches to summarize and identify novel genes and pathways associated with acute and chronic postsurgical pain. Journal of Clinical Anesthesia. 2020; 62:109738.

Huang, Y; Arora, K; Mun, KS; Yang, F; Yarlagadda, S; Jegga, A; Weaver, TE; Naren, AP. 586 ER LUMINAL ERAD AS A NOVEL TARGET TO RESCUE MUTANT CFTR IN THE INTESTINE. Gastroenterology. 2020; 158:s-125.

Deng, S; Essandoh, K; Wang, X; Li, Y; Huang, W; Chen, J; Peng, J; Jiang, D; Mu, X; Wang, C; et al. Tsg101 positively regulates P62-Keap1-Nrf2 pathway to protect hearts against oxidative damage. Redox Biology. 2020; 32:101453.

Haberman, Y; Minar, PP; Karns, R; Dexheimer, PJ; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; et al. 935 PRE-TREATMENT MUCOSAL INFLAMMATORY AND WOUND HEALING GENE PROGRAMS REVEAL MECHANISMS ASSOCIATED WITH FUTURE STRICTURING BEHAVIOR DURING FIVE YEAR FOLLOW-UP IN PEDIATRIC CROHN'S DISEASE. Gastroenterology. 2020; 158:s-187-s-188.

Haberman Ziv, Y; Minar, P; Karns, R; Dexheimer, P; Ghandikota, S; Tegge, S; Shapiro, D; Shuler, B; Venkateswaran, S; Braun, T; et al. DOP89 Pre-treatment mucosal inflammatory and wound healing gene programmes reveal mechanisms associated with future stricturing behaviour during 5-year follow-up in paediatric Crohn’s disease. Journal of Crohn's and Colitis. 2020; 14:s127.

Wang, Y; Yella, JK; Ghandikota, S; Cherukuri, TC; Ediga, HH; Madala, SK; Jegga, AG. Pan-transcriptome-based candidate therapeutic discovery for idiopathic pulmonary fibrosis. Theraputic Advances in Respiratory Disease. 2020; 14:1753466620971143.