PhD, Genomic Medicine / Bioinformatics,
Medical College of Georgia at Augusta University, Augusta, GA
With a background in computer science and a PhD in Genomic Medicine, I have experience in both the computational and biological aspects of biomedical research. My research focus is on the development of biologically meaningful algorithms for comprehensive analysis and the visualization of high-throughput data by incorporating biological knowledge and rigorous computational methods. In the last decade, biomedical research has been revolutionized by the advent of high-throughput technologies which can generate large amounts of data. Unlocking the meaningful biological information contained inside high-throughput data is a big challenge for bench biologists. In order to facilitate the analysis of such complex data, it is crucial to develop statistical tools as well as efficient algorithms and methods to extract useful information. My primary area of research is bioinformatics, where I apply computational, mathematical, and statistical methods to solve complex biological problems. Long term goals of my lab are to solve the challenges in the analysis of data from many high-throughput technologies, especially mass spectrometry-based proteomics, and to implement these solutions in usable software tools.
I work with an interdisciplinary team to carry out bioinformatics analysis and to pursue research projects in collaboration with other biologists. Currently, I am developing analytical methods for the large-scale measurements that are part of several Cancer and Diabetes projects. In our center (CBGM: Center for Biotechnology and Genomic Medicine), I am providing bioinformatics support for several long-term studies including The Environmental Determinants of Diabetes in the Young (TEDDY), the Phenome and Genome of Diabetes Autoimmunity (PAGODA), the Diabetic Complications Consortium (DiaComp), the Mouse Metabolic Phenotype Consortium (MMPC) and Biomarkers and Therapeutics in Cancer (BAT Cancer).
Post Translational Modification Analysis: Glycosylation and Phosphorylation
Glycan Identification & Characterization
Orbitrap Fusion™ Tribrid™ Mass Spectrometer
Proteomic Biomarkers for Glaucomatous Optic Neuropathy
Targeting Interleukin-6 Trans-signaling in Diabetic Retinopathy
Proteomic, Glycomic, and Glycoproteomic Profiling in Patients with Diabetic Retinopathy
Unraveling the role of genetics in the pathogenesis of diabetic retinopathy
Complete List of Published Work in MyBibliography:
Bhagirath D, Liston M, Akoto T, Lui B, Bensing BA, Sharma A, Saini S. Novel, non-invasive markers for detecting therapy induced neuroendocrine differentiation in castration-resistant prostate cancer patients. Sci Rep. 2021 Apr 15;11(1):8279.
Kodeboyina SK, Lee TJ, Bollinger K, Ulrich L, Bogorad D, Estes A, Zhi W, Sharma S, Sharma A. Aqueous Humor Proteomic Alterations Associated with Visual Field Index Parameters in Glaucoma Patients: A Pilot Study. J Clin Med. 2021 Mar 12;10(6):1180.
Bonifacio E, Weiß A, Winkler C, Hippich M, Rewers MJ, Toppari J, Lernmark Å, She JX, Hagopian WA, Krischer JP, Vehik K, Schatz DA, Akolkar B, Ziegler AG; TEDDY Study Group. An Age-Related Exponential Decline in the Risk of Multiple Islet Autoantibody Seroconversion During Childhood. Diabetes Care. 2021 Feb 24:dc202122. doi: 10.2337/dc20-2122.
Robinson R, Brown D, Churchwell L, Lee TJ, Kodeboyina SK, Bloom J, Sharma A, Sharma S. RNA-Seq analysis reveals gene expression changes induced by IL-6 trans-signaling activation in retinal endothelial cells. Cytokine. 2021 Mar;139:155375.
Kolhe R, Owens V, Sharma A, Lee TJ, Zhi W, Ghilzai U, Mondal AK, Liu Y, Isales CM, Hamrick MW, Hunter M, Fulzele S. Sex-Specific Differences in Extracellular Vesicle Protein Cargo in Synovial Fluid of Patients with Osteoarthritis. Life (Basel). 2020 Dec 10;10(12):337.
Kodeboyina SK, Lee TJ, Churchwell L, Ulrich L, Bollinger K, Bogorad D, Estes A, Zhi W, Sharma S, Sharma A. The Constitutive Proteome of Human Aqueous Humor and Race Specific Alterations. Proteomes. 2020 Nov 18;8(4):34.
Sharma A, Cox J, Glass J, Lee TJ, Kodeboyina SK, Zhi W, Ulrich L, Lukowski Z, Sharma S. Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy. Proteomes. 2020 Sep 13;8(3):25.
Robinson R, Youngblood H, Iyer H, Bloom J, Lee TJ, Chang L, Lukowski Z, Zhi W, Sharma A, Sharma S. Diabetes Induced Alterations in Murine Vitreous Proteome Are Mitigated by IL-6 Trans-Signaling Inhibition. Invest Ophthalmol Vis Sci. 2020 Sep 1;61(11):2.
Vehik K, Bonifacio E, Lernmark Å, Yu L, Williams A, Schatz D, Rewers M, She JX, Toppari J, Hagopian W, Akolkar B, Ziegler AG, Krischer JP; TEDDY Study Group. Hierarchical Order of Distinct Autoantibody Spreading and Progression to Type 1 Diabetes in the TEDDY Study. Diabetes Care. 2020 Sep;43(9):2066-2073.
Robinson R, Srinivasan M, Shanmugam A, Ward A, Ganapathy V, Bloom J, Sharma A, Sharma S. Interleukin-6 trans-signaling inhibition prevents oxidative stress in a mouse model of early diabetic retinopathy. Redox Biol. 2020 Jul;34:101574.
Fulzele S, Sahay B, Yusufu I, Lee TJ, Sharma A, Kolhe R, Isales CM. COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile. Aging Dis. 2020 May 9;11(3):509-522.
Wallbillich JJ, Tran PM, Bai S, Tran LK, Sharma AK, Ghamande SA, She JX. Identification of a transcriptomic signature with excellent survival prediction for squamous cell carcinoma of the cervix. Am J Cancer Res. 2020 May 1;10(5):1534-1547.
Vashishtha A, Lee TJ, Sharma A, Wallbillich JJ. Changes in microRNA expression associated with metastasis and survival in patients with uveal melanoma. Oncotarget. 2020 Apr 21;11(16):1435-1447.
Li Q, Parikh H, Butterworth MD, Lernmark Å, Hagopian W, Rewers M, She JX, Toppari J, Ziegler AG, Akolkar B, Fiehn O, Fan S, Krischer JP; TEDDY Study Group. Longitudinal Metabolome-Wide Signals Prior to the Appearance of a First Islet Autoantibody in Children Participating in the TEDDY Study. Diabetes. 2020 Mar;69(3):465-476.
Liu X, Vehik K, Huang Y, Elding Larsson H, Toppari J, Ziegler AG, She JX, Rewers M, Hagopian WA, Akolkar B, Krischer JP; TEDDY Study Group. Distinct Growth Phases in Early Life Associated With the Risk of Type 1 Diabetes: The TEDDY Study. Diabetes Care. 2020 Mar;43(3):556-562.
Youngblood H, Robinson R, Sharma A, Sharma S. Proteomic Biomarkers of Retinal Inflammation in Diabetic Retinopathy. International Journal of Molecular Sciences Int J Mol Sci. 2019 Sep 25;20(19).
Zhu H, Bhatt B, Sivaprakasam S, Cai Y, Liu S, Kodeboyina S, Patel N, Savage N, Sharma A, Kaufman R, Li H, and Singh N. Ufbp1 promotes plasma cell development and ER expansion by modulating distinct branches of UPR. Nature Communications, 2019 Mar 6; 10(1):1084.
Sharma A, Valle ML, Beveridge C, Liu Y, Sharma S. Unraveling the role of genetics in the pathogenesis of diabetic retinopathy. Eye (Lond). 2019.
Valle ML, Dworshak J, Sharma A, Ibrahim AS, Al-Shabrawey M, Sharma S.Inhibition of interleukin-6 trans-signaling prevents inflammation and endothelial barrier disruption in retinal endothelial cells. Exp Eye Res. 2019; 178:27-36.
Venugopal N*, Yeh J*, Kodeboyina SK, Lee T, Sharma S, Patel N, Sharma A. Differences in early stage gene expression profiles in lung adenocarcinoma and lung squamous cell carcinoma. Oncology Letters.
Dimri M, Humphries A, Laknaur A, Elattar S, Lee TJ, Sharma A, Kolhe R, Satyanarayana A. Nqo1 ablation inhibits activation of the PI3K/Akt and MAPK/ERK pathways and blocks metabolic adaptation in hepatocellular carcinoma. Hepatology 2019.
Sharma S, Bollinger KE, Kodeboyina SK, Zhi W, Patton J, Bai S, Edwards B, Ulrich L, Bogorad D, Sharma A*. A. Proteomic Alterations in Aqueous Humor from Patients with Primary Open Angle Glaucoma. Invest Ophthalmol. Vis. Science (IOVS). 2018 April
Tailor P, Kodeboyina SK, Bai S, Patel N, Sharma S, Ratnani A, Copland J, She JX, Sharma A*. Diagnostic and prognostic biomarker potential of kallikrein family genes in different cancer types. Oncotarget. 2018 March 06;9:17876-17888.
Purohit S, Li T, Guan W, Song X, Song J, Tian Y, Li L, Sharma A, Dun B, Mysona D, Ghamande S, Rungruang B, Cummings RD, Wang PG, She JX. Multiplex glycan bead array for high throughput and high content analyses of glycan binding proteins. Nature Communications. 2018 Jan 17;9(1):258.
Guo D, Xu Q, Pabla S, Koomen J, Biddinger P, Sharma A, Pabla S, Pacholczyk R, Chang CC, Friedrich K, Mohammed K, Smallridge RC, Copland JA, She JX, Weinberger PM. Cytokeratin-8 in Anaplastic Thyroid Carcinoma: More Than a Simple Structural Cytoskeletal Protein. Int J Mol Sci. 2018 Feb 14;19(2).
Purohit S, Sharma A, Zhi W, Bai S, Hopkins D, Steed L, Bode B, Anderson SW, Reed JC, Steed RD, She JX. Proteins of TNF-α and IL6 Pathways Are Elevated in Serum of Type-1 Diabetes Patients with Microalbuminuria. Front Immunol. 2018 Jan 31;9:154.
Sharma A, Liu X, Hadley D, Hagopian W, Chen WM, Onengut-Gumuscu S, Törn C, Steck AK, Frohnert BI, Rewers M, Ziegler AG, Lernmark Å, Toppari J, Krischer JP, Akolkar B, Rich SS, She JX; TEDDY Study Group. Identification of non-HLA genes associated with development of islet autoimmunity and type 1 diabetes in the prospective TEDDY cohort. Journal of Autoimmunity. 2018 Jan 5.
Kvirkvelia N, McMenamin M, Warren M, Jadeja R, Kodeboyina SK, Sharma A, Zhi W, O’Conor P, Raju R, Lucas R, Madaio M. Kidney Targeted Inhibition of Protein Kinase C-α Ameliorates Nephrotoxic Nephritis with Restoration of Mitochondrial Dysfunction. Kidney International. 2018
Mysona D, Pyrzak A, Allen J, Powell M, Kleven D, Zhi W, Sharma A, Bai S, She JX, Rungruang B, Ghamande S. Proteomic approach to identify biomarkers for invasive cervix cancer - A prospective pilot study. Journal of European Gynaecologic Oncology. 2017
Weinberger P, Ponny SR, Xu H, Bai S, Smallridge RC, Copland JA, Sharma A*. Cell Cycle M-phase Genes are Highly Upregulated in Anaplastic Thyroid Carcinoma. 2017 Feb;27(2):236-252.
Ma R, Xu H, Wu J, Sharma A, Bai S, Dun B, Jing C, Cao H, Wang Z, She JX, Feng J. Identification of serum proteins and multivariate models for diagnosis and therapeutic monitoring of lung cancer. Oncotarget. 2017 Jan 21.
Wu J, Li S, Ma R, Sharma A, Bai S, Dun B, Cao H, Jing C, She J, Feng J. Tumor profiling of co-regulated receptor tyrosine kinase and chemoresistant genes reveal different targeting options for lung and gastroesophageal cancers. Am J Transl Res. 2016 Dec 15;8(12):5729-5740.
Törn C, Liu X, Hagopian W, Lernmark Å, Simell O, Rewers M, Ziegler AG, Schatz D, Akolkar B, Onengut-Gumuscu S, Chen WM, Toppari J, Mykkänen J, Ilonen J, Rich SS, She JX, Sharma A, Steck A, Krischer J; TEDDY Study Group. Complement gene variants in relation to autoantibodies to beta cell specific antigens and type 1 diabetes in the TEDDY Study. Sci Rep. 2016 Jun 16; 6:27887.
Sharma A, Liu X, Hadley D, Hagopian W, Liu E, Chen WM, Onengut-Gumuscu S, Simell V, Rewers M, Ziegler AG, Lernmark Å, Simell O, Toppari J, Krischer JP, Akolkar B, Rich SS, Agardh D, She JX. Identification of Non-HLA Genes Associated with Celiac Disease and Country-Specific Differences in a Large, International Pediatric Cohort. PloS one. 2016 Mar 25; 11(3):e0152476.
Lavoie TN, Carcamo WC, Wanchoo A, Sharma A, Gulec A, Berg KM, Stewart CM, Nguyen CQ. IL-22 regulation of functional gene expression in salivary gland cells. Genomics data. 2016 Mar; 7:178-84.
Sharma A¶, Purohit S¶, Sharma S, Bai S, Zhi W, Ponny SR, Hopkins D, Steed L, Bode B, Anderson SW, She JX. IGF-binding proteins in type 1 diabetes are more severely altered in the presence of complications. Frontiers in endocrinology. 2016 Jan 29; 7:2.
Purohit S¶, Sharma A¶, Hopkins D, Steed L, Bode B, Anderson SW, Reed JC, Steed RD, Yang T, She JX. Large scale discovery and validation studies demonstrate significant reductions in circulating levels of IL8, IL-1Ra, MCP-1 and MIP-1β in type-1 diabetes patients. J Clin Endocrinol Metab 2015 Sep; 100(9):E1179-87.
Li S≠, Ma R≠, Wu JZ, Xiao X, Wu W, Li G, Chen B, Sharma A, Bai S, Dun BY, She JX and Tang JH. Delineation of gastric cancer subtypes by co-regulated expression of receptor tyrosine kinases and chemosensitivity genes. American Journal of Translational Research. 2015 Aug; 7(8):1429-39.
Sharma S, Purohit S, Sharma A, Hopkins D, Steed L, Bode B, Anderson SW, Caldwell R, She JX. Elevated Serum Levels of Soluble TNF Receptors and Adhesion Molecules Are Associated with Diabetic Retinopathy in Patients with Type-1 Diabetes. Mediators of Inflammation. 2015
Liu H, Wang Y, Sharma A, Mao R, Jiang N, Dun B, She JX. Derivatives containing both coumarin and benzimidazole potently induce caspase-dependent apoptosis of cancer cells through inhibition of PI3K-AKT-mTOR signaling. Anti-Cancer Drugs. 2015 Jul; 26(6):667-77.
Wang J, Ma R, Sharma A，He M, Xue J, Wu J, Dun B, Li G, Wang X, Ji M, She JX, Tang J. Inflammatory Serum Proteins Are Severely Altered in Metastatic Gastric Adenocarcinoma Patients from the Chinese Population. PLoS One. 2015 Apr; 10(4):e0123985.
Purohit S, Sharma A, She JX. Luminex and Other Multiplex High Throughput Technologies for the Identification of, and Host Response to, Environmental Triggers of Type 1 Diabetes. BioMed Research International 2015
Xu H, Wu J, Chen B, Li M, Tian Y, He M, Xue J, Wang J, Bai S, Sharma A, Liu H, Tang J, She JX. Serum Dickkopf-1 (DKK1) is significantly lower in patients with lung cancer but is rapidly normalized after treatment. Am J Transl Res. 2014 Nov 22; 6(6):850-6
Zhi W, Ferris D, Sharma A,Purohit S, Santos C, He M, Ghamande S, She JX.
Twelve serum proteins progressively increase with disease stage in squamous cellcervical cancer patients. Int J Gynecol Cancer.2014 Jul;24(6):1085-92. doi: 10.1097/IGC.0000000000000153.
Jin Y, Sharma A,Bai S, Davis C, Liu H, Hopkins D, Barriga K, Rewers M, She JX.
Risk of type 1 diabetes progression in islet autoantibody-positive children can be further stratified using expression patterns of multiple genes implicated inperipheral blood lymphocyte activation and function.Diabetes. 2014Jul;63(7):2506-15. doi: 10.2337/db13-1716. Epub 2014 Mar 4.
Dun B, Sharma A,Xu H, Liu H, Bai S, Zeng L, She JX.
Transcriptomic changes induced by mycophenolic acid in gastric cancer cells. Am J Transl Res. 2013Dec 1;6(1):28-42. eCollection 2013.
Dun B, Sharma A,Teng Y, Liu H, Purohit S, Xu H, Zeng L, She JX.
Mycophenolicacid inhibits migration and invasion of gastric cancer cells via multiplemolecular pathways. PLoS One. 2013 Nov15;8(11):e81702. doi: 10.1371/journal.pone.0081702
Wang J, Sharma A,Ghamande SA, Bush S, Ferris D, Zhi W, He M, Wang M, Wang X, Miller E, HopkinsD, Macfee M, Guan R, Tang J, SheJX.
Serum protein profile at remission can accurately assess therapeutic outcomes andsurvival for serous ovarian cancer. PLoS One. 2013 Nov11;8(11):e78393. doi: 10.1371/journal.pone.0078393
Dun B, Xu H, Sharma A,Liu H, Yu H, Yi B, Liu X, He M, Zeng L, She JX.
Delineation of biological and molecular mechanisms underlying the diverse anticanceractivities of mycophenolic acid. Int J Clin Exp Pathol.2013 Nov 15;6(12):2880-6
Jin Y*, Sharma A*, Carey C*, Hopkins D, Wang X, Robertson DG, Bode B, Anderson SW, Reed JC, Steed RD, Steed L, She JX.
The expression of inflammatory genes is upregulated in peripheral blood of patients with type 1 Diabetes.Diabetes Care, 36:1–9, 2013.
Chen B, Yi B, Mao R, Liu H, Wang J, Sharma A, Peiper S, Leonard WJ, She JX.
Enhanced T cell lymphoma in NOD.Stat5b transgenic mice is caused by hyperactivation of Stat5b in CD8+ thymocytes. PLoS One. 2013;8(2):e56600, 2013; PMID: 23457589.
Lu S*, Purohit S*, Sharma A*, Zhi W*, He M, Wang Y, Li CJ, She JX.
Serum Insulin-like growth factor binding protein 6 (IGFBP6) is increased in patients with type 1 diabetes and its complications. Int J Clin Exp Med. 2012; 5(3): 229–237; PMID: 22837797.
Zhi W*, Sharma A*, Purohit S, Miller E, Bode B, Anderson SW, Reed JC, Steed RD, Steed L, Hopkins D, She JX.
Discovery and validation of serum protein changes in type 1 diabetes patients using high throughput two dimensional liquid chromatography-mass spectrometry and immunoassays. Molecular & Cellular Proteomics, 2011: 10: M111.012203. (Impact Factor 9.876); PMID: 21900154.
Sharma A, Zhao J, Podolsky R, McIndoe RA.
ParaSAM: a parallelized version of the significance analysis of microarrays algorithm. Bioinformatics 2010: 26: 1465-7; PMID: 20400455.
Sharma A*, Bartell SM*, Baile CA, Chen B, Podolsky RH, McIndoe RA, She JX.
Hepatic gene expression profiling reveals key pathways involved in leptin-mediated weight loss in ob/ob mice. PLoS.One. 2010: 5(8): e12147; PMID: 20808936.
Sharma A, Podolsky R, Zhao J, McIndoe RA.
A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets. Bioinformatics 2009: 25: 1152-7; PMID: 19261720.
Kraj P*, Sharma A*, Garge N, Podolsky R, McIndoe RA.
ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use. BMC Bioinformatics 2008: 9: 200; PMID:18416829
Zhou L, Wang H, Zhong X, Jin Y, Mi QS, Sharma A, McIndoe RA, Garge N, Podolsky R, She JX.
The IL-10 and IFN-gamma pathways are essential to the potent immunosuppressive activity of cultured CD8+ NKT-like cells. Genome Biology. 2008: 9: R119; PMID:18664279.
Nguyen CQ, Sharma A, She JX, McIndoe RA, Peck AB.
Differential gene expressions in the lacrimal gland during development and onset of keratoconjunctivitis sicca in Sjogren's syndrome (SJS)-like disease of the C57BL/6.NOD-Aec1Aec2 mouse. Exp.Eye Res. 2009: 88: 398-409; PMID: 19103199.
Nguyen CQ, Sharma A, Lee BH, She JX, McIndoe RA, Peck AB.
Differential gene expression in the salivary gland during development and onset of xerostomia in Sjogren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse. Arthritis Res.Ther. 2009: 11: R56; PMID:19379516.
Peck AB, Saylor BT, Nguyen L, Sharma A, She JX, Nguyen CQ, McIndoe RA.
Gene expression profiling of early phase Sjögren’s syndrome in C57BL/6.NOD-Aec1Aec2 mice identifies focal adhesion (FA) maturation associated with infiltrating leukocytes. (Invest Ophthalmol. Vis. Sci. 2011: 52(8): 5647-55; PMID: 21666236.
Peck AB, Nguyen CQ, Sharma A, McIndoe RA, She JX.
The interferon-signature of Sjögren’s Syndrome: What is it and what does it mean? (J Clin Rheumatol & Musculoskeleton Med. 09-May-2011).