Research Publications
2024
• Mukherjee A, Verma A, Das T, Ghosh B, Ghosh Z. Circulating microRNAs in Body Fluid: "Fingerprint" RNA Snippets Deeply Impact Reproductive Biology. Reprod Sci. 2024 Dec 10. doi: 10.1007/s43032-024-01753-y. Epub ahead of print. PMID: 39658771. (IF:2.6)
• Chakrabarty, J., Parveen, R., Datta, S., Ghosh, B., Roy, V., Ghosh, Z., & Chaudhuri, S. (2024). ULTRAPETALA 1 Regulates The Growth and Development of Rice Plants to Promote Resilience to Salinity Stress. Environmental and Experimental Botany, 105780. (IF:5.7)
• Debsharma, S., Pramanik, S., Bindu, S., Mazumder, S., Das, T., Pal, U., Saha, D., De, R., Nag, S., Banerjee, C., Maiti, N.C., Ghosh, Z., Bandyopadhyay, U. 2024. NSAID targets SIRT3 to trigger mitochondrial dysfunction and gastric cancer cell death. Iscience 27, no. 4 (2024).(IF:5.8). https://doi.org/10.1016/j.isci.2024.109384
• Das, G, Das, T, Parida, S, Ghosh, Z. LncRTPred: Predicting RNA–RNA mode of interaction mediated by lncRNA. IUBMB Life. 2024.(IF:4.6). https://doi.org/10.1002/iub.2778
2023
• Birari, P., Mal, S., Majumder, D., Sharma, A.K., Kumar, M., Das, T., Ghosh, Z., Jana, K., Gupta, U.D., Kundu, M. and Basu, J., Nur77 influences immunometabolism to regulate the release of proinflammatory cytokines and the formation of lipid bodies during Mycobacterium tuberculosis infection of macrophages. Pathogens and disease, p.ftad033.(IF:3.3). https://doi.org/10.1093/femspd/ftad033
• Ghosh, B., Das, T., Das, G., Chowdhury, N., Bagchi, A., & Ghosh, Z. (2023). Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection. Current Bioinformatics, 18(9), 760-773. (IF:4).
• Gupta, P., Das, G., Chattopadhyay, T., Ghosh, Z., & Mallick, B. TarpiD, a database of putative and validated targets of piRNAs. Molecular Omics.(IF: 2.9). PMID: 37427797.
• Sarkar, A., Das, T., Das, G., & Ghosh, Z. MicroRNA mediated gene regulatory circuits leads to machine learning based preliminary detection of acute myeloid leukemia. Computational biology and chemistry, 104, 107859.(IF: 3.1). PMID: 37031648.
• Debsharma S, Pramanik S, Bindu S, Mazumder S, Das T, Saha D, De R, Nag S, Banerjee C, Siddiqui AA, Ghosh Z, Bandyopadhyay U. Honokiol, an inducer of sirtuin-3, protects against non-steroidal anti-inflammatory drug-induced gastric mucosal mitochondrial pathology, apoptosis and inflammatory tissue injury. Br J Pharmacol. 2023 Mar 13. doi: 10.1111/bph.16070. Epub ahead of print.(IF: 7.3). PMID: 36914615.
2022
• Acharya U, Das T, Ghosh Z, Ghosh A. Defense surveillance system at the interface: response of rice towards Rhizoctonia solani during sheath blight infection. Mol Plant Microbe Interact. 2022 Aug 23. doi: 10.1094/MPMI-07-22-0153-R. Epub ahead of print. (IF: 4.171). PMID: 36000178.
• Ghosh B, Sarkar A, Mondal S, Bhattacharya N, Khatua S, Ghosh Z. piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. RNA Biol. 2021 Dec 29:1-14. doi: 10.1080/15476286.2021.2010960. Epub ahead of print. (IF: 4.652). PMID: 34965192.
• Debnath, S., Sarkar, A., Mukherjee, D.D., Ray, S., Mahata, B., Mahata, T., Parida, P.K., Das, T., Mukhopadhyay, R., Ghosh, Z. and Biswas, K., 2022. Eriodictyol mediated selective targeting of the TNFR1/FADD/TRADD axis in cancer cells induce apoptosis and inhibit tumor progression and metastasis. Translational Oncology, 21, pp.101433-101433. (IF: 4.243). PMID: 35462210.
• Dey, S., Sarkar, A., Chowdhury, S., Singh, R., Mukherjee, A., Ghosh Z. and Kundu, P., 2022. Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato. Plant Molecular Biology. (IF: 4.076). PMID: 35499677.
2021
• Ganguly P, Roy D, Das T, Kundu A, Ghosh Z, Cartieaux F, DasGupta M. The natural antisense transcript DONE40 derived from the lncRNA ENOD40 locus interacts with SET domain protein ASHR3 during inception of symbiosis in Arachis hypogaea. Mol Plant Microbe Interact. 2021 May 2. doi: 10.1094/MPMI-12-20-0357-R. Epub ahead of print. (IF: 3.696), PMID: 33934615.
• Das, G., Das, T., Chowdhury, N., Chatterjee, D., Bagchi, A. & Ghosh, Z. (2021) Repurposed drugs and nutraceuticals targeting envelope protein: A possible therapeutic strategy against COVID-19, Genomics. (IF: 5.736). PMID: 33189776.
• Das, T., Deb, A., Parida, S., Mondal, S., Khatua, S. & Ghosh, Z. (2021) LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients, RNA biology, 1-16. (IF: 4.652). PMID: 33112702 .
2020
• Pal, S., Mondal, S., Das, G., Khatua, S. & Ghosh, Z. (2020) Big data in biology: The hope and present-day challenges in it, Gene Reports. 21, 100869.(IF: 0.61).
• Kumar, M., Majumder, D., Mal, S., Chakraborty, S., Gupta, P., Jana, K., Gupta, U. D., Ghosh, Z., Kundu, M. & Basu, J. (2020) Activating transcription factor 3 modulates the macrophage immune response to Mycobacterium tuberculosis infection via reciprocal regulation of inflammatory genes and lipid body formation, Cellular microbiology. 22, e13142. (IF: 4.060). PMID: 31709711.
• Subuddhi, A., Kumar, M., Majumder, D., Sarkar, A., Ghosh, Z., Vasudevan, M., Kundu, M. & Basu, J. (2020) Unraveling the role of H3K4 trimethylation and lncRNA HOTAIR in SATB1 and DUSP4-dependent survival of virulent Mycobacterium tuberculosis in macrophages, Tuberculosis. 120, 101897. (IF: 2.576) .PMID: 32090865
• Banerjee, K., Jana, T., Ghosh, Z. & Saha, S. (2020) PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines, Journal of biosciences. 45. (IF 1.720). PMID:32345779
2019
• Mondal S., Maji R. K., Ghosh Z and Khatua S (2019). “ParStream-seq: An improved method of handling next generation sequence data.” Genomics 111(6): 1641-1650. (IF 7.890). PMID: 30448525
• Chakraborty S. and Ghosh Z (2019). “A systemic insight into astrocytoma biology across different grades.” J Cell Physiol 234(4): 4243-4255. (IF 4.020). PMID: 30146735
• Parida S., Chakraborty S, Maji R K and Ghosh Z (2019). “Elucidating the gene regulatory networks modulating cancer stem cells and non-stem cancer cells in high grade serous ovarian cancer.” Genomics 111(1): 103-113. (IF 7.890). PMID: 29355597
2018
• Sen K., Bhattacharyya D, Sarkar A, J. Das, Maji N, Basu M, Ghosh Z and Ghosh T C (2018). “Exploring the major cross-talking edges of competitive endogenous RNA networks in human Chronic and Acute Myeloid Leukemia.” Biochim Biophys Acta Gen Subj 1862(9): 1883-1892. (IF 4.008). PMID: 29902552
• Datta C, Subuddhi A, Kumar M, Lepcha T T, Chakraborty S, Jana K, Ghosh Z, A. K. Mukhopadhyay, Basu J and Kundu M (2018). “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 20(9): e12859. (IF 4.228). PMID: 29749704
• Maji R K., Khatua S and Ghosh Z (2018). “A supervised ensemble approach for sensitive microRNA target prediction.” IEEE/ACM Trans Comput Biol Bioinform. (IF 2.850). PMID: 30040648
• Sarmah D., Agrawal V, Rane P, Bhute S, Watanabe M, Kalia K, Ghosh Z, K. R. Dave, D. R. Yavagal and P. Bhattacharya (2018). “Mesenchymal Stem Cell Therapy in Ischemic Stroke: A Meta-analysis of Preclinical Studies.” Clin Pharmacol Ther 103(6): 990-998. (IF 6.565). PMID: 29090465
• Parida P K, Mahata B, Santra A, Chakraborty S, Ghosh Z, Raha S, Misra A K, Biswas K and Jana K (2018). “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 9(5): 448. (IF 5.910). PMID: 29670107
2017
• Deb A, Sarkar A and Ghosh Z (2017). “Dissecting the variation in transcriptional circuits between naive and primed pluripotent states.” FEBS Lett 591(15): 2362-2375. (IF 6.750). PMID: 28649717
• Sarkar D., Maji R K, Dey S, Sarkar A, Ghosh Z and Kundu K (2017). “Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease.” DNA Res 24(3): 235-250. (IF 4.009). PMID: 28338918
• Sahu, S. Kumar K M, Chakraborty S, Banerjee S K, Kumar R, Gupta P, Jana K, Gupta U D, Ghosh Z, Kundu M and Basu J (2017). “MicroRNA 26a (miR-26a)/KLF4 and CREB-C/EBPbeta regulate innate immune signaling, the polarization of macrophages and the trafficking of Mycobacterium tuberculosis to lysosomes during infection.” PLoS Pathog 13(5): e1006410. (IF 6.180). PMID: 28558034
• Roy J., Sarkar A, Parida S, Ghosh Z and Mallick B (2017). “Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis.” Mol Biosyst 13(3): 565-576. (IF 2.83). PMID: 28127595
2016
• Sen K., Sarkar A, Maji R K, Ghosh Z, Gupta S and Ghosh T C (2016). “Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line.” Mol Biosyst 12(12): 3633-3642.(IF 2.83). PMID: 27730241
• Kundu M., Mahata B, Banerjee A, Chakraborty S, Debnath S, Ray S S, Ghosh Z and Biswas K (2016). “Ganglioside GM2 mediates migration of tumor cells by interacting with integrin and modulating the downstream signaling pathway.” Biochim Biophys Acta 1863(7 Pt A): 1472-1489. (IF 4.008). PMID: 27066976
2015
• 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 and Saha V (2015). “Stromal cell-mediated mitochondrial redox adaptation regulates drug resistance in childhood acute lymphoblastic leukemia.” Oncotarget 6(40): 43048-43064. (IF 3.710). PMID: 26474278
• Halder P, Kumar R, Jana K, Chakraborty S, Ghosh Z, Kundu M and 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 67(9): 726-736. (IF 3.09). PMID: 26337784
• Kumar M, Sahu S K, Kumar R, Subuddhi A, Maji R K, Jana K, Gupta P, Raffetseder J, Lerm M, Ghosh Z, Loo G, Beyaert R, Gupta U D, Kundu M and Basu J (2015). “MicroRNA let-7 modulates the immune response to Mycobacterium tuberculosis infection via control of A20, an inhibitor of the NF-kappaB pathway.” Cell Host Microbe 17(3): 345-356. (IF 15.923). PMID: 25683052
2014
• Chakraborty S., Deb A, Maji R K, Saha S and Ghosh Z (2014). “LncRBase: an enriched resource for lncRNA information.” PLoS One 9(9): e108010. (IF 2.740). PMID: 25233092
• Sarkar A., Maji R K, Saha S and Ghosh Z (2014). “piRNAQuest: searching the piRNAome for silencers.” BMC Genomics 15: 555. (IF 3.530). PMID: 24997126
• Maji R K, Sarkar A, Khatua S, Das Sgupta S and Ghosh Z (2014). “PVT: an efficient computational procedure to speed up next-generation sequence analysis.” BMC Bioinformatics 15: 167. (IF 2.511). PMID: 24894600
2013
• Hu S., Wilson K D, Ghosh Z, Han L, Wang Y, Lan F, Ransohoff K J, Burridge P and Wu J C (2013). “MicroRNA-302 increases reprogramming efficiency via repression of NR2F2.” Stem Cells 31(2): 259-268. (IF 5.614). PMID: 23136034
2012
• Kumar R., Halder P, Sahu S K, Kumari M M, Jana K, Ghosh Z, Sharma P, Kundu M and 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 4.228). PMID: 22712528
• Reddy S., Zhao M, Hu D Q, Fajardo G, Hu S, Ghosh Z, Rajagopalan V, Wu J C and Bernstein D (2012). “Dynamic microRNA expression during the transition from right ventricular hypertrophy to failure.” Physiol Genomics 44(10): 562-575. (IF 2.581). PMID: 22454450
2011
• Li Z., Hu S, Ghosh Z, Han Z and Wu J C (2011). “Functional characterization and expression profiling of human induced pluripotent stem cell- and embryonic stem cell-derived endothelial cells.” Stem Cells Dev 20(10): 1701-1710. (IF 3.082). PMID: 21235328
• Ghosh Z., Huang M, Hu S, Wilson K D, Dey D and Wu J C (2011). “Dissecting the oncogenic and tumorigenic potential of differentiated human induced pluripotent stem cells and human embryonic stem cells.” Cancer Res 71(14): 5030-5039. (IF 7.070). PMID: 21646469
• Mallick B. and Ghosh Z (2011). “A complex crosstalk between polymorphic microRNA target sites and AD prognosis.” RNA Biol 8(4): 665-673. (IF 4.200). PMID: 21659796
• Pearl J. I., Lee A S, Leveson-Gower D B, Sun N, Ghosh Z, Lan F, Ransohoff J, Negrin R S, Davis M Mand Wu J C (2011). “Short-term immunosuppression promotes engraftment of embryonic and induced pluripotent stem cells.” Cell Stem Cell 8(3): 309-317. (IF 13.250). PMID: 21362570
2010
• Wilson K. D., Hu S, Venkatasubrahmanyam S,. Fu J D, Sun N,. Abilez O J, . Baugh J J, Jia F, Ghosh Z,. Li R A, Butte A J and Wu J C (2010). “Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499.” Circ Cardiovasc Genet 3(5): 426-435. (IF 4.864). PMID: 20733065
• Hu S., Huang M, Li Z, Jia F, Ghosh Z, Lijkwan M A, Fasanaro P, Sun N, Wang X, Martelli F, Robbins R C and Wu J C (2010). “MicroRNA-210 as a novel therapy for treatment of ischemic heart disease.” Circulation 122(11 Suppl): S124-131. (IF 23.603). PMID: 20837903
• Ghosh Z., Wilson K D, Wu Y, Hu S, Quertermous T and Wu J C (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 2.740). PMID: 20126639
2009
• Mallick B., Ghosh Z and Chakrabarti J (2009). “MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells.” PLoS One 4(11): e7837. ( IF 2.740). PMID: 19915717
2008
• Mallick B., Ghosh Z and Chakrabarti J (2008). “Structural determinants characteristic to AARS subclasses and tRNA-splicing endonuclease in eukaryotes.” J Biomol Struct Dyn 26(2): 223-234. (IF 3.220). PMID: 18597544
• Mallick B., Ghosh Z and Chakrabarti J (2008). “MicroRNA switches in Trypanosoma brucei.” Biochem Biophys Res Commun 372(3): 459-463. (IF 2.985). PMID: 18510949
• Kohrer C, Srinivasan G, Mandal D, Mallick B, Ghosh, Z., Chakrabarti J and Rajbhandary U L (2008). “Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui.” RNA 14(1): 117-126. (IF 3.63). PMID: 17998287
2006
• Ghosh, Z., Chakrabarti J, Mallick B, Das S, Sahoo S and Sethi H S (2006). “tRNA-isoleucine-tryptophan composite gene.” Biochem Biophys Res Commun 339(1): 37-40. (IF 2.985). PMID: 16307727
2005
• Das G S, Chakrabarti J, Ghosh Z, Sahoo S and 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 1.823). PMID: 16388144
• Mukherjee S, De S, Ghosh Z and Dasgupta S (2005). “A docking interaction study of the effect of critical mutations in ribonuclease a on protein-ligand binding.” Biochem Mol Biol Educ 33(5): 335-343. (IF 0.924). PMID: 21638595
• Mallick B., Chakrabarti J, Das S and Ghosh Z (2005). “TRNomics: a comparative analysis of Picrophilus torridus with other archaeal thermoacidophiles.” Indian J Biochem Biophys 42(4): 238-242. (IF 0.537). PMID: 23923548
• Mallick B, Kumar M, Sahoo S, Ghosh Z and Das S (2005). “Identity elements of archaeal tRNA.” DNA Res 12(4): 235-246. (IF 4.009). PMID: 16769686
List of any books/chapters/reviews published
Books
1. Regulatory RNAs: Basics, Methods & Applications (2012) Mallick B. and Ghosh Z. (Eds) Springer-Verlag, Heidelberg, Germany. ISBN-978-3-642-22516-1 (Hardcover).
2. Bioinformatics-Principles and Applications (2008) Ghosh Z. and Mallick B. Oxford University Press (First Print: 2008; Second Print: 2009) [ISBN-9780195692303].
Book Chapters
1. Mondal S., Bhattacharya N., Das T., Ghosh Z., Khatua S. (2021) Implication of Statistical Methods on Patient Data: An Approach for Cancer Survivability Prediction. In: Bhatia S., Dubey A.K., Chhikara R., Chaudhary P., Kumar A. (eds) Intelligent Healthcare. EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-67051-1_4
2. Sarkar A and Ghosh Z. (2019) Rejuvenation of piRNAs in emergence of cancer and other diseases in AGO-driven Non-Coding RNAs: Codes to Decode the Therapeutics of Diseases, Elsevier. Pages 319-333
3. Chakraborty S and Ghosh Z. (2018) MicroRNAs Shaping Cellular Reprogramming in AGO-driven Non-Coding RNAs: Codes to Decode the Therapeutics of Diseases, Elsevier. Pages 75-97
4. Ghosh Z and Mallick B (2012) Renaissance of RNA regulators. In Ghosh/Mallick (Eds.) Regulatory RNAs: Basics, Methods and Applications, Springer-Verlag, 2011. Pages 3-22
Reviews
• Kaur H., Sarmah D, Saraf J, Vats K, Kalia K, Borah A, Yavagal D R, Dave K R, Ghosh Z and Bhattacharya P (2018). "Noncoding RNAs in ischemic stroke: time to translate." Ann N Y Acad Sci 1421(1): 19-36. (IF 4.320). PMID: 29683506
• Ghosh Z and Mallick B (2014). Cancer stem cells and regulatory RNAs crosstalk: Fostering possibilities for cancer therapies. BioScience 64(12):1138-1149. (IF 8.282)[Advance Access: doi:10.1093/biosci/biu149]. (IF 5.970)
• Mallick B and Ghosh, Z. (2012). "Probing Evolutionary Biography of MicroRNAs and Associated Factors." Curr Genomics 13(2): 144-152. (IF 2.220). PMID: 23024606
• Mallick B, Chakrabarti, J and Ghosh, Z. (2011). "MicroRNA reins in embryonic and cancer stem cells." RNA Biol 8(3): 415-426. (IF 4.200). PMID: 21525784
• Ghosh Z., Mallick B and Chakrabarti J (2009). "Cellular versus viral microRNAs in host-virus interaction." Nucleic Acids Res 37(4): 1035-1048. (IF 11.501). PMID: 19095692
• Ghosh Z., Chakrabarti J and Mallick B (2007). "miRNomics-The bioinformatics of microRNA genes." Biochem Biophys Res Commun 363(1): 6-11. ( IF 2.985). PMID: 17714687
