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13. Mishra D, Shekhar S, Subba P, Prasad TSK, Chakraborty S, Chakraborty N. Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery. Plant J. 2024;119(5):2217-2235. doi:10.1111/tpj.16913
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16. Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res. 2024;23(8):3217-3234. doi:10.1021/acs.jproteome.3c00781
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20. Khan S, Mishra RK. Multigenerational Effect of Heat Stress on the Drosophila melanogaster Sperm Proteome. J Proteome Res. 2024;23(6):2265-2278. doi:10.1021/acs.jproteome.4c00205
21. Aggarwal S, Gupta P, Dhawan U, Yadav AK. The language of posttranslational modifications and deciphering it from proteomics data. In: Transcription and Translation in Health and Disease. Elsevier; 2023. doi:10.1016/B978-0-323-99521-4.00012-X
22. Babele P, Yadav AK. Back2Basics: mass-to-charge ratio (m/z) in proteomics. J Proteins Proteomics. 2023;14(4). doi:10.1007/s42485-023-00115-7
23. Kumari S, Bandyopadhyay B, Singh A, et al. Extracellular vesicles recovered from plasma of severe dengue patients induce CD4+ T cell suppression through PD-L1/PD-1 interaction. mBio. 2023;14(6):e0182323. doi:10.1128/mbio.01823-23
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25. Raj A, Aggarwal S, Kumar D, Yadav AK, Dash D. Proteogenomics 101: a primer on database search strategies. J Proteins Proteomics. 2023;14(4):287-301. doi:10.1007/s42485-023-00118-4
26. Raj A, Aggarwal S, Singh P, Yadav AK, Dash D. PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects. Comput Struct Biotechnol J. 2023;23:711-722. Published 2023 Dec 26. doi:10.1016/j.csbj.2023.12.033
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28. Bihani A, Avvaru AK, Mishra RK. Biochemical Deconstruction and Reconstruction of Nuclear Matrix Reveals the Layers of Nuclear Organization. Mol Cell Proteomics. 2023;22(12):100671. doi:10.1016/j.mcpro.2023.100671
29. Phanindhar K, Mishra RK. Auxin-inducible degron system: an efficient protein degradation tool to study protein function. Biotechniques. 2023;74(4):186-198. doi:10.2144/btn-2022-0108
30. Sureka R, Avvaru AK, Sowpati DT, Pathak RU, Mishra RK. Structural and developmental dynamics of Matrix associated regions in Drosophila melanogaster genome. BMC Genomics. 2022;23(1):725. Published 2022 Oct 25. doi:10.1186/s12864-022-08944-4
31. Aggarwal S, Raj A, Kumar D, Dash D, Yadav AK. False discovery rate: the Achilles' heel of proteogenomics. Brief Bioinform. 2022;23(5):bbac163. doi:10.1093/bib/bbac163
32. Sharma KB, Aggarwal S, Yadav AK, Vrati S, Kalia M. Studying Autophagy Using a TMT-Based Quantitative Proteomics Approach. Methods Mol Biol. 2022;2445:183-203. doi:10.1007/978-1-0716-2071-7_12
33. Polepalli S, Singh R, Naskar S, et al. Rapid and deep plasma proteomics workflows for robust identification and quantification of biomarkers of sickle cell anaemia. J Proteins Proteomics. 2022;13(4):205-218
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35. Taunk K, Porto-Figueira P, Pereira JAM, et al. Urinary Volatomic Expression Pattern: Paving the Way for Identification of Potential Candidate Biosignatures for Lung Cancer. Metabolites. 2022;12(1):36. Published 2022 Jan 4. doi:10.3390/metabo12010036
36. Lande NV, Barua P, Gayen D, et al. Dehydration-responsive chickpea chloroplast protein, CaPDZ1, confers dehydration tolerance by improving photosynthesis. Physiol Plant. 2022;174(1):e13613. doi:10.1111/ppl.13613
37. Kumar S, Lande NV, Barua P, Pareek A, Chakraborty S, Chakraborty N. Proteomic dissection of rice cytoskeleton reveals the dominance of microtubule and microfilament proteins, and novel components in the cytoskeleton-bound polysome. Plant Physiol Biochem. 2022;170:75-86. doi:10.1016/j.plaphy.2021.11.037
38. Rathi D, Verma JK, Pareek A, Chakraborty S, Chakraborty N. Dissection of grasspea (Lathyrus sativus L.) root exoproteome reveals critical insights and novel proteins. Plant Sci. 2022;316:111161. doi:10.1016/j.plantsci.2021.111161
39. Sureka R, Mishra R. Identification of Evolutionarily Conserved Nuclear Matrix Proteins and Their Prokaryotic Origins. J Proteome Res. 2021;20(1):518-530. doi:10.1021/acs.jproteome.0c00550
40. Puri D, Swamy CVB, Dhawan J, Mishra RK. Comparative nuclear matrix proteome analysis of skeletal muscle cells in different cellular states. Cell Biol Int. 2021;45(3):580-598. doi:10.1002/cbin.11499
41. Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nat Commun. 2021;12(1):6094. Published 2021 Oct 19. doi:10.1038/s41467-021-26234-7
42. Pandey M, Bansal S, Bar S, et al. miR-125-chinmo pathway regulates dietary restriction-dependent enhancement of lifespan in Drosophila. Elife. 2021;10:e62621. Published 2021 Jun 8. doi:10.7554/eLife.62621
43. Sharma KB, Chhabra S, Aggarwal S, et al. Proteomic landscape of Japanese encephalitis virus-infected fibroblasts. J Gen Virol. 2021;102(9):10.1099/jgv.0.001657. doi:10.1099/jgv.0.001657
44. Chanukuppa V, Taware R, Taunk K, et al. Proteomic Alterations in Multiple Myeloma: A Comprehensive Study Using Bone Marrow Interstitial Fluid and Serum Samples. Front Oncol. 2021;10:566804. Published 2021 Jan 29. doi:10.3389/fonc.2020.566804
45. Mohan N, Jhandai S, Bhadu S, et al. Acclimation response and management strategies to combat heat stress in wheat for sustainable agriculture: A state-of-the-art review. Plant Sci. 2023;336:111834. doi:10.1016/j.plantsci.2023.111834
46. Mishra D, Shekhar S, Chakraborty S, Chakraborty N. Wheat 2-Cys peroxiredoxin plays a dual role in chlorophyll biosynthesis and adaptation to high temperature. Plant J. 2021;105(5):1374-1389. doi:10.1111/tpj.15119
47. Aggarwal S, Banerjee SK, Talukdar NC, Yadav AK. Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. Front Genet. 2020;11:356. Published 2020 Apr 30. doi:10.3389/fgene.2020.00356
48. Aggarwal S, Kumar A, Jamwal S, Midha MK, Talukdar NC, Yadav AK. HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. ACS Omega. 2020;5(19):10857-10867. Published 2020 May 7. doi:10.1021/acsomega.0c00515
49. Roy S, Goel R, Aggarwal S, Asthana S, Yadav AK, Awasthi A. Proteome analysis revealed the essential functions of protein phosphatase PP2A in the induction of Th9 cells. Sci Rep. 2020;10(1):10992. Published 2020 Jul 3. doi:10.1038/s41598-020-67845-2
50. Bhattacharyya NP, Das S, Choudhury KR, Raychaudhuri S, Ghose J. Huntingtin yeast two-hybrid protein K (HYPK): an intrinsically unstructured heat shock inducible protein with diverse cellular and molecular functions. In: Heat Shock Proteins in Human Diseases. 2021:249-274
51. Rawat S, Ghosh S, Mondal D, Anusha V, Raychaudhuri S. Increased supraorganization of respiratory complexes is a dynamic multistep remodelling in response to proteostasis stress. J Cell Sci. 2020;133(18):jcs248492. Published 2020 Sep 24. doi:10.1242/jcs.248492
52. Taware R, More TH, Bagadi M, Taunk K, Mane A, Rapole S. Lipidomics investigations into the tissue phospholipidomic landscape of invasive ductal carcinoma of the breast. RSC Adv. 2020;11(1):397-407. Published 2020 Dec 22. doi:10.1039/d0ra07368g
53. Taware R, Taunk K, Kumar TVS, et al. Extracellular volatilomic alterations induced by hypoxia in breast cancer cells. Metabolomics. 2020;16(2):21. Published 2020 Jan 24. doi:10.1007/s11306-020-1635-x
54. Taunk K, Kalita B, Kale V, et al. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics. 2020;17(6):433-451. doi:10.1080/14789450.2020.1787157
55. Kalita B, Bano S, Vavachan VM, Taunk K, Seshadri V, Rapole S. Application of mass spectrometry based proteomics to understand diabetes: A special focus on interactomics. Biochim Biophys Acta Proteins Proteom. 2020;1868(10):140469. doi:10.1016/j.bbapap.2020.140469
56. Chanukuppa V, Paul D, Taunk K, et al. Proteomics and functional study reveal marginal zone B and B1 cell specific protein as a candidate marker of multiple myeloma. Int J Oncol. 2020;57(1):325-337. doi:10.3892/ijo.2020.5056
57. Kumar R, Barua P, Chakraborty N, Nandi AK. Systemic acquired resistance specific proteome of Arabidopsis thaliana. Plant Cell Rep. 2020;39(11):1549-1563. doi:10.1007/s00299-020-02583-3
58. Rai Y, Wardhan V, Gupta DB, Chakraborty N. Calcium-dependent changes in physicochemical properties and the proteome dynamics influence dehydration responses in rice. Environ Exp Bot. 2020;172:103965. doi:10.1016/j.envexpbot.2019.103965
59. Narula K, Elagamey E, Abdellatef MAE, et al. Chitosan-triggered immunity to Fusarium in chickpea is associated with changes in the plant extracellular matrix architecture, stomatal closure and remodeling of the plant metabolome and proteome. Plant J. 2020;103(2):561-583. doi:10.1111/tpj.14750
60. Sinha A, Haider T, Narula K, Ghosh S, Chakraborty N, Chakraborty S. Integrated Seed Proteome and Phosphoproteome Analyses Reveal Interplay of Nutrient Dynamics, Carbon-Nitrogen Partitioning, and Oxidative Signaling in Chickpea. Proteomics. 2020;20(8):e1900267. doi:10.1002/pmic.201900267
61. Barua P, Lande NV, Kumar S, Chakraborty S, Chakraborty N. Quantitative Phosphoproteomic Analysis of Legume Using TiO2-Based Enrichment Coupled with Isobaric Labeling. Methods Mol Biol. 2020;2107:395-406. doi:10.1007/978-1-0716-0235-5_22
62. Lande NV, Barua P, Gayen D, et al. Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses. Plant Physiol Biochem. 2020;146:337-348. doi:10.1016/j.plaphy.2019.11.034
63. Lande NV, Barua P, Gayen D, Kumar S, Chakraborty S, Chakraborty N. Proteomic dissection of the chloroplast: Moving beyond photosynthesis. J Proteomics. 2020;212:103542. doi:10.1016/j.jprot.2019.103542
64. Elagamey E, Narula K, Chakraborty N, Chakraborty S. Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies. Methods Mol Biol. 2020;2057:155-172. doi:10.1007/978-1-4939-9790-9_14
65. Aggarwal S, Talukdar NC, Yadav AK. Advances in Higher Order Multiplexing Techniques in Proteomics. J Proteome Res. 2019;18(6):2360-2369. doi:10.1021/acs.jproteome.9b00228
66. Sharma N, Aggarwal S, Kumar S, et al. Comparative analysis of homologous aminopeptidase PepN from pathogenic and non-pathogenic mycobacteria reveals divergent traits. PLoS One. 2019;14(4):e0215123. Published 2019 Apr 10. doi:10.1371/journal.pone.0215123
67. Sharma KB, Sharma M, Aggarwal S, et al. Quantitative Proteome Analysis of Atg5-Deficient Mouse Embryonic Fibroblasts Reveals the Range of the Autophagy-Modulated Basal Cellular Proteome. mSystems. 2019;4(6):e00481-19. Published 2019 Nov 5. doi:10.1128/mSystems.00481-19
68. Rawat S, Anusha V, Jha M, Sreedurgalakshmi K, Raychaudhuri S. Aggregation of Respiratory Complex Subunits Marks the Onset of Proteotoxicity in Proteasome Inhibited Cells. J Mol Biol. 2019;431(5):996-1015. doi:10.1016/j.jmb.2019.01.022
69. Saleh A, Subramaniam G, Raychaudhuri S, Dhawan J. Cytoplasmic sequestration of the RhoA effector mDiaphanous1 by Prohibitin2 promotes muscle differentiation. Sci Rep. 2019;9(1):8302. Published 2019 Jun 5. doi:10.1038/s41598-019-44749-4
70. Chanukuppa V, Paul D, Taunk K, et al. XPO1 is a critical player for bortezomib resistance in multiple myeloma: A quantitative proteomic approach. J Proteomics. 2019;209:103504. doi:10.1016/j.jprot.2019.103504
71. Chanukuppa V, More TH, Taunk K, et al. Serum metabolomic alterations in multiple myeloma revealed by targeted and untargeted metabolomics approaches: a pilot study. RSC Adv. 2019;9(51):29522-29532. Published 2019 Sep 18. doi:10.1039/c9ra04458b
72. Rathi D, Pareek A, Zhang T, et al. Metabolite signatures of grasspea suspension-cultured cells illustrate the complexity of dehydration response. Planta. 2019;250(3):857-871. doi:10.1007/s00425-019-03211-5
73. Gayen D, Barua P, Lande NV, et al. Dehydration-responsive alterations in the chloroplast proteome and cell metabolomic profile of rice reveals key stress adaptation responses. Environ Exp Bot. 2019;160:12-24. doi:10.1016/j.envexpbot.2019.01.003
74. Gayen D, Gayali S, Barua P, et al. Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes. J Proteomics. 2019;192:267-279. doi:10.1016/j.jprot.2018.09.008
75. Barua P, Lande NV, Subba P, et al. Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant Cell Environ. 2019;42(1):230-244. doi:10.1111/pce.13334
76. Narula K, Choudhary P, Ghosh S, Elagamey E, Chakraborty N, Chakraborty S. Comparative Nuclear Proteomics Analysis Provides Insight into the Mechanism of Signaling and Immune Response to Blast Disease Caused by Magnaporthe oryzae in Rice. Proteomics. 2019;19(3):e1800188. doi:10.1002/pmic.201800188