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Siddharth Pratap

TitleDirector of Bioinformatics, Director of Proteomics
Faculty RankAssistant Professor
InstitutionMeharry Medical College
DepartmentBioinformatics Core, Proteomics Core
AddressDept. of Microbiology & Immunonogy
rm# 4108 West Basic Science Building
1005 D.B. Todd Blvd
Nashville TN 37208
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    Other Positions
    TitleAssistant Professor
    InstitutionMeharry Medical College
    DepartmentSchool of Graduate Sudies

    Collapse Affiliation 

    Collapse Biography 
    Collapse awards and honors
    1993 - 1995Howard Hughes Undergraduate Research Award, Indiana University
    1995Honorable mention for the design of novel biomedical device, Cook Inc.
    2000Woods Hole Immuno-Parasitology 2000, Trainee Presentation Award, Woods Hole, MA
    2008Oak Ridge National Labs Bioinformatics Summit, Cadiz, KY

    Collapse Overview 
    Collapse overview
    I have the expertise in BioMedical Informatics, Proteomics and Computational Biology to successfully fulfill my role in the Meharry Clinical and Translational Research Center (MeTRC). As the director of the Meharry Microarray-Bioinformatics Core and the MeTRC Biomedical Informatics key activity, I have created a comprehensive bioinformatics analysis infrastructure at Meharry Medical College. I have also been active in launching new programs and capabilities as evidenced by my lead role in the Meharry Proteomics Core, in which I serve as the Managing Director. Additionally, I have been successful in expanding Meharry’s educational training in Translational research by initiating a new course in Bioinformatics as part of the School of Graduate Studies and Research curriculum. My experience has allowed me to have excellent multi-disciplinary, multi-institutional interactions. Together, we have effectively incorporated basic science, clinical investigation, and bioinformatics, thus allowing for a translational approach to research in health disparities. I believe that the current project is an excellent area for me to become involved as my experience fits it effectively.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Rayford KJ, Cooley A, Strode AW, Osi I, Arun A, Lima MF, Misra S, Pratap S, Nde PN. Trypanosoma cruzi dysregulates expression profile of piRNAs in primary human cardiac fibroblasts during early infection phase. Front Cell Infect Microbiol. 2023; 13:1083379. PMID: 36936778.
      Citations:    Fields:    Translation:HumansAnimalsCells
    2. Cooley A, Rayford KJ, Arun A, Villalta F, Lima MF, Pratap S, Nde PN. Trypanosoma cruzi Dysregulates piRNAs Computationally Predicted to Target IL-6 Signaling Molecules During Early Infection of Primary Human Cardiac Fibroblasts. Immune Netw. 2022 Dec; 22(6):e51. PMID: 36627941.
    3. Olokpa E, Mandape SN, Pratap S, Stewart MV. Metformin regulates multiple signaling pathways within castration-resistant human prostate cancer cells. BMC Cancer. 2022 Sep 29; 22(1):1025. PMID: 36175875.
      Citations:    Fields:    Translation:HumansCells
    4. Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLB, Witkowski L, Zouk H, Weng C, Leppig KA, Sleiman PMA, Hakonarson H, Williams MS, Luo Y, Jarvik GP, Green RC, Chung WK, Gharavi AG, Lennon NJ, Rehm HL, Gibbs RA, Peterson JF, Roden DM, Wiesner GL, Denny JC. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. JAMA Oncol. 2022 06 01; 8(6):835-844. PMID: 35446370.
      Citations: 4     Fields:    Translation:Humans
    5. Beasley HK, Widatalla SE, Whalen DS, Williams SD, Korolkova OY, Namba C, Pratap S, Ochieng J, Sakwe AM. Identification of MAGEC2/CT10 as a High Calcium-Inducible Gene in Triple-Negative Breast Cancer. Front Endocrinol (Lausanne). 2022; 13:816598. PMID: 35355564.
      Citations:    Fields:    Translation:HumansCells
    6. Arun A, Rayford KJ, Cooley A, Rana T, Rachakonda G, Villalta F, Pratap S, Lima MF, Sheibani N, Nde PN. Thrombospondin-1 expression and modulation of Wnt and hippo signaling pathways during the early phase of Trypanosoma cruzi infection of heart endothelial cells. PLoS Negl Trop Dis. 2022 01; 16(1):e0010074. PMID: 34986160.
      Citations: 3     Fields:    Translation:AnimalsCells
    7. Kaddour H, Kopcho S, Lyu Y, Shouman N, Paromov V, Pratap S, Dash C, Kim EY, Martinson J, McKay H, Epeldegui M, Margolick JB, Stapleton JT, Okeoma CM. HIV-infection and cocaine use regulate semen extracellular vesicles proteome and miRNAome in a manner that mediates strategic monocyte haptotaxis governed by miR-128 network. Cell Mol Life Sci. 2021 Dec 22; 79(1):5. PMID: 34936021.
      Citations:    Fields:    Translation:HumansCells
    8. Tripathi A, Singha UK, Cooley A, Gillyard T, Krystofiak E, Pratap S, Davis J, Chaudhuri M. Trypanosoma brucei Tim50 Possesses PAP Activity and Plays a Critical Role in Cell Cycle Regulation and Parasite Infectivity. mBio. 2021 10 26; 12(5):e0159221. PMID: 34517757.
      Citations: 2     Fields:    Translation:AnimalsCells
    9. Rayford KJ, Cooley A, Rumph JT, Arun A, Rachakonda G, Villalta F, Lima MF, Pratap S, Misra S, Nde PN. piRNAs as Modulators of Disease Pathogenesis. Int J Mol Sci. 2021 Feb 27; 22(5). PMID: 33673453.
      Citations: 12     Fields:    Translation:HumansAnimals
    10. Myers JN, Harris KL, Rekhadevi PV, Pratap S, Ramesh A. Benzo(a)pyrene-induced cytotoxicity, cell proliferation, DNA damage, and altered gene expression profiles in HT-29 human colon cancer cells. Cell Biol Toxicol. 2021 12; 37(6):891-913. PMID: 33411230.
      Citations: 6     Fields:    Translation:HumansCells
    11. Rayford KJ, Cooley A, Arun A, Rachakonda G, Kleschenko Y, Villalta F, Pratap S, Lima MF, Nde PN. Trypanosoma cruzi Modulates PIWI-Interacting RNA Expression in Primary Human Cardiac Myocytes during the Early Phase of Infection. Int J Mol Sci. 2020 Dec 11; 21(24). PMID: 33322418.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    12. Arun A, Rayford KJ, Cooley A, Rachakonda G, Villalta F, Pratap S, Lima MF, Sheibani N, Nde PN. Thrombospondin-1 Plays an Essential Role in Yes-Associated Protein Nuclear Translocation during the Early Phase of Trypanosoma cruzi Infection in Heart Endothelial Cells. Int J Mol Sci. 2020 Jul 12; 21(14). PMID: 32664627.
      Citations: 5     Fields:    Translation:AnimalsCells
    13. Hall T, Jenkins CA, Hulgan T, Furukawa S, Turner M, Pratap S, Sterling TR, Tabatabai M, Berthaud V. Hepatitis C Coinfection and Mortality in People Living with HIV in Middle Tennessee. AIDS Res Hum Retroviruses. 2020 03; 36(3):193-199. PMID: 31789047.
      Citations: 1     Fields:    Translation:Humans
    14. Kaddour H, Lyu Y, Welch JL, Paromov V, Mandape SN, Sakhare SS, Pandhare J, Stapleton JT, Pratap S, Dash C, Okeoma CM. Proteomics Profiling of Autologous Blood and Semen Exosomes from HIV-infected and Uninfected Individuals Reveals Compositional and Functional Variabilities. Mol Cell Proteomics. 2020 01; 19(1):78-100. PMID: 31676584.
      Citations: 13     Fields:    Translation:HumansCells
    15. Tripathi A, Singha UK, Paromov V, Hill S, Pratap S, Rose K, Chaudhuri M. Erratum for Tripathi et al., "The Cross Talk between TbTim50 and PIP39, Two Aspartate-Based Protein Phosphatases, Maintains Cellular Homeostasis in Trypanosoma brucei". mSphere. 2019 Sep 04; 4(5). PMID: 31484745.
      Citations:    Fields:    
    16. Tripathi A, Singha UK, Paromov V, Hill S, Pratap S, Rose K, Chaudhuri M. The Cross Talk between TbTim50 and PIP39, Two Aspartate-Based Protein Phosphatases, Maintains Cellular Homeostasis in Trypanosoma brucei. mSphere. 2019 08 07; 4(4). PMID: 31391278.
      Citations: 4     Fields:    Translation:AnimalsCells
    17. Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR. Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility. Front Microbiol. 2018; 9:3220. PMID: 30666239.
    18. Suman S, Rachakonda G, Mandape SN, Sakhare SS, Villalta F, Pratap S, Lima MF, Nde PN. Phospho-proteomic analysis of primary human colon epithelial cells during the early Trypanosoma cruzi infection phase. PLoS Negl Trop Dis. 2018 09; 12(9):e0006792. PMID: 30222739.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    19. Walker MY, Pratap S, Southerland JH, Farmer-Dixon CM, Lakshmyya K, Gangula PR. Role of oral and gut microbiome in nitric oxide-mediated colon motility. Nitric Oxide. 2018 02 28; 73:81-88. PMID: 28602746.
      Citations: 26     Fields:    Translation:Humans
    20. Matthews QL, Farrow AL, Rachakonda G, Gu L, Nde P, Krendelchtchikov A, Pratap S, Sakhare SS, Sabbaj S, Lima MF, Villalta F. Epitope Capsid-Incorporation: New Effective Approach for Vaccine Development for Chagas Disease. Pathog Immun. 2016 Fall-Winter; 1(2):214-233. PMID: 27709126.
    21. Xie Y, Lu W, Liu S, Yang Q, Goodwin JS, Sathyanarayana SA, Pratap S, Chen Z. MMP7 interacts with ARF in nucleus to potentiate tumor microenvironments for prostate cancer progression in vivo. Oncotarget. 2016 Jul 26; 7(30):47609-47619. PMID: 27356744.
      Citations: 17     Fields:    Translation:HumansCells
    22. Udoko AN, Johnson CA, Dykan A, Rachakonda G, Villalta F, Mandape SN, Lima MF, Pratap S, Nde PN. Early Regulation of Profibrotic Genes in Primary Human Cardiac Myocytes by Trypanosoma cruzi. PLoS Negl Trop Dis. 2016 Jan; 10(1):e0003747. PMID: 26771187.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    23. Addai AB, Pandhare J, Paromov V, Mantri CK, Pratap S, Dash C. Cocaine modulates HIV-1 integration in primary CD4+ T cells: implications in HIV-1 pathogenesis in drug-abusing patients. J Leukoc Biol. 2015 Apr; 97(4):779-90. PMID: 25691383.
      Citations: 17     Fields:    Translation:HumansCells
    24. Mantri CK, Chen CH, Dong X, Goodwin JS, Pratap S, Paromov V, Xie H. Fimbriae-mediated outer membrane vesicle production and invasion of Porphyromonas gingivalis. Microbiologyopen. 2015 Feb; 4(1):53-65. PMID: 25524808.
      Citations: 37     Fields:    Translation:HumansCells
    25. Farrow AL, Rachakonda G, Gu L, Krendelchtchikova V, Nde PN, Pratap S, Lima MF, Villalta F, Matthews QL. Immunization with Hexon modified adenoviral vectors integrated with gp83 epitope provides protection against Trypanosoma cruzi infection. PLoS Negl Trop Dis. 2014 Aug; 8(8):e3089. PMID: 25144771.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    26. Goode G, Pratap S, Eltom SE. Depletion of the aryl hydrocarbon receptor in MDA-MB-231 human breast cancer cells altered the expression of genes in key regulatory pathways of cancer. PLoS One. 2014; 9(6):e100103. PMID: 24932473.
      Citations: 12     Fields:    Translation:HumansCells
    27. Chaudhuri S, Pratap S, Paromov V, Li Z, Mantri CK, Xie H. Identification of a diguanylate cyclase and its role in Porphyromonas gingivalis virulence. Infect Immun. 2014 Jul; 82(7):2728-35. PMID: 24733094.
      Citations: 9     Fields:    Translation:HumansCells
    28. Mandape SN, Marshall DR, Dent LL, Pratap S. Draft Genome Sequence of Multidrug-Resistant Acinetobacter baumannii Strain MMC4, Isolated from a Patient in Tennessee. Genome Announc. 2014 Feb 20; 2(1). PMID: 24558237.
    29. Johnson CA, Rachakonda G, Kleshchenko YY, Nde PN, Madison MN, Pratap S, Cardenas TC, Taylor C, Lima MF, Villalta F. Cellular response to Trypanosoma cruzi infection induces secretion of defensin a-1, which damages the flagellum, neutralizes trypanosome motility, and inhibits infection. Infect Immun. 2013 Nov; 81(11):4139-48. PMID: 23980110.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    30. Pratap S, Brown LE, Izban MG, Nowicki S, Nowicki BJ. Accurate preterm labor diagnosis using a CD55-TLR4 combination biomarker model. J Biomed Sci Eng. 2013 Mar; 6:253-257. PMID: 23667715.
    31. Nde PN, Lima MF, Johnson CA, Pratap S, Villalta F. Regulation and use of the extracellular matrix by Trypanosoma cruzi during early infection. Front Immunol. 2012; 3:337. PMID: 23133440.
      Citations: 22     Fields:    
    32. Watson K, Koumangoye R, Thompson P, Sakwe AM, Patel T, Pratap S, Ochieng J. Fetuin-A triggers the secretion of a novel set of exosomes in detached tumor cells that mediate their adhesion and spreading. FEBS Lett. 2012 Sep 21; 586(19):3458-63. PMID: 22980907.
      Citations: 22     Fields:    Translation:HumansCells
    33. Johnson CA, Kleshchenko YY, Ikejiani AO, Udoko AN, Cardenas TC, Pratap S, Duquette MA, Lima MF, Lawler J, Villalta F, Nde PN. Thrombospondin-1 interacts with Trypanosoma cruzi surface calreticulin to enhance cellular infection. PLoS One. 2012; 7(7):e40614. PMID: 22808206.
      Citations: 15     Fields:    Translation:AnimalsCells
    34. Jules GE, Pratap S, Ramesh A, Hood DB. In utero exposure to benzo(a)pyrene predisposes offspring to cardiovascular dysfunction in later-life. Toxicology. 2012 May 16; 295(1-3):56-67. PMID: 22374506.
      Citations: 19     Fields:    Translation:AnimalsCells
    35. Dey A, Mantri CK, Pandhare-Dash J, Liu B, Pratap S, Dash C. Downregulation of APOBEC3G by xenotropic murine leukemia-virus related virus (XMRV) in prostate cancer cells. Virol J. 2011 Dec 12; 8:531. PMID: 22152111.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    36. Pawelczyk E, Nowicki BJ, Izban MG, Pratap S, Sashti NA, Sanderson M, Nowicki S. Spontaneous preterm labor is associated with an increase in the proinflammatory signal transducer TLR4 receptor on maternal blood monocytes. BMC Pregnancy Childbirth. 2010 Oct 21; 10:66. PMID: 20964862.
      Citations: 18     Fields:    Translation:HumansCells
    37. Dent LL, Marshall DR, Pratap S, Hulette RB. Multidrug resistant Acinetobacter baumannii: a descriptive study in a city hospital. BMC Infect Dis. 2010 Jul 07; 10:196. PMID: 20609238.
      Citations: 53     Fields:    Translation:HumansCells
    38. Nde PN, Johnson CA, Pratap S, Cardenas TC, Kleshchenko YY, Furtak VA, Simmons KJ, Lima MF, Villalta F. Gene network analysis during early infection of human coronary artery smooth muscle cells by Trypanosoma cruzi and Its gp83 ligand. Chem Biodivers. 2010 May; 7(5):1051-64. PMID: 20491065.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    39. Cardenas TC, Johnson CA, Pratap S, Nde PN, Furtak V, Kleshchenko YY, Lima MF, Villalta F. REGULATION of the EXTRACELLULAR MATRIX INTERACTOME by Trypanosoma cruzi. Open Parasitol J. 2010; 4:72-76. PMID: 21499436.
    40. Nowicki S, Izban MG, Pawelczyk E, Agboto VK, Pratap S, Olson G, Nowicki B. Preterm labor: CD55 in maternal blood leukocytes. Am J Reprod Immunol. 2009 May; 61(5):360-7. PMID: 19341386.
      Citations: 9     Fields:    Translation:HumansCells
    41. Ochieng J, Pratap S, Khatua AK, Sakwe AM. Anchorage-independent growth of breast carcinoma cells is mediated by serum exosomes. Exp Cell Res. 2009 Jul 01; 315(11):1875-88. PMID: 19327352.
      Citations: 44     Fields:    Translation:HumansCells
    42. Augustine SA, Kleshchenko YY, Nde PN, Pratap S, Ager EA, Burns JM, Lima MF, Villalta F. Molecular cloning of a Trypanosoma cruzi cell surface casein kinase II substrate, Tc-1, involved in cellular infection. Infect Immun. 2006 Jul; 74(7):3922-9. PMID: 16790765.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    43. Nde PN, Simmons KJ, Kleshchenko YY, Pratap S, Lima MF, Villalta F. Silencing of the laminin gamma-1 gene blocks Trypanosoma cruzi infection. Infect Immun. 2006 Mar; 74(3):1643-8. PMID: 16495535.
      Citations: 25     Fields:    Translation:HumansAnimals
    44. Boczko EM, Cooper TG, Gedeon T, Mischaikow K, Murdock DG, Pratap S, Wells KS. Structure theorems and the dynamics of nitrogen catabolite repression in yeast. Proc Natl Acad Sci U S A. 2005 Apr 19; 102(16):5647-52. PMID: 15814615.
      Citations: 11     Fields:    Translation:Animals
    45. Villalta F, Zhang Y, Bibb KE, Pratap S, Burns JM, Lima MF. Signal transduction in human macrophages by gp83 ligand of Trypanosoma cruzi: trypomastigote gp83 ligand up-regulates trypanosome entry through protein kinase C activation. Mol Cell Biol Res Commun. 1999 Jul; 2(1):64-70. PMID: 10527894.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
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