Thomas Jefferson University

Ramkrishna Mitra

TitleAsst Professor
InstitutionThomas Jefferson University
DepartmentPharmacology and Exp Therapeut
Address130 S. 9th Street
Philadelphia PA 19107
Phone215-503-7247
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    Collapse Biography 
    Collapse education and training
    Jadavpur University (Research work done at Indian Statistical Institute), Kolkata, IndiaPh.D.2011 Engineering
    Stanford University, CA, USAPost-doc2012 Bioinformatics
    Vanderbilt University, TN, USAPost-doc2016 Bioinformatics

    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.
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    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. Ramteke P, Watson B, Toci M, Tran VA, Johnston S, Tsingas M, Barve RA, Mitra R, Loeser RF, Collins JA, Risbud MV. SIRT6 loss causes intervertebral disc degeneration in mice by promoting senescence and SASP status. bioRxiv. 2024 Sep 09. PMID: 39314282.
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    2. Naranjo NM, Kennedy A, Testa A, Verrillo CE, Altieri AD, Kean R, Hooper DC, Yu J, Zhao J, Abinader O, Pickles MW, Hawkins A, Kelly WK, Mitra R, Languino LR. Neuroendocrine gene subsets are uniquely dysregulated in prostate adenocarcinoma. Cancer Biol Ther. 2024 Dec 31; 25(1):2364433. PMID: 38926911.
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    3. Adams CM, McBride A, Michener P, Shkundina I, Mitra R, An HH, Porcu P, Eischen CM. Identifying Targetable Vulnerabilities to Circumvent or Overcome Venetoclax Resistance in Diffuse Large B-Cell Lymphoma. Cancers (Basel). 2024 Jun 03; 16(11). PMID: 38893249.
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    4. Calbert ML, Chandramouly G, Adams CM, Saez-Ayala M, Kent T, Tyagi M, Ayyadevara VSSA, Wang Y, Krais JJ, Gordon J, Atkins J, Toma MM, Betzi S, Boghossian AS, Rees MG, Ronan MM, Roth JA, Goldman AR, Gorman N, Mitra R, Childers WE, Gra?a X, Skorski T, Johnson N, Hurtz C, Morelli X, Eischen CM, Pomerantz RT. 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress. Mol Cancer Ther. 2023 Dec 08. PMID: 38064712.
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    5. Mitra R, Adams CM, Eischen CM. Decoding the lncRNAome Across Diverse Cellular Stresses Reveals Core p53-effector Pan-cancer Suppressive lncRNAs. Cancer Res Commun. 2023 05; 3(5):842-859. PMID: 37377895.
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    6. Adams CM, Mitra R, Xiao Y, Michener P, Palazzo J, Chao A, Gour J, Cassel J, Salvino JM, Eischen CM. Targeted MDM2 degradation reveals a new vulnerability for p53 inactivated triple negative breast cancer. Cancer Discov. 2023 Feb 03. PMID: 36734633.
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    7. Liu H, Yuan M, Mitra R, Zhou X, Long M, Lei W, Zhou S, Huang YE, Hou F, Eischen CM, Jiang W. CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research. Genome Med. 2022 10 13; 14(1):118. PMID: 36229842.
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    8. Haizhou Liu, Mengqin Yuan, Ramkrishna Mitra (co-first author), Xu Zhou, Min Long, Wanyue Lei, Shunheng Zhou, Yu-e Huang, Fei Hou, Christine M. Eischen & Wei Jiang. CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research. Genome Medicine. 2022; 14. View Publication.
    9. Mitra R, Adams CM, Eischen CM. Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs. Elife. 2022 06 13; 11. PMID: 35695878.
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    10. Mitra R, Adams CM, Eischen CM. Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs. eLife. 2022; 11::e77357. View Publication.
    11. Yousef M, Goy G, Mitra R, Eischen CM, Jabeer A, Bakir-Gungor B. miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking. PeerJ. 2021; 9:e11458. PMID: 34055490.
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    12. Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterle M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers (Basel). 2020 Sep 10; 12(9). PMID: 32927769.
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    13. Mitra R, Adams CM, Jiang W, Greenawalt E, Eischen CM. Pan-cancer analysis reveals cooperativity of both strands of microRNA that regulate tumorigenesis and patient survival. Nat Commun. 2020 Feb 20; 11(1):968. PMID: 32080184.
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    14. Qin G, Mallik S, Mitra R, Li A, Jia P, Eischen CM, Zhao Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep. 2020 Jan 21; 10(1):852. PMID: 31965022.
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    15. Adams CM, Mitra R, Vogel AN, Liu J, Gong JZ, Eischen CM. Targeting BCL-W and BCL-XL as a therapeutic strategy for Hodgkin lymphoma. Leukemia. 2019 Oct 21. PMID: 31636344.
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    16. Stier MT, Mitra R, Nyhoff LE, Goleniewska K, Zhang J, Puccetti MV, Casanova HC, Seegmiller AC, Newcomb DC, Kendall PL, Eischen CM, Peebles RS. IL-33 Is a Cell-Intrinsic Regulator of Fitness during Early B Cell Development. J Immunol. 2019 Aug 07. PMID: 31391233.
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    17. Greenawalt EJ, Edmonds MD, Jain N, Adams CM, Mitra R, Eischen CM. Targeting of SGK1 by miR-576-3p inhibits lung adenocarcinoma migration and invasion. Mol Cancer Res. 2018 Sep 26. PMID: 30257988.
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    18. Mitra R, Chen X, Greenawalt EJ, Maulik U, Jiang W, Zhao Z, Eischen CM. Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. Nat Commun. 2017 Nov 17; 8(1):1604. PMID: 29150601.
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    19. Adams CM, Mitra R, Gong JZ, Eischen CM. Non-Hodgkin and Hodgkin Lymphomas Select for Overexpression of BCLW. Clin Cancer Res. 2017 Nov 15; 23(22):7119-7129. PMID: 28855351.
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    20. Feeley KP, Adams CM, Mitra R, Eischen CM. Mdm2 Is Required for Survival and Growth of p53-Deficient Cancer Cells. Cancer Res. 2017 Jun 02. PMID: 28576884.
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    21. Adams CM, Kim AS, Mitra R, Choi JK, Gong JZ, Eischen CM. BCL-W has a fundamental role in B cell survival and lymphomagenesis. J Clin Invest. 2017 Feb 01; 127(2):635-650. PMID: 28094768.
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    22. Grieb BC, Boyd K, Mitra R, Eischen CM. Haploinsufficiency of the Myc regulator Mtbp extends survival and delays tumor development in aging mice. Aging (Albany NY). 2016 Oct 30; 8(10):2590-2602. PMID: 27803394.
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    23. Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z. The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development. Mol Cancer Ther. 2016 Dec; 15(12):2977-2986. PMID: 27784795.
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    24. Liu S, Yin F, Zhao M, Zhou C, Ren J, Huang Q, Zhao Z, Mitra R, Fan W, Fan M. The homing and inhibiting effects of hNSCs-BMP4 on human glioma stem cells. Oncotarget. 2016 Apr 05; 7(14):17920-31. PMID: 26908439; PMCID: PMC4951260.
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    25. Edmonds MD, Boyd KL, Moyo T, Mitra R, Duszynski R, Arrate MP, Chen X, Zhao Z, Blackwell TS, Andl T, Eischen CM. MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer. J Clin Invest. 2016 Jan; 126(1):349-64. PMID: 26657862.
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    26. Jiang W, Mitra R, Lin CC, Wang Q, Cheng F, Zhao Z. Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. Brief Bioinform. 2016 11; 17(6):996-1008. PMID: 26655252.
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    27. Lin CC, Mitra R, Cheng F, Zhao Z. A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules. Mol Biosyst. 2015 Dec; 11(12):3244-52. PMID: 26448606; PMCID: PMC4643368.
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    28. Zhao M, Kim P, Mitra R, Zhao J, Zhao Z. TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res. 2016 Jan 04; 44(D1):D1023-31. PMID: 26590405; PMCID: PMC4702895.
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    29. Lin CC, Jiang W, Mitra R, Cheng F, Yu H, Zhao Z. Regulation rewiring analysis reveals mutual regulation between STAT1 and miR-155-5p in tumor immunosurveillance in seven major cancers. Sci Rep. 2015 Jul 09; 5:12063. PMID: 26156524; PMCID: PMC4496795.
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    30. Mitra R, Sun J, Zhao Z. microRNA regulation in cancer: One arm or two arms? Int J Cancer. 2015 Sep 15; 137(6):1516-8. PMID: 25758934; PMCID: PMC4497856.
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    31. Mitra R, Lin CC, Eischen CM, Bandyopadhyay S, Zhao Z. Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study. RNA. 2015 Jun; 21(6):1055-65. PMID: 25852169.
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    32. Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Sci Rep. 2015 Jan 23; 5:8004. PMID: 25614300; PMCID: PMC4648438.
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    33. Mitra R, Zhao Z. The oncogenic and prognostic potential of eight microRNAs identified by a synergetic regulatory network approach in lung cancer. Int J Comput Biol Drug Des. 2014; 7(4):384-93. PMID: 25539849; PMCID: PMC4779644.
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    34. Yu H, Mitra R, Yang J, Li Y, Zhao Z. Algorithms for network-based identification of differential regulators from transcriptome data: a systematic evaluation. Sci China Life Sci. 2014 Nov; 57(11):1090-102. PMID: 25326829; PMCID: PMC4779643.
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    35. Lin CC, Mitra R, Zhao Z. A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. PLoS One. 2014; 9(7):e103142. PMID: 25054916; PMCID: PMC4108425.
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    36. Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z. Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. RNA. 2014 Sep; 20(9):1356-68. PMID: 25024357.
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    37. Mitra R, Bandyopadhyay S. MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method. PLOS ONE. 2011; 6(9):e2458. View Publication.
    38. Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ. Development of the human cancer microRNA network. Silence. 2010 Feb 02; 1(1):6. PMID: 20226080; PMCID: PMC2835996.
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    39. Mitra R, Bandyopadhyay S, Maulik U, Zhang MQ. SFSSClass: an integrated approach for miRNA based tumor classification. BMC Bioinformatics. 2010 Jan 18; 11 Suppl 1:S22. PMID: 20122194; PMCID: PMC3009493.
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    40. Bandyopadhyay S, Mitra R. TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics Oxford Journal. 2009; 25(20):2625–2631. View Publication.
    41. Bandyopadhyay S, Mitra R. A parallel pairwise local sequence alignment algorithm. IEEE Trans Nanobioscience. 2009; 8(2):139-46. View Publication.
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