Zhumur Ghosh

Zhumur Ghosh
Professor

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Previous appointments:

Nov 2008- March 2009 Postdoc at Indian Association for the Cultivation of Science

March 2009- June 2010 Postdoc at Stanford University School of Medicine

June 2010 - Nov 2010    Assistant Professor, Indian Institute of Technology (IIT) Guwahati, India

Nov 2010-Jan 2014        Faculty Fellow, Bioinformatics Centre, Bose Institute

Jan2014-July 2018       Assistant Professor, Bioinformatics Centre, Bose Institute

July 2018-present        Associate Professor, Division of Bioinformatics, Bose Institute

Research interests:

Regulatory RNA and stem cells

Contact:

Address: Biological Sciences
Unified Academic Campus
Bose Institute
EN-80, Sector V
Bidhan Nagar
Kolkata - 700 091, India
E-Mail: zhumur[at]jcbose.ac.in
Phone: +91-33-25693220

Research:

Ghosh lab studies the role of regulatory RNAs towards modulating cancer stem cells. We are also interested to look into the role of these RNAs  in modulating cellular reprogramming towards shaping mammalian development. We use a combination of in silico and wet bench techniques to better understand the role of regulatory RNAs in stem cell biology. We are presently focused on miRNAs, piRNAs and long noncoding RNAs.

For more details please visit my home page http://bicresources.jcbose.ac.in/zhumur/lab/






Publications:

  1. Chakraborty S and Ghosh Z. A systemic insight into astrocytoma biology across different grades. J Cell Physiol 2018 Aug 26 https://doi.org/10.1002/jcp.27193 (doi: 10.1002/jcp.27193).
  2. Maji RK, Khatua S, Ghosh Z. A supervised ensemble approach for sensitive microRNA target prediction. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul 20. doi: 10.1109/TCBB.2018.2858252. PMID: 30040648
  3. Sen K, Bhattacharyya D, Sarkar A, Das J, Maji N, Basu M, Ghosh Z, Ghosh TC. Exploring the major cross-talking edges of competitive endogenous RNA networks in human Chronic and Acute Myeloid Leukemia. Biochim Biophys Acta. 2018 Sep;1862(9):1883-1892. doi: 10.1016/j.bbagen.2018.06.002. Epub 2018 Jun 15. PMID: 29902552
  4. Parida S, Chakraborty S, Maji RK, Ghosh Z. Elucidating the gene regulatory networks modulating cancer stem cells and non-stem cancer cells in high grade serous ovarian cancer. Genomics. 2018 (https://doi.org/10.1016/j.ygeno.2018.01.006)

5.    Datta C, Subuddhi A, Kumar M, Lepcha TT, Chakraborty S, Jana K, Ghosh Z, Mukhopadhyay AK, Basu J, Kundu M. Genome-wide mRNA-miRNA profiling uncovers a role of the microRNA miR-29b-1-5p/PHLPP1 signalling pathway in Helicobacter pylori-driven matrix metalloproteinase production in gastric epithelial cells.  Cell Microbiol. 2018 Sep;20(9):e12859. doi: 10.1111/cmi.12859. Epub 2018 May 25.

6.    Kaur H, Sarmah D, Saraf J, Vats K, Kalia K, Borah A, Yavagal DR, Dave KR, Ghosh Z, Bhattacharya P. Noncoding RNAs in ischemic stroke: time to translate. Ann N Y Acad Sci. 2018 Jun;1421(1):19-36. doi: 10.1111/nyas.13612. Epub 2018 Apr 23. Review.

7.    Parida PK, Mahata B, Santra A, Chakraborty S, Ghosh Z, Raha S, Misra AK, Biswas K, Jana K. Inhibition of cancer progression by a novel trans-stilbene derivative through disruption of microtubule dynamics, driving G2/M arrest, and p53-dependent apoptosis. Cell Death Dis. 2018 May1;9(5):448. doi: 10.1038/s41419-018-0476-2. PMID: 29670107

8.    Sarmah D, Agrawal V, Rane P, Bhute S, Watanabe M, Kalia K, Ghosh Z, Dave KR, Yavagal DR, Bhattacharya P. Mesenchymal Stem Cell Therapy in Ischemic Stroke: A Meta-analysis of Preclinical Studies. Clin Pharmacol Ther. 2018 Jun;103(6):990-998. doi: 10.1002/cpt.927. Epub 2017 Dec 14. Review. PMID:  29090465

  1. Deb A, Sarkar A and Ghosh Z. Dissecting the variation in transcriptional circuits between naive and primed pluripotent states. FEBS Lett. 2017 (DOI: 10.1002/1873-3468.12732) (IF 3.623)
  2. Sahu SK, Kumar M, Chakraborty S, Banerjee SK, Kumar R, Gupta P, Jana K, Gupta UD, Ghosh Z, Kundu M, Basu J. MicroRNA 26a (miR-26a)/KLF4 and CREB-C/EBPβ regulate innate immune signaling, the polarization of macrophages and the trafficking of Mycobacterium tuberculosis to lysosomes during infection. PLoS Pathog. 2017 May 30; 13(5):e1006410. doi: 10.1371/journal.ppat.1006410. PMID:    28558034
  3. Sarkar D, Maji R, Dey S, Sarkar A, Ghosh Z and Kundu P. Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease. DNA Research 2017 (Accepted) (IF 5.267).   
  4. Roy J, Sarkar A, Parida S, Ghozh Z, Mallick B. Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis. Mol Biosyst. 2017. DOI: 10.1039/C6MB00699J. (IF 2.86)

13. Sen K, Sarkar A, Maji RK, Ghosh Z, Gupta S, Ghosh TC. Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line. Mol Biosyst. 2016;12(12):3633-3642. (IF 2.86)

14. Kundu M, Mahata B, Banerjee A, Chakraborty S, Debnath S, Ray SS, Ghosh Z, Biswas K. Ganglioside GM2 mediates migration of tumor cells by interacting with integrin and modulating the downstream signaling pathway. Biochim Biophys Acta. 2016; S0167-4889(16)30085-4. PMID: 27066976. (IF 5.128)

  1. Liu J, Masurekar A, Johnson S, Chakraborty S, Griffiths J, Smith D, Alexander S, Dempsey C, Parker C, Harrison S, Li Y, Miller C, Di Y, Ghosh Z, Krishnan S, Saha V. Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia. Oncotarget. 2015; 6(40):43048-64. PMID: 26474278. (IF 6.359)
  2. Halder P, Kumar R, Jana K, Chakraborty S, Ghosh Z, Kundu M, Basu J (2015). Gene expression profiling of Mycobacterium tuberculosis Lipoarabinomannan-treated macrophages: A role of the Bcl-2 family member A1 in inhibition of apoptosis in mycobacteria-infected macrophages. IUBMB Life. (doi: 10.1002/iub.1430) (IF 3.143)
  3. Kumar M, Sahu SK, Kumar R, Subuddhi A, Maji RK, Jana K, Gupta P, Raffetseder J, Lerm M, Ghosh Z, van Loo G, Beyaert R, Gupta UD, Kundu M, Basu J (2015). MicroRNA let-7 modulates the immune response to Mycobacterium tuberculosis infection via control of A20, an inhibitor of the NF-κB pathway. Cell Host Microbe 17(3):345-56 (IF 12.194)
  4. Chakraborty S, Deb A, Maji R K, Saha S and Ghosh Z (2014). LncRBase: An Enriched Resource for lncRNA Information. PLoS One (DOI: 10.1371/journal.pone.0108010) (IF  3.5)
  5. Ghosh Z and Mallick B (2014). Cancer stem cells and regulatory RNAs crosstalk: Fostering possibilities for cancer therapies. BioScience 64(12):1138-1149. [Advance Access: doi:10.1093/biosci/biu149] (IF 5.43)
  6. Sarkar A, Maji RK, Saha S and Ghosh Z (2014). piRNAQuest: searching the piRNAome for silencers, BMC Genomics 15(1):555. [Epub ahead of print]. (IF 4.04)
  7. Maji RK, Sarkar A, Khatua S, Dasgupta S and Ghosh Z (2014). PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis. BMC Bioinformatics 15:167. (IF 2.67)
  8. Kumar R, Halder P, Sahu SK, Kumar M, Kumari M, Jana K, Ghosh Z, Sharma P, Kundu M, Basu J (2012). Identification of a novel role of ESAT-6-dependent miR-155 induction during infection of macrophages with Mycobacterium tuberculosis. Cell Microbiol. 14(10):1620-1631. (IF: 5.45)
  9. Hu S, Wilson KD, Ghosh Z, Han L, Wang Y, Lan F, Ransohoff KJ, Wu JC (2013). MicroRNA-302 increases reprogramming efficiency via repression of NR2F2. Stem Cells. 31(2):259-268. (IF: 7.78)
  10. Mallick B, Ghosh Z (2012) Probing evolutionary biography of microRNAs and associated factors. Curr Genomics. 13(2):144-152.
  11. Reddy S, Zhao M, Hu DQ, Fajardo G, Hu S, Ghosh Z, Rajagopalan V, Wu JC, Bernstein D (2012). Dynamic microRNA expression during the transition from right ventricular hypertrophy to failure. Physiol Genomics. 44(10):562-575. (IF: 2.73)
  12. Mallick B, Ghosh Z (2011). A complex crosstalk between polymorphic microRNA target sites and AD prognosis. RNA Biol. 8(4):665-673. (IF: 5.56).
  13. Ghosh Z, Huang M, Hu S, Wilson KD, Dey D, Wu JC (2011). Dissecting the oncogenic and tumorigenic potential of differentiated human induced pluripotent stem cells and human embryonic stem cells. Cancer Res. 71(14):5030-9. (IF: 7.85)
  14. Pearl JI, Leveson-Gower DB, Lee A, Sun N, Ghosh Z, Negrin RS, Davis MM, Wu JC (2011) Inducing immunotolerance to pluripotent stem cells for long-term engraftment. Cell Stem Cell 8 (3):309-317. (IF: 25.421).
  15. Li Z, Hu S, Ghosh Z, Han Z, Wu JC (2011). Functional comparison and expression profiling of human induced pluripotent stem cell- and embryonic stem cell-derived endothelial cells. Stem Cells Dev. 2011 Jan 14. [Epub ahead of print] PMID: 21235328. (IF: 4.146).
  16. Mallick B, Chakrabarti J, Ghosh Z (2011) microRNA reins in embryonic and cancer stem cells. RNA Biol. 8(3):415-426. (IF: 5.56).
  17. Hu S, Huang M, Li Z, Jia F, Ghosh Z, Lijkwan MA, Fasanaro P, Sun N, Wang X, Martelli F, Robbins RC, Wu JC (2010) MicroRNA-210 as a novel therapy for treatment of ischemic heart disease. Circulation 122(11 Suppl): S124-S31. (IF: 14.81).
  18. Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC (2010) Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Circ Cardiovasc Genet 3(5): 426-435.
  19. Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC (2010) Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PLoS One 5(2): e8975. (IF: 4.35).
  20. Ghosh Z, Mallick B, Gautheret D, Malhotra P, Sachidanandam R (2009) Regulatory RNomics and gene expression. J Biomed Biotechnol: 691286. [Editorial]
  21. Ghosh Z, Mallick B, Chakrabarti J (2009) MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells. PLoS One 4(11): e7837. (IF: 4.35).
  22. Ghosh Z, Mallick B, Chakrabarti J (2009) Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res. 37(4): 1035-48. (IF: 8.026).
  23. Mallick B, Ghosh Z, Chakrabarti J (2008) Structural determinants characteristic to AARS subclasses and tRNA-splicing endonuclease in eukaryotes. J Biomol Struct Dyn. 26(2): 223-34.
  24. Ghosh Z, Mallick B, Chakrabarti J (2008) MicroRNA switches in Trypanosoma brucei. Biochem Biophys Res Commun. 372(3): 459-463.  [Faculty 1000 Biology recommended]. (IF: 2.54).
  25. Koehrer C, Srinivasan G, Mandal D, Mallick B, Ghosh Z, Chakrabarti J, Rajbhandary UL (2008) Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. RNA. 14(1): 117-126. [Appeared on Cover page]. (IF: 5.19).
  26. Ghosh Z, Chakrabarti J, Mallick B (2007) miRNomics-The bioinformatics of microRNA genes. Biochem Biophys Res Commun. 363(1): 6-11. (IF: 2.54).
  27.  Mallick B, Chakrabarti J, Sahoo S, Ghosh Z, Das S (2005) Identity elements of archaeal tRNA. DNA Res. 12(4): 235-246. (IF: 4.91).
  28. Ghosh Z, Chakrabarti J, Mallick B, Das S, Sahoo S, Sethi HS (2006) tRNA-isoleucine-tryptophan composite gene. Biochem Biophys Res Commun. 339(1): 37-40. (IF: 2.54).
  29. Das S, Chakrabarti J, Ghosh Z, Sahoo S, Mallick B (2005) A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the ‘codon impact parameter’. J Biosci. 30(5): 699-709. (IF: 1.70).


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Recognition:

  • Associate Fellow, Indian Academy of Science, 2011-2014
  • Member of the National Academy of Science, 2017
  • SERB Woman Excellence Award, 2018
  • NASI Scopus Young Scientists Award, 2018

Teaching:

Students:

Image Name Designation Department Campus Contact number Email
profile image Gourab Das Senior Research Fellow Bioinformatics Centre Centenary gourab4gd@gmail.com
profile image Pritha Sengupta Junior Research Fellow Bioinformatics Centre Unified prithseng@gmail.com

Former:

Former lab members:

Sohini Chakraborty

Arijita Sarkar

Ranjan Kumar Maji

Aritra Deb



Group News:

Ghosh lab will be recruiting JRFs for an interdisciplinary project. Please check the link below for details:

http://bicresources.jcbose.ac.in/zhumur/lab/join_us.html