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From IISc
* Corresponding author
# Equal contribution
2020 to now
1. Pal, A., Ghorai, D., Ge, X., Sarkar, B., Sahu, A.K., Chaudhary, V., Sanyal, S., Singh, M. and Ghosh, A.* (2024) Second messenger c-di-AMP regulates multiple antibiotic sensitivity pathways in Mycobacterium smegmatis by discrete mechanisms. Manuscript in revision!
[Preprint]: https://www.biorxiv.org/content/10.1101/2023.07.05.547667v1
2. Rothweiler, U.*, Gundesø, S. E., Mikalsen, E. W., Svenning, S., Singh, M., Combes, F., Frida, P., Mangold, A., Piotrowski, Y., Schwab, F., Lanes, O., Striberny, B. K*. (2024) Using nucleolytic toxins as restriction enzymes enables new RNA applications. Nucleic Acids Research. Just accepted!
3. Kumar, N., Taneja, A., Ghosh, M., Rothweiler, U., Sundaresan N.R., and Singh, M.* (2024) Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Research. 2024, Feb 9;52(3):1450-1470. doi: 10.1093/nar/gkad1208.
[Preprint]: doi: https://doi.org/10.1101/2022.08.08.503141
4. Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A.* (2023) Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife. 12: e80218
5. Manikandan, P.#, Nadig, K.#, and Singh, M.* (2023) Large-scale Purification of Protein Toxin, RNA Antitoxin, and Ribonucleoprotein Type III Toxin-Antitoxin Complex from E. coli for Biophysical Studies. Bio-protocol. 2023 Jul 5;13(13):e4763. doi: 10.21769/BioProtoc.4763. eCollection 2023 Jul 5.
6. Wang, Y., He, Y., Wang, Y., Yang, Y., Singh, M., Eichhorn, C.D., Cheng, X., Xiao, Y., Zhou, J.H., and Feigon, J.* (2023) Structure of LARP7 protein p65–telomerase RNA complex in telomerase revealed by cryo-EM and NMR. Journal of Molecular Biology. Mar 20; 168044. doi: 10.1016/j.jmb.2023.168044.
7. Maulik, A.*, Bandopadhyay, D., and Singh, M.* (2023) A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK. Current Research in Structural Biology. 28 Feb; 5, 100099. https://doi.org/10.1016/j.crstbi.2023.100099.
[Preprint]: doi: https://doi.org/10.1101/2021.03.24.436769
8. Kumar, N., Ghosh, M., Maninandan, P., Basak, S., Deepa, A., and Singh, M.* (2022) Resonance assignment and secondary structure of the tandem harmonin homology domains of human RTEL1. Biomolecular NMR Assignments. Apr;16(1):159-164. doi: 10.1007/s12104-022-10074-7.
9. Manikandan, P., Sandhya, S., Nadig, K., Paul S., Srinivasan N., Rothweiler U.*, and Singh, M.* (2022) Identification, functional characterization, assembly, and structure of ToxIN type III toxin-antitoxin complex from E. coli. Nucleic Acids Research. Feb 22;50(3):1687-1700. doi: 10.1093/nar/gkab1264.
Highlighted on the cover page of journal 'RNA'. Issue: March 2023; 29 (3)
https://rnajournal.cshlp.org/content/29/3.cover-expansion
10. Giri, M., Gupta, P., Maulik, A., Gracias, M., and Singh, M.* (2022). Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b. Protein Science. May;31(5):e4294. doi: 10.1002/pro.4294.
11. Jadhav, P.V. #, Sinha, V.K#., Chugh, S., Kotyada, C., Bachhav, D., Singh, R., Rothweiler, U.*, and Singh, M.* (2020). 2.09 Å resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin. Biochemical Journal. 2020 Oct 30;477(20):4001-4019. doi: 10.1042/BCJ20200363.
12. Ghosh, M. and Singh, M.* (2020) Structure specific recognition of telomere repeats containing RNA by the RGG-box of hnRNPA1. Nucleic Acids Research. May 7;48(8):4492-4506. doi: 10.1093/nar/gkaa134.
2014 to 2019
13. Giri, M.# Maulik, A.#, and Singh, M.* (2019) Signatures of specific DNA binding by the AT-rich interaction domain of BAF250a. Biochemistry. Jan 14. 59(1):100-113. doi: 10.1021/acs.biochem.9b00852.
This manuscript was featured in ‘Future of Biochemistry – Asia Pacific’ issue of the journal.
14. Ravi V., Jain A., Khan D., Ahamed F., Mishra S., Giri M., Inbaraj M., Krishna S., Sarikhani M., Maity S., Kumar S., Shriniwas P.A., Shah R.A., Dave1 P., Rajendran R., Desingu P.A., Varshney U., Das S., Kolthur-Seetharam U., Rajakumari S., Singh M. and Sundaresan N.R.* (2019) SIRT6 transcriptionally regulates global protein synthesis through transcription factor Sp1 independent of its deacetylase activity. Nucleic Acids Research. Aug 2. pii: gkz648. doi: 10.1093/nar/gkz648.
15. Maulik, A.# Giri, M.# and Singh, M.* (2019) Molecular Determinants of Complex Formation between DNA and the AT-rich Interaction Domain of BAF250a. Febs Letters. Jul 19. 593(19):2716-2729. doi: 10.1002/1873-3468.
This article was selected and featured as 'Editor's Choice' article in Febs Letters !
16. Bastiray, A. Giri, M. and Singh, M.* (2018) Sequential backbone resonance assignment of AT-rich interaction domain of human BAF200. Biomolecular NMR Assignments. Dec 10. doi: 10.1007/s12104-018-9862-z.
17. Sandhya, S#., Maulik, A#. Giri, M. and Singh, M.* (2018) Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. Plos One. Oct. 11. 13(10):e0205267. doi: 10.1371/journal.pone.0205267. eCollection 2018.
18. Ghosh, M. and Singh, M.* (2018) RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain. Nucleic Acids Research. Nov 2. 46(19):10246-10261. doi: 10.1093/nar/gky854.
19. Sarikhani, M., Mishra, S., Maity, S., Kotyada, C., Wolfgeher, D., Gupta, M.P., Singh, M. and Sundaresan, N.R.* (2018) SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation. eLife. Mar 5;7. pii: e32952. doi: 10.7554/eLife.32952.
20. Sarikhani, M., Mishra, S., Desingu, P.A., Kotyada, C., Wolfgeher, D., G
upta, M.P., Singh, M. and Sundaresan, N.R.* (2018) SIRT2 regulates oxidative stress-induced cell death through deacetylation of c-Jun NH2-terminal kinase. Cell Death and Differentiation. Feb 15. doi: 10.1038/s41418-018-0069-8.
21. Kotyada, C., Maulik, A., Srivastava, A. and Singh, M.* (2017) Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A. ACS Omega, 2, 6691-6702.
22. Singh, M., Wang, Z., Cascio, D. and Feigon, J.* (2015) Structure and interactions of the CS domain of human H/ACA RNP assembly protein Shq1. Journal of Molecular Biology, 427, 807-823.
Before IISc
(before 2014)
23. Singh, M., Choi, C.P. and Feigon, J.* (2013) xRRM: a new class of RRM found in the telomerase La family protein p65. RNA Biology, 10, 353-359.
24. Singh, M., Wang, Z., Koo, B.K., Patel, A., Cascio, D., Collins, K. and Feigon, J.* (2012) Structural basis for telomerase RNA recognition and RNP assembly by the holoenzyme La family protein p65. Molecular cell, 47, 16-26.
25. Singh, M. #, Gonzales, F.A. #, Cascio, D., Heckmann, N., Chanfreau, G. and Feigon, J.* (2009) Structure and functional studies of the CS domain of the essential H/ACA ribonucleoparticle assembly protein SHQ1. The Journal of Biological Chemistry, 284, 1906-1916.
26. Singh, M., Popowicz, G.M., Krajewski, M. and Holak, T.A.* (2007) Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex. Chembiochem : a European Journal of Chemical Biology, 8, 1308-1316.
27. Singh, M., D'Silva, L. and Holak, T.A.* (2006) DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein. Biological Chemistry, 387, 1469-1478.
28. Smialowski, P., Singh, M., Mikolajka, A., Majumdar, S., Joy, J.K., Nalabothula, N., Krajewski, M., Degenkolbe, R., Bernard, H.U. and Holak, T.A.* (2005) NMR and mass spectrometry studies of putative interactions of cell cycle proteins pRb and CDK6 with cell differentiation proteins MyoD and ID-2. Biochimica et Biophysica Acta, 1750, 48-60.
29. Singh, M., Krajewski, M., Mikolajka, A. and Holak, T.A.* (2005) Molecular determinants for the complex formation between the retinoblastoma protein and LXCXE sequences. The Journal of Biological Chemistry, 280, 37868-37876.
30. D'Silva, L., Ozdowy, P., Krajewski, M., Rothweiler, U., Singh, M. and Holak, T.A.* (2005) Monitoring the effects of antagonists on protein-protein interactions with NMR spectroscopy. Journal of the American Chemical Society, 127, 13220-13226.
* Corresponding author
# Equal contribution
2020 to now
1. Pal, A., Ghorai, D., Ge, X., Sarkar, B., Sahu, A.K., Chaudhary, V., Sanyal, S., Singh, M. and Ghosh, A.* (2024) Second messenger c-di-AMP regulates multiple antibiotic sensitivity pathways in Mycobacterium smegmatis by discrete mechanisms. Manuscript in revision!
[Preprint]: https://www.biorxiv.org/content/10.1101/2023.07.05.547667v1
2. Rothweiler, U.*, Gundesø, S. E., Mikalsen, E. W., Svenning, S., Singh, M., Combes, F., Frida, P., Mangold, A., Piotrowski, Y., Schwab, F., Lanes, O., Striberny, B. K*. (2024) Using nucleolytic toxins as restriction enzymes enables new RNA applications. Nucleic Acids Research. Just accepted!
3. Kumar, N., Taneja, A., Ghosh, M., Rothweiler, U., Sundaresan N.R., and Singh, M.* (2024) Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Research. 2024, Feb 9;52(3):1450-1470. doi: 10.1093/nar/gkad1208.
[Preprint]: doi: https://doi.org/10.1101/2022.08.08.503141
4. Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A.* (2023) Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife. 12: e80218
5. Manikandan, P.#, Nadig, K.#, and Singh, M.* (2023) Large-scale Purification of Protein Toxin, RNA Antitoxin, and Ribonucleoprotein Type III Toxin-Antitoxin Complex from E. coli for Biophysical Studies. Bio-protocol. 2023 Jul 5;13(13):e4763. doi: 10.21769/BioProtoc.4763. eCollection 2023 Jul 5.
6. Wang, Y., He, Y., Wang, Y., Yang, Y., Singh, M., Eichhorn, C.D., Cheng, X., Xiao, Y., Zhou, J.H., and Feigon, J.* (2023) Structure of LARP7 protein p65–telomerase RNA complex in telomerase revealed by cryo-EM and NMR. Journal of Molecular Biology. Mar 20; 168044. doi: 10.1016/j.jmb.2023.168044.
7. Maulik, A.*, Bandopadhyay, D., and Singh, M.* (2023) A cytosine-patch sequence motif identified in the conserved region of lincRNA-p21 interacts with the KH3 domain of hnRNPK. Current Research in Structural Biology. 28 Feb; 5, 100099. https://doi.org/10.1016/j.crstbi.2023.100099.
[Preprint]: doi: https://doi.org/10.1101/2021.03.24.436769
8. Kumar, N., Ghosh, M., Maninandan, P., Basak, S., Deepa, A., and Singh, M.* (2022) Resonance assignment and secondary structure of the tandem harmonin homology domains of human RTEL1. Biomolecular NMR Assignments. Apr;16(1):159-164. doi: 10.1007/s12104-022-10074-7.
9. Manikandan, P., Sandhya, S., Nadig, K., Paul S., Srinivasan N., Rothweiler U.*, and Singh, M.* (2022) Identification, functional characterization, assembly, and structure of ToxIN type III toxin-antitoxin complex from E. coli. Nucleic Acids Research. Feb 22;50(3):1687-1700. doi: 10.1093/nar/gkab1264.
Highlighted on the cover page of journal 'RNA'. Issue: March 2023; 29 (3)
https://rnajournal.cshlp.org/content/29/3.cover-expansion
10. Giri, M., Gupta, P., Maulik, A., Gracias, M., and Singh, M.* (2022). Structure and DNA binding analysis of AT-rich interaction domain present in human BAF-B specific subunit BAF250b. Protein Science. May;31(5):e4294. doi: 10.1002/pro.4294.
11. Jadhav, P.V. #, Sinha, V.K#., Chugh, S., Kotyada, C., Bachhav, D., Singh, R., Rothweiler, U.*, and Singh, M.* (2020). 2.09 Å resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin. Biochemical Journal. 2020 Oct 30;477(20):4001-4019. doi: 10.1042/BCJ20200363.
12. Ghosh, M. and Singh, M.* (2020) Structure specific recognition of telomere repeats containing RNA by the RGG-box of hnRNPA1. Nucleic Acids Research. May 7;48(8):4492-4506. doi: 10.1093/nar/gkaa134.
2014 to 2019
13. Giri, M.# Maulik, A.#, and Singh, M.* (2019) Signatures of specific DNA binding by the AT-rich interaction domain of BAF250a. Biochemistry. Jan 14. 59(1):100-113. doi: 10.1021/acs.biochem.9b00852.
This manuscript was featured in ‘Future of Biochemistry – Asia Pacific’ issue of the journal.
14. Ravi V., Jain A., Khan D., Ahamed F., Mishra S., Giri M., Inbaraj M., Krishna S., Sarikhani M., Maity S., Kumar S., Shriniwas P.A., Shah R.A., Dave1 P., Rajendran R., Desingu P.A., Varshney U., Das S., Kolthur-Seetharam U., Rajakumari S., Singh M. and Sundaresan N.R.* (2019) SIRT6 transcriptionally regulates global protein synthesis through transcription factor Sp1 independent of its deacetylase activity. Nucleic Acids Research. Aug 2. pii: gkz648. doi: 10.1093/nar/gkz648.
15. Maulik, A.# Giri, M.# and Singh, M.* (2019) Molecular Determinants of Complex Formation between DNA and the AT-rich Interaction Domain of BAF250a. Febs Letters. Jul 19. 593(19):2716-2729. doi: 10.1002/1873-3468.
This article was selected and featured as 'Editor's Choice' article in Febs Letters !
16. Bastiray, A. Giri, M. and Singh, M.* (2018) Sequential backbone resonance assignment of AT-rich interaction domain of human BAF200. Biomolecular NMR Assignments. Dec 10. doi: 10.1007/s12104-018-9862-z.
17. Sandhya, S#., Maulik, A#. Giri, M. and Singh, M.* (2018) Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. Plos One. Oct. 11. 13(10):e0205267. doi: 10.1371/journal.pone.0205267. eCollection 2018.
18. Ghosh, M. and Singh, M.* (2018) RGG-box in hnRNPA1 specifically recognizes the telomere G-quadruplex DNA and enhances the G-quadruplex unfolding ability of UP1 domain. Nucleic Acids Research. Nov 2. 46(19):10246-10261. doi: 10.1093/nar/gky854.
19. Sarikhani, M., Mishra, S., Maity, S., Kotyada, C., Wolfgeher, D., Gupta, M.P., Singh, M. and Sundaresan, N.R.* (2018) SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation. eLife. Mar 5;7. pii: e32952. doi: 10.7554/eLife.32952.
20. Sarikhani, M., Mishra, S., Desingu, P.A., Kotyada, C., Wolfgeher, D., G
upta, M.P., Singh, M. and Sundaresan, N.R.* (2018) SIRT2 regulates oxidative stress-induced cell death through deacetylation of c-Jun NH2-terminal kinase. Cell Death and Differentiation. Feb 15. doi: 10.1038/s41418-018-0069-8.
21. Kotyada, C., Maulik, A., Srivastava, A. and Singh, M.* (2017) Mechanistic Insights into the Differential Catalysis by RheB and Its Mutants: Y35A and Y35A-D65A. ACS Omega, 2, 6691-6702.
22. Singh, M., Wang, Z., Cascio, D. and Feigon, J.* (2015) Structure and interactions of the CS domain of human H/ACA RNP assembly protein Shq1. Journal of Molecular Biology, 427, 807-823.
Before IISc
(before 2014)
23. Singh, M., Choi, C.P. and Feigon, J.* (2013) xRRM: a new class of RRM found in the telomerase La family protein p65. RNA Biology, 10, 353-359.
24. Singh, M., Wang, Z., Koo, B.K., Patel, A., Cascio, D., Collins, K. and Feigon, J.* (2012) Structural basis for telomerase RNA recognition and RNP assembly by the holoenzyme La family protein p65. Molecular cell, 47, 16-26.
25. Singh, M. #, Gonzales, F.A. #, Cascio, D., Heckmann, N., Chanfreau, G. and Feigon, J.* (2009) Structure and functional studies of the CS domain of the essential H/ACA ribonucleoparticle assembly protein SHQ1. The Journal of Biological Chemistry, 284, 1906-1916.
26. Singh, M., Popowicz, G.M., Krajewski, M. and Holak, T.A.* (2007) Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex. Chembiochem : a European Journal of Chemical Biology, 8, 1308-1316.
27. Singh, M., D'Silva, L. and Holak, T.A.* (2006) DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein. Biological Chemistry, 387, 1469-1478.
28. Smialowski, P., Singh, M., Mikolajka, A., Majumdar, S., Joy, J.K., Nalabothula, N., Krajewski, M., Degenkolbe, R., Bernard, H.U. and Holak, T.A.* (2005) NMR and mass spectrometry studies of putative interactions of cell cycle proteins pRb and CDK6 with cell differentiation proteins MyoD and ID-2. Biochimica et Biophysica Acta, 1750, 48-60.
29. Singh, M., Krajewski, M., Mikolajka, A. and Holak, T.A.* (2005) Molecular determinants for the complex formation between the retinoblastoma protein and LXCXE sequences. The Journal of Biological Chemistry, 280, 37868-37876.
30. D'Silva, L., Ozdowy, P., Krajewski, M., Rothweiler, U., Singh, M. and Holak, T.A.* (2005) Monitoring the effects of antagonists on protein-protein interactions with NMR spectroscopy. Journal of the American Chemical Society, 127, 13220-13226.
