Publications

Click here to see a list of my most recent publications

Previous Publications

2025

  1. Bell MB, Kane MS, Ouyang X, Young ME, Jegga AG, Chatham JC, Darley-Usmar V, Zhang J. 2025. Brain Transcriptome Changes Associated With an Acute Increase of Protein O-GlcNAcylation and Implications for Neurodegenerative Disease. J Neurochem. 169(1):e16302. doi: 10.1111/jnc.16302.

2024

  1. 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. 2024.  Roles of cMyBP-C phosphorylation on cardiac contractile dysfunction in Db/Db mice. Journal of Molecular and Cellular Cardiology Plus 100075, https://doi.org/10.1016/j.jmccpl.2024.100075.

  2. Ghandikota SK, Jegga AG. 2024. Application of artificial intelligence and machine learning in drug repurposing, Progress in Molecular Biology and Translational Science, Academic Press, https://doi.org/10.1016/bs.pmbts.2024.03.030.

  3. Feng Y, Cai L, Pook M, Liu F, Chang CH, Mouti MA, Nibhani R, Wu S, Deng S, Militi S, Dunford J, Philpott M, Fan Y, Fan GC, Liu Q, Qi J, Sadayappan S, Jegga AG, Oppermann U, Wang Y, Huang W, Jiang L, Pauklin S. 2024. BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma. Gastroenterology 166(1):139-154. https://doi.org/10.1053/j.gastro.2023.09.021

2023

  1. Nguyen V, Gao C, Hochman ML, Kravitz J, Chen EH, Friedman HI, Wenceslau CF, Chen D, Wang Y, Nelson JS, Jegga AG*, Tan W.* 2023. Endothelial cells differentiated from patient dermal fibroblast-derived induced pluripotent stem cells resemble vascular malformations of Port Wine Birthmark. Br J Dermatol. doi: 10.1093/bjd/ljad330. *Co-senior author.

  2. Nguyen V, Kravitz J, Gao C, Hochman ML, Meng D, Chen D, Wang Y, Jegga AG, Nelson JS, Tan W. 2023. Perturbations of Glutathione and Sphingosine Metabolites in Port Wine Birthmark Patient-Derived Induced Pluripotent Stem Cells. Metabolites. 13(9):983. https://doi.org/10.3390/metabo130909.

  3. Braun T, Sosnovski KE, Amir A, BenShoshan M, VanDussen KL, Karns R, Levhar N, Abbas-Egbariya H, Hadar R, Efroni G, Castel D, Avivi C, Rosen MJ, Grifiths AM, Walters TD, Mack DR, Boyle BM, Ali SA, Moore SR, Schirmer M, Xavier RJ, Kugathasan S, Jegga AG, Weiss B, Mayer C, Barshack I, Ben-Horin S, Ulitsky I, Beucher A, Ferrer J, Hyams JS, Denson LA, Haberman Y. 2023. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn disease, and celiac disease. JCI Insight. Jun 1:e170181. doi: 10.1172/jci.insight.170181.

  4. Bell M, Ouyang X, Shelton AK, Huynh NV, Mueller T, Chacko BK, Jegga AG, Chatham JC, Miller CR, Darley-Usmar V, Zhang J. 2023. Relationships between gene expression and behavior in mice in response to systemic modulation of the O-GlcNAcylation pathway. J Neurochem. doi: 10.1111/jnc.15835.

  5. Zeighami Y, Bakken TE, Nickl-Jockschat T, Peterson Z, Jegga AG, Miller JA, Schulkin J, Evans AC, Lein ES, Hawrylycz M. 2023. A comparison of anatomic and cellular transcriptome structures across 40 human brain diseases. PLoS Biol. 21(4):e3002058. doi: 10.1371/journal.pbio.3002058.

  6. Tsai C, Saito T, Sarangdhar M, Abu-El-Haija M, Wen L, Lee B, Yu M, Lipata DA, Manohar M, Barakat1 MT, Contrepois K, Tran TH, Theoret Y, Bo N, Ding Y, Stevenson K, Ladas EJ, Silverman LB, Quadro L, Anthony TG, Jegga AG*, Husain SZ*. 2023. A systems approach points to a therapeutic role for retinoids in asparaginase-associated pancreatitis. Science Translational Medicine. *Co-corresponding author. doi:10.1126/scitranslmed.abn2110.

  7. Khandelwal P, Lounder DT, Bartlett A, Haberman Y, Jegga AG, Ghandikota S, Koo J, Luebbering N, Leino D, Abdullah S, Loveless M, Minar P, Lake K, Litts B, Karns R, Nelson AS, Denson LA, Davies SM. 2023. Transcriptome analysis in acute gastrointestinal graft-versus host disease reveals a unique signature in children and shared biology with pediatric inflammatory bowel disease. Haematologica. doi: 10.3324/haematol.2022.282035.

2022

  1. Ghandikota S, Yella JK and Jegga AG. 2022. Multimodal feature learning framework for disease biomarker discovery. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, pp. 3252-3259, doi: 10.1109/BIBM55620.2022.9995233.

  2. Yella JK, Ghandikota S and Jegga AG. 2022. GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022, pp. 1957-1965, doi: 10.1109/BIBM55620.2022.9995245.

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

  4. Kalim KW, Yang JQ, Wunderlich M, Modur V, Nguyen P, Li Y, Wen T, Davis AK, Verma R, Lu QR, Jegga AG, Zheng Y, Guo F. 2022. Targeting of Cdc42 GTPase in regulatory T cells unleashes antitumor T-cell immunity. J Immunother Cancer 10(11):e004806.

  5. Mun KS, Nathan JD, Jegga AG, Wikenheiser-Brokamp KA, Abu-El-Haija M, Naren AP 2022. Personalized medicine approaches in cystic fibrosis related pancreatitis. Am J Transl Res. 14(10):7612-7620.

  6. Ghandikota S, Jegga AG. 2022. gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks. AMIA Annu Symp Proc. 2022:206-215.

  7. Desai DA, Rao VJ, Jegga AG, Dhandapany PS, Sadayappan S. 2022. Heterogeneous Distribution of Genetic Mutations in Myosin Binding Protein-C Paralogs. Front Genet. 13:896117. doi: 10.3389/fgene.2022.896117.

  8. Mun KS, Nathan JD, Lin TK, Elder DA, Jegga AG, Naren AP, Abu-El-Haija M. 2022. Is There a Benefit From Islet Autotransplantation in Patients With Type 1 Diabetes Mellitus Undergoing Total Pancreatectomy? Pancreas 51(4):399-403. doi: 10.1097/MPA.0000000000002017.

  9. Clarkston K, Karns R, Jegga AG, Sharma M, Fox S, Ojo BA, Minar P, Walters TD, Griffiths AM, Mack DR, Boyle B, LeLeiko NS, Markowitz J, Rosh JR, Patel AS, Shah S, Baldassano RN, Pfefferkorn M, Sauer C, Kugathasan S, Haberman Y, Hyams JS, Denson LA, Rosen MJ. 2022. Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis. J Crohns Colitis. doi: 10.1093/ecco-jcc/jjac075.

  10. Ghandikota S, Sharma M, Ediga HH, Madala SK, Jegga AG. 2022. Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. International Journal of Molecular Sciences 23(10): 5447. https://doi.org/10.3390/ijms23105447

  11. Zeighami Y, Bakken TE, Nickl-Jockschat T, Peterson Z, Jegga AG, Miller JA, Evans AC, Lein ES, Hawrylycz M. 2022. Structural and cellular transcriptome foundations of human brain disease. bioRxiv 2021.05.12.443911; doi: https://doi.org/10.1101/2021.05.12.443911

  12. Feng Y, Cai L, Hong W, Zhang C, Tan N, Wang M, Wang C, Liu F, Wang X, Ma J, Gao C, Kumar M, Mo Y, Geng Q, Luo C, Lin Y, Chen H, Wang SY, Watson MJ, Jegga AG, Pedersen RA, Fu JD, Wang ZV, Fan GC, Sadayappan S, Wang Y, Pauklin S, Huang F, Huang W, Jiang L. 2022. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation. 2022 Apr 11. doi: 10.1161/CIRCULATIONAHA.121.055781.

  13. Jurickova I, Bonkowski E, Angerman E, Novak E, Huron A, Akers G, Iwasawa K, Braun T, Hadar R, Hooker M, Han S, Cutler DJ, Okou DT, Kugathasan S, Jegga A, Wells J, Takebe T, Mollen KP, Haberman Y, Denson LA. 2022. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflamm Bowel Dis. doi: 10.1093/ibd/izac037

2021

  1. Yella JK and Jegga AG. 2021. Magic bullets: Drug repositioning and drug combinations. In Reference Module in Biomedical Sciences, Elsevier, doi: 10.1016/B978-0-12-820472-6.00116-X

  2. Ghandikota S, Sharma M, Jegga AG. 2021. Computational workflow for functional characterization of COVID-19 through secondary data analysis. STAR Protocols. doi: 10.1016/j.xpro.2021.100873.

  3. Bradford L, Ross MK, Minso J, Cernelc-Kohan M, Shayan K, Wong SS, Li X, Rivier L, Jegga AG, Deutsch GH, Vece TJ, Loughlin CE, Gower WA, Hurley C, Furman W, Stokes D, Hagood JS. 2021. Interstitial Lung Disease in Children with Rubinstein- Taybi Syndrome. Pediatr Pulmonol. doi: 10.1002/ppul.25709.

  4. Huynh VN, Wang S, Ouyang X, Wani WY, Johnson MS, Chacko BK, Jegga AG, Qian W-J, Chatham JC, Darley-Usmar VM and Zhang J 2021. Defining the Dynamic Regulation of OGlcNAc Proteome in the Mouse Cortex---the O-GlcNAcylation of Synaptic and Trafficking Proteins Related to Neurodegenerative Diseases. Front. Aging 2:757801. doi: 10.3389/fragi.2021.757801

  5. Gajjala PR, Kasam RK, Soundararajan D, Sinner D, Huang SK, Jegga AG, Madala SK. 2021. Dysregulated overexpression of Sox9 induces fibroblast activation in pulmonary fibrosis. JCI Insight. doi:10.1172/jci.insight.152503.

  6. Kumar A, Elko E, Bruno SR, Mark ZF, Chamberlain N, Mihavics BK, Chandrasekaran R, Walzer J, Ruban M, Gold C, Lam YW, Ghandikota S, Jegga AG, Villalobos JG, Janssen-Heininger YMW, Anathy V. 2021. Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis. Thorax doi:10.1136/thoraxjnl-2021-216882.

  7. Niklinska-Schirtz BJ, Venkateswaran S, Anbazhagan M, Kolachala VL, Prince J, Dodd A, Chinnadurai R, Gibson G, Denson LA, Cutler DJ, Jegga AG, Matthews JD, Kugathasan S. 2021. Ileal derived organoids from Crohn’s disease patients show unique transcriptomic and secretomic signatures. Cellular and Molecular Gastroenterology and Hepatology. doi.org/10.1016/j.jcmgh.2021.06.018

  8. Yella JK, Jegga A. 2021. MGATRx: Discovering Drug Repositioning Candidates Using Multi-view Graph Attention. IEEE/ACM Trans Comput Biol Bioinform. doi: 10.1109/TCBB.2021.3082466.

  9. Ebrahimpour A, Wang M, Li L, Jegga AG, Bonnen MD, Eissa NT, Raghu G, Jyothula S, Kheradmand F, Hanania NA, Rosas IO, Ghebre YT. 2021. Esomeprazole attenuates inflammatory and fibrotic response in lung cells through the MAPK/Nrf2/HO1 pathway. J Inflamm (Lond). 18(1):17. doi:10.1186/s12950-021-00284-6.

  10. Ghandikota S, Sharma M, Jegga AG. 2021. Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. Patterns doi.org/10.1016/j.patter.2021.100247.

  11. Chidambaran V, Pilipenko V, Jegga AG, Geisler K and Martin LJ 2021. Systems Biology Guided Gene Enrichment Approaches Improve Prediction of Chronic Post-surgical Pain After Spine Fusion. Front. Genet. 12:594250. doi: 10.3389/fgene.2021.594250.

  12. Yombo DJK, Odayar V, Gupta N, Jegga AG and Madala SK 2021. The Protective Effects of IL-31RA Deficiency During Bleomycin-Induced Pulmonary Fibrosis. Front. Immunol. 12:645717. doi: 10.3389/fimmu.2021.645717

  13. Haberman Y, Iqbal NT, Ghandikota S, Mallawaarachchi I, Braun T, Dexheimer PJ, Rahman N, Hadar R, Sadiq K, Ahmad Z, Idress R, Iqbal J, Ahmed S, Hotwani A, Umrani F, Ehsan L, Medlock G, Syed S, Moskaluk C, Ma JZ, Jegga AG, Moore SR, Ali SA, Denson LA. 2021. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology doi.org/10.1053/j.gastro.2021.01.221.

  14. Ta AD, Ollberding NJ, Karns R, Haberman Y, Alazraki AL, Hercules D, Baldassano R, Markowitz J, Heyman MB, Kim S, Kirschner B, Shapiro JM, Noe J, Oliva-Hemker M, Otley A, Pfefferkorn M, Kellermayer R, Snapper S, Rabizadeh S, Xavier R, Dubinsky M, Hyams J, Kugathasan S, Jegga AG, Dillman JR, Denson LA. 2021. Association of Baseline Luminal Narrowing With Ileal Microbial Shifts and Gene Expression Programs and Subsequent Transmural Healing in Pediatric Crohn Disease. Inflamm Bowel Dis. doi: 10.1093/ibd/izaa339.

2020

  1. Ghandikota S, Jegga AG. 2020. A multi-context feature learning approach to identify disease-specific gene neighborhoods. BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. doi:10.1145/3388440.3412419.

  2. Wang Y, Yella JK, Ghandikota S, Cherukuri TC, Ediga HH, Madala SK, Jegga AG. 2020. Pan-transcriptome-based candidate therapeutic discovery for idiopathic pulmonary fibrosis. Ther Adv Respir Dis. doi:10.1177/1753466620971143.

  3. Kasam RK, Ghandikota S, Soundararajan D, Reddy GB, Huang SK, Jegga AG*, Madala SK*. 2020. Inhibition of Aurora Kinase B attenuates fibroblast activation and pulmonary fibrosis. EMBO Molecular Medicine doi/10.15252/emmm.202012131. *Co-corresponding author.

  4. Haberman Y, Minar P, Karns R, Dexheimer PJ, Ghandikota S, Tegge S, Shapiro D, Shuler B, Venkateswaran S, Braun T, Ta A, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Dotson JL, Mack DR, Kellermayer R, Griffiths AM, Heyman MB, Baker SS, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva- Hemker M, Ziring D, Gokhale R, Kim S, Guthery SL, Cohen SA, Snapper S, Aronow BJ, Stephens M, Gibson G, Dillman JR, Dubinsky M, Hyams JS, Kugathasan S, Jegga AG, Denson LA. 2020. Mucosal Inflammatory and Wound Healing Gene Programs Reveal Targets for Stricturing Behavior in Pediatric Crohn's Disease. J Crohns Colitis. doi: 10.1093/ecco-jcc/jjaa166.

  5. Yella JK, Jegga AG 2020. MGATRx: Discovering drug repositioning candidates using multi-view graph. In Proceedings of BIOKDD’20: International Workshop on Data Mining for Bioinformatics. San Diego, CA, USA. doi.org/10.1101/2020.06.29.171876

  6. Kasam RK, Gajjala PR, Jegga AG, Courtney JA, Randell SH, Kramer EL, Clancy JP, Madala SK. 2020. Fibrocyte accumulation in the lungs of cystic fibrosis patients. Journal of Cystic Fibrosis. doi: 10.1016/j.jcf.2020.06.011

  7. Ouyang X, Ahmad I, Johnson M, Redmann M, Craver J, Wani WY, Benavides GA, Chacko B, Li P, Young M, Jegga AG, Darley-Usmar V, and Zhang J. 2020. Nuclear receptor binding factor 2 (NRBF2) is required for learning and memory. Laboratory Investigation doi: 10.1038/s41374-020-0433-4

  8. Li Y, Deng S, Wang X, Huang W, Chen J, Robbins N, Mu X, Essandoh K, Peng T, Jegga AG, Rubinstein J, Adams DE, Wang Y, Peng J, Fan GC. 2020. Sectm1a Deficiency Aggravates Inflammation-Triggered Cardiac Dysfunction through Disruption of LXRa  Signaling in Macrophages. Cardiovasc Res. doi: 10.1093/cvr/cvaa067.

  9. Chidambaran V, Ashton M, Martin LJ, Jegga AG. 2020. Systems biology-based approaches to summarize and identify novel genes and pathways associated with acute and chronic postsurgical pain. J Clin Anesth. 62:109738. doi:10.1016/j.jclinane.2020.109738.

  10. Deng S, Essandoh K, Wang X, Li Y, Huang W, Chen J, Peng J, Jiang DS, Mu X, Wang C, Peng T, Guan JL, Wang Y, Jegga A, Huang K, Fan GC. 2020. Tsg101 positively regulates P62-Keap1-Nrf2 pathway to protect hearts against oxidative damage. Redox Biol. doi:10.1016/j.redox.2020.101453.

  11. Treble-Barna A, Pilipenko V, Wade SL, Jegga A, Yeates KO, Taylor HG, Martin LJ, Kurowski BG. 2020. The Cumulative Influence of Inflammatory Response Genetic Variation on Long-Term Neurobehavioral Outcomes following Pediatric Traumatic Brain Injury Relative to Orthopedic Injury: An Exploratory Polygenic Risk Score. J Neurotrauma. doi:10.1089/neu.2019.6866.

2019

  1. Pan H, Deutsch GH, Wert SE; Ontology Subcommittee; NHLBI Molecular Atlas of Lung Development Program Consortium. 2019. Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung. J Biomed Semantics 10(1):18. doi:10.1186/s13326-019-0209-1.

  2. Wang Y, Yella JK, Ghandikota S, Cherukuri TC, Madala SK, Jegga AG. 2019. Pan-transcriptome-based Candidate Therapeutic Discovery for Idiopathic Pulmonary Fibrosis. bioRxiv doi: https://doi.org/10.1101/824367

  3. Huang Y, Arora K, Mun KS, Yang F, Moon C, Yarlagadda S, Jegga A, Weaver T, Naren AP. 2019. Targeting DNAJB9, a novel ER luminal co-chaperone, to rescue ΔF508-CFTR. Sci Rep. 9(1): 9808. doi: 10.1038/s41598-019-46161-4.

  4. Kasam RK, Reddy GB, Jegga AG, Madala SK. 2019. Dysregulation of mesenchymal cell survival pathways in severe fibrotic lung disease: The effect of nintedanib therapy. Frontiers in Pharmacology doi: 10.3389/fphar.2019.00532.

  5. Kurowski BG, Treble-Barna A, Pilipenko V, Wade SL, Yeates KO, Taylor HG, Martin LJ, Jegga AG. 2019. Genetic influences on behavioral outcomes after childhood TBI: A novel systems biology-informed approach. Frontiers in Genetics doi: 10.3389/fgene.2019.00481.

  6. Wang Y, Yella J, Jegga AG. 2019. Transcriptomic data mining and repurposing for computational drug discovery. Methods Mol Biol. 1903:73-95.

2018

  1. Sontake V, Kasam RK, Sinner D, Korfhagen TR, Reddy GB, White ES, Jegga AG, Madala SK. 2018. Wilms’ tumor 1 drives fibroproliferation and myofibroblast transformation in severe fibrotic lung disease. JCI Insight 3(16): e121252.

  2. Hankey W, Chen, Bergman MJ, Fernandez MO, Hancioglu B, Lan X, Jegga AG, Jie Zhang J, Jin VX, Aronow BJ, Wang Q, Groden J. 2018. Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. Oncotarget 9:31214-31230.

  3. Peng J, Li Y, Wang X, Deng S, Holland J, Yates E, Chen J, Gu H, Essandoh K, Mu X, Wang B, McNamara RK, Peng T, Jegga AG, Liu T, Nakamura, Huang K, Perez-Tilve D, Fan GC. 2018. An Hsp20-FBXO4 Axis Regulates Adipocyte Function through Modulating PPARγ Ubiquitination. Cell Reports 23 (12): 3607-3620.

  4. Chen J, Xu H, Jegga AG, Kejian Z, White PS, Ge Z. 2018.  Novel phenotype-disease matching tool for rare genetic diseases. Genetics in Medicine. doi: https://doi.org/10.1038/s41436-018-0050-4

  5. Yella JK, Yaddanapudi S, Wang Y, Jegga AG 2018. Changing Trends in Computational Drug Repositioning. Pharmaceuticals 11, 57.

  6. Wang Y, Arora K, Yang F, Shin W, Chen J, Kihara D, Naren AP, Jegga AG 2018. PP-2, a src-kinase inhibitor, is a potential corrector for F508del-CFTR in cystic fibrosis. BioRxiv doi: https://doi.org/10.1101/288324

  7. Kronk CJ, Jegga AG. 2018. GNOMICS: A one-stop shop for biomedical and genomic data. AMIA Summits on Translational Science Proceedings. 2017:118-123.

  8. Jiang A, Jegga AG. 2018. Characterizing drug-related adverse events by joint analysis of biomedical and genomic data: A case study of drug-induced pulmonary fibrosis. AMIA Summits on Translational Science Proceedings. 2017:91-97.

2017

  1. Smith, E. A., Krumpelbeck, E. F., Jegga, A. G., Prell, M., Matrka, M. M., Kappes, F., Greis, K. D., Ali, A. M., Meetei, A. R. and Wells, S. I. 2017. The nuclear DEK interactome supports multi-functionality: “The DEK Interactome”. Proteins. doi:10.1002/prot.25411

  2. Wang Y, Yella J, Chen J, McCormack F, Madala S, Jegga AG. 2017. Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers. BMC Pulmonary Medicine 17: 133. doi: 10.1186/s12890-017-0472-9.

  3. Luo Z, Jegga AG, Bezerra JA. 2017. Gene-disease associations identify a connectome with shared molecular pathways in human cholangiopathies. Hepatology doi: 10.1002/hep.29504.

  4. Angel PM, Narmoneva DA, Sewell-Loftin MK, Munjal C, Dupuis L, Landis BJ, Jegga A, Kern CB, Merryman WD, Baldwin HS, Bressan GM, Hinton RB. 2017. Proteomic Alterations Associated with Biomechanical Dysfunction are Early Processes in the Emilin1 Deficient Mouse Model of Aortic Valve Disease. Ann Biomed Eng. doi: 10.1007/s10439-017-1899-0.

  5. Landis BJ, Schubert JA, Lai D, Jegga AG, Shikany AR, Foroud T, Ware SM, Hinton RB. 2017. Exome sequencing identifies candidate genetic modifiers of syndromic and familial thoracic aortic aneurysm severity. J Cardiovasc Transl Res. doi:10.1007/s12265-017-9753-1.

  6. Kurowski BG, Treble-Barna A, Pitzer AJ, Wade SL, Martin LJ, Jegga AG. 2017. Applying systems biology methodology to identify genetic factors possibly associated with recovery after traumatic brain injury. Journal of Neurotrauma doi:10.1089/neu.2016.4856.

  7. Smith E, Gole B, Willis N, Soria R, Starnes L, Krumpelbeck E, Jegga AG, Ali A, Guo H, Meetei R, Andreassen P, Kappes F, Vinnedge LP, Daniel J, Scully R, Wiesmüller L, and Wells S. 2017. DEK is required for homologous recombination repair of DNA breaks. Scientific Reports doi: 10.1038/srep44662.

  8. Sontake V, Wang Y, Kasam RK, Sinner D, Reddy GB, Naren AP, McCormack FX, White ES, Jegga AG* and Madala S* 2017. Hsp90 regulation of fibroblast activation in pulmonary fibrosis. JCI Insight 2017;2(4):e91454. doi:10.1172/jci.insight.91454. *Co-corresponding author.

  9. Munjal C, Jegga AG, Opoka AM, Stoilov I, Norris RA, Thomas CJ, Smith JM, Mecham RP, Bressan GM, Hinton RB. 2017. Inhibition of MAPK-Erk pathway in vivo attenuates aortic valve disease processes in Emilin1 deficient mouse model. Physiological Reports doi: 10.14814/phy2.13152.

  10. Malavia T, Chaparala S, Wood J, Chowdari K, Prasad K, McClain L, Jegga AG, Ganapathiraju MK, and Nimgaonkar VL. 2017. Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic and protein interaction data. NPJ Schizophrenia 3, Article number: 11; doi:10.1038/s41537-017-0010-z

2016

  1. Lynch TL 4th, Ismahil MA, Jegga AG, Zilliox MJ, Troidl C, Prabhu SD, Sadayappan S. Cardiac inflammation in genetic dilated cardiomyopathy caused by MYBPC3 mutation. J Mol Cell Cardiol. 2016 Dec 9. pii: S0022-2828(16)30444-8. doi:10.1016/j.yjmcc.2016.12.002.

  2. Jegga AG. 2016. Bioinformatics and orphan diseases. In Pediatric Biomedical Informatics, Translational Bioinformatics 10: 313-338, J.J. Hutton (ed.), Springer Publishers. DOI 10.1007/978-981-10-1104-7_16

  3. Sarangdhar M, Gudivada RC, Shrestha RB, Wang Y, and Jegga AG. 2016. Network Analyses of Biomedical and Genomic Big Data. In Big Data of Complex Networks. Dehmer M, Emmert-Streib F, Pickl S, Holzinger A (Eds). Chapman & Hall/CRC Big Data Series, CRC Press, Taylor and Francis Group.Print ISBN: 978-1-4987-2361-9; eBook ISBN: 978-1-4987-2362-6.

  4. Malek E, Abdel-Malek M, Jagannathan S, Vad N, Karns R, Jegga AG, Broyl A, van Duin M, Sonneveld P, Cottini F, Anderson K, and Driscoll J. 2016. Pharmacogenomics and chemical library screens reveal a novel SCFSKP2 inhibitor that overcomes bortezomib resistance in multiple myeloma. Leukemia doi: 10.1038/leu.2016.258.

  5. Singh B, Jegga AG, Shanmukhappa KS, Edukulla R, Khurana GH, Medvedovic M, Dillon SR, Madala SK. 2016. IL-31-driven skin remodeling involves epidermal cell proliferation and thickening that lead to impaired skin-barrier function. PLoS One 11(8): e0161877. doi:10.1371/journal.pone.0161877.

  6. Bian F, Gao F, Kartashov AV, Jegga AG, Barski A, Das S. 2016. Polycomb repressive complex 1 controls uterine decidualization. Scientific Reports 6:26061. doi:10.1038/srep26061

  7. Sarangdhar M, Tabar S, Schmidt C, Kushwaha A, Shah K, Dahlquist JE, Jegga AG, Aronow BJ. 2016. Data mining differential clinical outcomes associated with drug regimens using adverse event reporting data. Nature Biotechnology 34(7):697-700. doi:10.1038/nbt.3623.

2015

  1. Hawrylycz M, Miller J, Menon V, Feng D, Dolbeare T, Guillozet-Bongaarts A, Jegga AG, Aronow BJ, Lee C, Bernard A, Glasser M, Dierker D, Menche J, Collman F, Grange P, Berman K, Mihalas S, Yao Z, Stewart L, Barabási A, Schulkin J, Phillips J, Ng L, Dang C, Haynor D, Jones A, Van Essen D, Koch C, Lein E. 2015. Canonical Genetic Signatures of the Adult Human Brain. Nature Neuroscience doi:10.1038/nn.4171.

  2. Adams AK, Bolanos LC, Dexheimer PJ, Karns RA, Aronow BJ, Komurov K, Jegga AG, Casper KA, Patil YJ, Wilson KM, Starczynowski DT, Wells SI. 2015. IRAK1 is a novel DEK transcriptional target and is essential for head and 1 neck cancer cell survival. Oncotarget.

  3. Miethke AG, Zhang W, Simmons J, Taylor A, Shi T, Shanmukhappa SK, Karns R, White S, Jegga AG, Lages CS, Nkinin S, Keller BT, Setchell KD. 2015. Pharmacological inhibition of ASBT changes bile composition and blocks progression of sclerosing cholangitis in mdr2 knockout mice. Hepatology. doi: 10.1002/hep.27973.

  4. Cha J, Burnum-Johnson KE, Bartos A, Li Y, Baker ES, Tilton SC, Webb-Robertson BJ, Piehowski PD, Monroe ME, Jegga AG, Murata S, Hirota Y, Dey SK. 2015. Muscle segment homeobox genes direct embryonic diapause by limiting inflammation in the uterus. J Biol Chem. pii: jbc.M115.655001.

  5. Patchala J and Jegga AG. 2015. Concept Modeling-based Drug Repositioning. AMIA 2015 Joint Summits on Translational Science. AMIA Jt Summits Transl Sci Proc. 2015: 222-226.

  6. Zhu C, Wu C, Jegga AG. 2015. Network Biology Methods for Drug Repositioning. In Post-Genomic Approaches in Drug and Vaccine Development (eds. Sakharkar KR, Sakharkar MK, Chandra R): 5, 115. River Publishers, Denmark.

  7. Edukulla R, Singh B, Jegga AG, Sontake V, Dillon SR, Madala SK. 2015. Th2 cytokines augment IL-31/IL-31RA interactions via STAT6-dependent IL-31RA expression. J. Biol. Chem. doi:10.1074/jbc.M114.622126.

  8. Chung Gilbert S, Nivarthi H, Mayhew CN, Lo YH, Noah TK, Vallance J, Rülicke T, Müller M, Jegga AG, Tang W, Zhang D, Helmrath M, Shroyer N, Moriggl R, Han X. 2015. Activated STAT5 confers resistance to intestinal injury by increasing intestinal stem cell proliferation and regeneration. Stem Cell Reports pii:S2213-6711(14)00381-6. doi: 10.1016/j.stemcr.2014.12.004.

  9. Chung D, Gao F, Jegga AG, Das SK. 2014. Estrogen mediated epithelial proliferation in the uterus is directed by stromal Fgf10 and Bmp8a. Molecular and Cellular Endocrinology. DOI: 10.1016/j.mce.2014.11.002.

2014

  1. Karns R, Tabar S, Bardes EE, Jegga AG and Aronow BJ 2014. How Do Bioinformatics Approaches Apply to the Analysis and Understanding of Disease Pathology?  In: Pathobiology of Human Disease (McManus LM, Mitchell RN eds.). Elsevier, San Diego. pp. 4140-4157.

  2. Jegga AG. 2014. Candidate Gene Discovery and Prioritization in Rare Diseases. Methods in Molecular Biology, 1168: 295-313. In Clinical Bioinformatics 2nd ed. (ed. Trent R). Springer Protocols, Humana Press.

  3. Wu C, Bardes EE, Jegga AG, Aronow BJ. 2014. ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. Nucleic Acids Research DOI: 10.1093/nar/gku409

  4. Wu C, Zhu C, Jegga AG. 2014. Integrative Literature and Data Mining to Rank Disease Candidate Genes. Methods Mol Biol. 1159: 207-226.

  5. Zhu C, Wu C, Aronow BJ, Jegga AG. 2014. Computational approaches for human disease gene prediction and ranking. Advances in Experimental Medicine and Biology 799: 69-84. In: Systems Analysis of Human Multigene Disorders, Springer Science+Business Media New York 2014 DOI 10.1007/978-1-4614-8778-4_4

  6. Bessho K, Mourya R, Shivakumar P, Walters S, Magee JC, Rao M, Jegga AG, Bezerra JA. 2014. Gene expression signature for biliary atresia and a role for Interleukin-8 in pathogenesis of experimental disease. Hepatology. doi: 10.1002/hep.27045.

  7. Velu CS, Cahubey A, Phelan JD, Horman SR, Wunderlich M, Guzman ML, Jegga AG, Zeleznik-Le NJ, Chen J, Mulloy JC, Cancelas JA, Jordan CT, Aronow BJ, Marcuccu G, Bhat B, Gebelein B, Grimes HL. 2014. Therapeutic antagonists of microRNAs deplete leukemia-initiating cell activity. Journal of Clinical Investigation doi:10.1172/JCI66005.

  8. Brundage M, Tandon P, Eaves D, Williams J, Miller S, Hennigan R, Jegga AG, Cripe T, Ranter N. 2014. MAF mediates crosstalk between Ras-MAPK and mTOR signaling in NF1. Oncogene doi: 10.1038/onc.2013.506.

  9. Feng Y, Huang W, Meng W, Jegga AG, Wang Y, Cai W, Kim HW, Wen Z, Rao F, Modi RM, Yu X, Ashraf M. 2014. Heat shock improves sca-1+ stem cells survival and directs ischemic cardiomyocytes towards a prosurvival phenotype via exosomal transfer: a critical role for HSF1/miR-34a/HSP70 pathway. Stem Cells DOI: 10.1002/stem.1571.

2013

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

  2. Jegga AG, Aronow BJ. 2013 Evolutionarily Conserved Noncoding DNA. In: Encyclopedia of Life Sciences (eLS 2013). John Wiley & Sons Ltd: Chichester DOI: 10.1002/9780470015902.a0006126.pub3

  3. Sarangdhar M, Kushwaha A, Dahlquist J, Jegga AG, Aronow BJ. 2013. Using systems biology-based analysis approaches to identify mechanistically significant adverse drug reactions: Pulmonary complications from combined use of anti-TNFa agents and corticosteroids. AMIA Summits on Translational Science Proceedings 2013:151-155.

  4. Bessho K, Shanmukhappa K, Sheridan R, Shivakumar P, Mourya R, Walters S, Kaimal V, Dilbone E, Jegga AG and Bezerra JA 2013. Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia. BMC Systems Biology 7: 104.

  5. Wu C, Bakshi A, Aronow B, Jegga A, Bhatnagar R. 2013. A biclustering algorithm to discover functional modules from ENCODE ChIP-Seq data.  IEEE 13th International Conference on Data Mining Workshops (ICDMW), 7-10 Dec 2013. pp. 96-103. 10.1109/ICDMW.2013.96.

  6. Bisio A, Sanctis V, Vescovo V, Denti MA, Jegga AG, Inga A, Ciribilli Y. 2013. Identification of new p53 target microRNAs by bioinformatics and functional analysis. BMC Cancer 13(1): 552.

  7. Brown EB, Layne JE, Zhu C, Jegga AG, Rollmann SM. 2013. Genome-wide Association Mapping of Natural Variation in Odor-guided Behavior in Drosophila. Genes Brain Behav. doi: 10.1111/gbb.12048

  8. Rajan S, Pena JR, Jegga AG, Aronow BJ, Wolska BM, Wieczorek DF. 2013. Microarray Analysis of Active Cardiac Remodeling Genes in a Familial Hypertrophic Cardiomyopathy Mouse Model Rescued by a Phospholamban Knockout. Physiol Genomics. 2013 Jun 25. [Epub ahead of print].

  9. Li Q, Deleger L, Lingren T, Zhai H, Kaiser M, Stoutenborough L, Jegga AG, Cohen KB, Solti I. 2013. Mining FDA drug labels for medical conditions. BMC Med Inform Decis Mak. 13(1): 53.

2012

  1. Zhu C, Kushwaha A, Berman K, Jegga AG 2012. A vertex similarity-based framework to discover and rank orphan disease-related genes. BMC Systems Biology 6(Suppl 3):S8.

  2. Jegga AG, Zhu C, Aronow BJ. 2012. Orphan Diseases, Bioinformatics and Drug Discovery. In Pediatric Biomedical Informatics - Computer Applications in Pediatric Research, Series: Translational Bioinformatics, Vol. 2. pp: 287-307. (Ed. Hutton JJ). Springer Science.

  3. Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q, Marsolo K, Jegga A, Kaiser M, Stoutenborough L, Solti I. 2012. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc. 2012 Aug 2. [Epub ahead of print].

  4. Xie H, Sun X, Piao Y, Jegga AG, Handwerger S, Ko MS, Dey SK. 2012. Silencing or amplification of endocannabinoid signaling in blastocysts via CB1 compromises trophoblast cell migration. J Biol Chem. 2012 Jul 24. [Epub ahead of print].

  5. Park JK, Martin LJ, Zhang X, Jegga AG, Benson DW. 2012. Genetic variants in SCN5A promoter are associated with arrhythmia phenotype severity in patients with heterozygous loss of function mutation. Heart Rhythm. Feb 24. [Epub ahead of print].

2011

  1. Willson TA, Kuhn BR, Jurickova I, Gerad S, Moon D, Bonkowski E, Carey R, Collins M, Xu H, Jegga AG, Guthery SL, Denson LA. STAT3 2011. Genotypic Variation and Cellular STAT3 Activation and Colon Leukocyte Recruitment in Pediatric Crohn Disease. J Pediatr Gastroenterol Nutr. Dec 22. [Epub ahead of print]

  2. Ma X, Gao F, Rusie A, Hemingway J, Ostmann AB, Sroga JM, Jegga AG, Das SK. 2011. Decidual cell polyploidization necessitates mitochondrial activity. PLoS One 6(10):e26774.

  3. Zhang M, Zhu C, Jacomy A, Lu LJ, Jegga AG. 2011 The orphan disease networks. American Journal of Human Genetics 88 (6): 755-766.

  4. Ren J, Jegga AG, Zhang M, Deng J, Liu J, Gordon CB, Aronow BJ, Lu LJ, Zhang B, and Ma J. 2011. A Drosophila model of the neurodegenerative disease SCA17 reveals a role of RBP-J/Su(H) in modulating the pathological outcome Hum. Mol. Genet. June 8, 2011 doi:10.1093/hmg/ddr251.

  5. Saradana D, Zhu C, Zhang M, Gudivada RC, Yang L, Jegga AG. 2011. Drug repositioning for orphan diseases. Briefings in Bioinformatics. April 18, 2011 [Epub ahead of print].

  6. Chen J and Jegga AG. 2011 Protein Network Analysis for Disease Gene Identification and Prioritization. In Applied Statistics for Network Biology: Methods in Systems Biology (eds. M. Dehmer, F. Emmert-Streib, A. Graber and A. Salvador), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527638079.ch18

  7. Yang L, Wang K, Chen J, Jegga AG, Luo H, Shi L, Wan C, Guo X, Qin S, He G, Feng G, He L. 2011. Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome - clozapine-induced agranulocytosis as a case study. PLoS Computational Biology 7(3): e1002016.

  8. Yang L, Wang KJ, Wang LS, Jegga AG, Qin SY, He G, Chen J, Xiao Y, He L. 2011. Chemical-protein interactome and its application in off-target identification. Interdiscip Sci. 3(1):22-30.

  9. Jegga AG, Schneider L, Ouyang X, and Zhang J. 2011. Systems biology of the autophagy-lysosomal pathway. Autophagy Volume 7, Issue 5 May 2011 (advance access).

  10. Kaimal V, Sardana D, Bardes EE, Gudivada RC, Chen J, Jegga AG. 2011. Integrative systems biology approaches to identify and prioritize disease and drug candidate genes. Methods Mol Biol. 700: 241-259.

  11. Rankin SA, Kormish J, Kofron M, Jegga AG, Zorn AM. 2011. A gene regulatory network controlling hhex transcription in the anterior endoderm of the organizer. Dev Biol. Jan 4. [Epub ahead of print].

2010

  1. Alqadah F, Bhatnagar R, Jegga AG. 2010. A novel framework for detecting maximally banded matrices in binary data. Statistical Analysis and Data Mining Article first published online : 7 Sept. 2010, DOI: 10.1002/sam.10089.

  2. Zhang X, Wang X, Zhu H, Zhu C, Wang Y, Pu WT, Jegga AG, Fan GC. 2010 Synergistic effects of the GATA-4-mediated miR-144/451 cluster in protection against simulated ischemia/reperfusion-induced cardiomyocyte death. J Mol Cell Cardiol. 49(5):841-50.

  3. Maldonado AR, Klanke C, Jegga AG, Aronow BJ, Mahller YY, Cripe TP, Crombleholme TM. 2010. Molecular engineering and validation of an oncolytic herpes simplex virus type 1 transcriptionally targeted to midkine-positive tumors. J Gene Med. 12(7): 613-623.

  4. Sardana D, Vasa, S, Vepachedu N, Chen, J, Gudivada RC, Aronow BJ, Jegga AG. 2010. PhenoHM: Human-Mouse Comparative Phenome-Genome Server. Nucleic Acids Research 38 Suppl:W165-74 doi:10.1093/nar/gkq472.

  5. Moyer K, Kaimal V, Pacheco C, Mourya R, Xu H, Shivakumar P, Chakraborty R, Rao M, Magee JC, Bove K, Aronow BJ, Jegga AG, Bezerra JA. 2010. Staging of biliary atresia at diagnosis by molecular profiling of the liver. Genome Med. 2(5):33.

  6. Kaimal V, Bardes E, Tabar S, Jegga AG, Aronow BJ. 2010. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Research 38 Suppl:W96-102doi:10.1093/nar/gkq418.

  7. Takemoto CM, Brandal S, Jegga AG, Lee YN, Shahlaee A, Ying Y, Dekoter R, McDevitt MA. PU.1 Positively Regulates GATA-1 Expression in Mast Cells. J Immunol. 184(8):4349-61.

2009

  1. Gowrisankar S, Jegga AG. 2009. Regression based predictor for p53 transactivation. BMC Bioinformatics 10:215.

  2. Miller SJ, Jessen WJ, Mehta T, Hardiman A, Sites E, Kaiser S, Jegga AG, Li H, Upadhyaya M, Giovannini M, Muir D, Wallace MR, Lopez E, Serra E, Nielsen GP, Lazaro C, Stemmer-Rachamimov A, Page G, Aronow BJ, Ratner N. 2009 Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene. EMBO Molecular Medicine 1: 236-248 doi: 10.1002/emmm.200900027

  3. Chen J, Bardes EE, Aronow BJ, Jegga AG 2009. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Research doi: 10.1093/nar/gkp427.

  4. Qu XA, Gudivada RC, Jegga AG, Neumann EK, Aronow BJ. 2009. Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. BMC Bioinformatics 10 Suppl 5:S4.

  5. Chen J, Aronow BJ, Jegga AG 2009. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10: 73.

  6. Gu Y, Harley ITW, Henderson LB, Aronow BJ, Vietor I, Huber LA, Harley JB, Kilpatrick JR, Langefeld CD, Williams AH, Jegga AG, Chen J, Wills-Karp M, Arshad SH, Ewart SL, Thio CL, Flick LM, Filippi MD, Grimes LH, Drumm ML, Cutting GR, Knowles MR, Karp CL. 2009. IFRD1 polymorphisms in cystic fibrosis with potential link to altered neutrophil function. Nature 458(7241): 1039-1042.

2008

  1. Brunskill EW, Aronow BJ, Georgas K, Rumballe B, Valerius TM, Aronow J, Kaimal V, Jegga AG, Grimmond S, McMahon AP, Patterson LT, Little MH and Potter SS. 2008. Atlas of gene expression in the developing kidney at microanatomic resolution. Developmental Cell15(5): 781-791.

  2. Gudivada RC, Qu XA, Chen J, Jegga AG, Neumann EK, Aronow BJ. 2008. Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge. J Biomed Inform. [Epub ahead of print]

  3. Jegga AG and Aronow BJ 2008 Evolutionarily Conserved Noncoding DNA. In: Handbook of Human Molecular Evolution, David N. Cooper and Hildegard Kehrer-Sawatzki (Editors) Wiley Publishers; 1 edition (October 20, 2008).

  4. Jegga AG and Aronow BJ 2008 Evolutionarily Conserved Noncoding DNA. In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0006126.pub2

  5. Takemoto CM, Lee YN, Jegga AG, Zablocki D, Brandal S, Shahlaee A, Huang S, Ye Y, Gowrisankar S, Huynh J, McDevitt MA. Mast cell transcriptional networks. Blood Cells Mol Dis. 2008 Apr 10; [Epub ahead of print]

  6. Kamath MB, Houston IB, Janovski AJ, Zhu X, Gowrisankar S, Jegga AG and DeKoter RP 2008. Myeloid gene activation and T cell/natural killer cell gene repression in cells expressing two distinct PU.1 concentrations. Leukemia; doi:10.1038/leu.2008.67.

  7. Sinha AU, Kaimal V, Chen J and Jegga AG 2008. Dissecting microregulation of a master regulatory network. BMC Genomics 9:88;doi:10.1186/1471-2164-9-88.

  8. Jegga AG, Inga A, Menendez D, Aronow BJ and Resnick MA 2008. Functional evolution of the p53 regulatory network through its target response elements. Proc Natl Acad Sci U S A. 105 (3): 945-950. Epub 2008 Jan 10.

  9. Gudivada RC, Fu Y, Jegga AG, Qu XA, Neumann EK, Aronow BJ. 2008. Mining human phenome to investigate modularity of complex disorders. Summit on Translat Bioinforma. 2008:31-5.

2007

  1. Chen J, Xu H, Aronow BJ, Jegga AG 2007. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics 8(1): 392 [Epub ahead of print]; doi:10.1186/1471-2105-8-392

  2. Jegga AG, Chen J, Gowrisankar S, Deshmukh M, Kaimal V, Gudivada R, Kong S and Aronow BJ 2007. GenomeTrafac: A genome-wide database for the detection of conserved transcription factor binding site clusters in both conventional and microRNA mouse-human gene orthologs. Nucleic Acids Research 35 (Database issue): D116-D121; doi:10.1093/nar/gkl1011.

  3. Jegga AG, Gowrisankar S, Chen J and Aronow BJ 2007. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Research 35 (Database issue): D700-D706; doi:10.1093/nar/gkl826.

  4. Liu C, Aronow BJ, Jegga AG, Wang N, Miethke A, Mourya R, Bezerra JA 2007. Novel resequencing chip customized to diagnose mutations in patients with inherited syndromes of intrahepatic cholestasis. Gastroenterology 132(1):119-126. Epub 2006 Oct 21.

  5. Diwan A, Koesters AG, Odley AM, Pushkaran S, Baines CP, Spike BT, Daria D, Jegga AG, Geiger H, Aronow BJ, Molkentin JD, Macleod KF, Kalfa TA, Dorn GW 2nd. 2007. Unrestrained erythroblast development in Nix-/- mice reveals a mechanism for apoptotic modulation of erythropoiesis. Proc Natl Acad Sci U S A. 2007 104(16):6794-6799 [Epub ahead of print] [Pdf].

  6. Markey MP, Bergseid J, Bosco EE, Stengel K, Xu H, Mayhew CN, Schwemberger SJ, Braden WA, Jiang Y, Babcock G, Jegga AG, Aronow BJ, Reed MF, Wang JYJ and Knudsen ES 2007. Loss of the retinoblastoma tumor suppressor: differential action on transcriptional programs related to cell cycle control and immune function. Oncogene 26(43): 6307-6318 [Epub ahead of print].

  7. Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, et al. 2007. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biol. 8(7): R131 [Epub ahead of print]

  8. Jegga AG, Aronow B, Handwerger 2007. Microarray-based Gene Expression Analysis of Endocrine Systems: Principles of Experimental Design and Interpretation In Genomics in Endocrinology: DNA Microarray Analysis in Endocrine Health and Disease Series (Contemporary Endocrinology) Handwerger S and Aronow B (Eds.). Humana Press, USA (October 1, 2007) (In press) (Hardcover ISBN: 978-1-58829-651-1).

  9. Jegga AG, Chen J, Gowrisankar S, Deshmukh M and Aronow BJ. GenomeTrafac: A Whole-Genome Resource for the Detection of Conserved Transcription Factor Binding Site Motifs and Clusters in Promoters and Flanking Regions of Known Human-Mouse Gene Orthologs. In Applications of Statistical and Machine Learning Methods in Bioinformatics; Series: Advances in Computational and Systems Biology, Vol 1 (eds. Meller J and Nowak W), 2007 Peter Lang Publishing Group.

2006

  1. Miller SJ, Rangwala F, Williams J, Ackerman P, Kong S, Jegga AG, Kaiser S, Aronow BJ, Frahm S, Kluwe L, Mautner V, Upadhyaya M, Muir D, Wallace M, Hagen J, Quelle DE, Watson MA, Perry A, Gutmann DH, and Ratner N. 2006. Large-Scale molecular comparison of human schwann cells to malignant peripheral nerve sheath tumor cell lines and tissues. Cancer Research 66 (5): 2584-91.

2005

  1. Jegga AG, Gupta A, Gowrisankar S, Deshmukh MA, Connolly S, Finley K, Aronow BJ 2005. CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. Nucleic Acids Research33 (Web Server Issue): W408-W11. [Pdf]

  2. Jegga AG, Kong S, Zhang J, Moseley A, Gupta A, Williams SS, Genter MB and Aronow1 BJ 2005. Comparative Genomics of Tissue Specific Gene Expression In Gene Expression and Regulation (ed. J, Ma), Springer, USA. (see at amazon.com)

  3. Vukkadapu SS, Belli JM, Ishii K, Jegga AG, Hutton JJ, Aronow BJ, Katz JD. Dynamic interaction between T cell-mediated beta cell damage and beta cell repair in the run-up to autoimmune diabetes of the NOD mouse 2005. Physiol Genomics. 21(2): 201-11.

2004

  1. Hutton JJ, Jegga AG, Kong S, Gupta A, Ebert C, Williams S, Katz JD and Aronow BJ 2004. Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genomics 5(1): 82 [Oct 25, 2004; Epub ahead of print].

  2. Zhang J, Moseley A, Jegga AG, Gupta A, Witte DP, Sartor M, Medvedovic M, Williams SS, Ley-Ebert C, Coolen L, Egnaczyk G, Genter MB, Lehman M, Lingrel J, Maggio J, Parysek L, Walsh R, Xu M, Aronow BJ. 2004. Neural system-enriched gene expression, relationship to biological pathways and neurological diseases. Physiological Genomics 18:167-83 [Pdf].

  3. Livingston RJ, Von Niederhausern A, Jegga AG, Crawford DC, Carlson CS, Rieder MJ, Gowrisankar S, Aronow BJ, Weiss RB, Nickerson DA. 2004. Pattern of Sequence Variation Across 213 Environmental Response Genes. Genome Res. 14:1821-31. Epub 2004 Sep 13 [Pdf].

  4. Kim J.-w., Zeller KI, Wang Y, Jegga AG, Aronow BJ, O'Donnell KA, and Dang CV 2004. Evaluation of Myc E-Box Phylogenetic Footprints in Glycolytic Genes by Chromatin Immunoprecipitation Assays. Mol. Cell. Biol. 24: 5923-5936 [Pdf].

  5. Bonizzi G, Bebien M, Otero DC, Johnson-Vroom KE, Cao Y, Vu D, Jegga AG, Aronow BJ, Ghosh VG, Rickert RC and Karin M 2004. Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers. EMBO J. 23(21): 4202-4210 [Pdf].

2003

  1. Jegga AG and Aronow BJ 2003. Evolutionarily Conserved Noncoding DNA. In Nature Encyclopedia of the Human Genome, Vol 2, pp 347-354. Nature Publishing Group, England and In Encycyclopedia of Life Sciences. John Wiley and Sons, Ltd: Chichester [Pdf].

  2. Zeller KI, Jegga AG, Aronow BJ, O'Donnell KA and Dang CV 2003. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biology 4: R69 [Pdf].

  3. Genter MB, Van Veldhoven PP, Jegga AG, Sakthivel B, Kong S, Stanley K, Witte DP, Ebert CL, Aronow BJ. 2003. Microarray-based discovery of highly expressed olfactory mucosal genes: potential roles in the various functions of the olfactory system. Physiol Genomics 16: 67-81. Epub 2003 Oct 21. [Pdf].

2002

  1. Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP and Aronow BJ 2002. Detection and visualization of compositionally similar cis-regulatory element clusters in orthologous and coordinately expressed genes. Genome Research 12 (9): 1408-1417 [Pdf].

  2. Bates MD, Erwin CR, Sanford LP, Wiginton D, Bezerra JA, Schatzman LC, Jegga AG, Ley-Ebert C, Williams SS, Steinbrecher KA, Warner BW, Cohen MB and Aronow BJ. 2002. Novel genes and functional relationships in the adult mouse gastrointestinal tract identified by microarray analysis. Gastroenterology 122 (5):1467-1482 [Pdf].

  3. Warren MA, Koshoffer A, Aronow BJ, Jegga AG, Brackenbury R (2002). Structure of the 5' Portion of the Human Plakoglobin Gene. J Invest Dermatol 119 (1):196-197.

<2002

  1. Jegga AKG and Raghavender KBP 1997. Abdominal wall reconstruction with external abdominal oblique myofascial flap in dogs: an experimental study. Indian Journal of Veterinary Surgery 18 (1): 12-14.