* Equal contribution; # Corresponding author

A. Journal Publications [58]​

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1. Das S, Kannihalli A, Banerjee S, Chakraborty N, Ray S#. A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology. Funct Integr Genomics. 2025 Feb 19;25(1):41. doi: 10.1007/s10142-025-01554-9.

2. Bhatnagar A, Raj G, Das S, Kannihali A, Rajakumara E, Murray G, Ray S#. Integrated bioinformatics and interaction analysis to advance chronotherapies for mental disorders. Front Pharmacol. 2024 Dec 5;15:1444342. doi: 10.3389/fphar.2024.1444342.

3. Das S, Khan R, Banerjee S, Ray S, Ray S#. Alterations in Circadian Rhythms, Sleep, and Physical Activity in COVID-19: Mechanisms, Interventions, and Lessons for the Future. Mol Neurobiol. 2024 May 3. doi: 10.1007/s12035-024-04178-5. 

4. Ghosh, P. K., Rao, M. J., Putta, C. L., Ray, S., & Rengan, A. K. (2024). Telomerase: a nexus between cancer nanotherapy and circadian rhythm. Biomaterials science, 12(9), 2259–2281. https://doi.org/10.1039/d4bm00024b

5.  Kunjulakshmi R, Kumar A, et al., Ray S, Tiwari B, Kumar R. AagingBase: A Comprehensive Database of Anti-aging Peptides. Database 2024, doi: 10.1093/database/baae016.

6. Bhatnagar A, Murray G, Ray S#. Circadian biology to advance therapeutics for mood disorders. Trends Pharmacol Sci 2023 Aug 28:S0165-6147(23)00170-0.

7. Rankawat S, Kundal K, Chakraborty S, Kumar R, Ray S#. A comprehensive rhythmicity analysis of host proteins and immune factors involved in malaria pathogenesis to decipher the importance of host circadian clock in malaria. Front Immunol 2023 Aug 10;14:1210299.

8. Chakraborty S, Kannihalli A, Mohanty A, Ray S#. The promise of proteomics and metabolomics for unraveling the mechanism and side effect landscape of beta-adrenoreceptor antagonists in cardiovascular therapeutics. Omics 2023, 27(3), 87–92.

9. Banerjee S, Ray S#. Circadian medicine for aging attenuation and sleep disorders: Prospects and challenges. Prog Neurobiol 2023, 220, 102387.

10. Banerjee S, Chakraborty S, Ray S#. Systems biology of Covid-19 and human diseases: beyond a birds eye view, and toward One Health. Omics 2023, 27(1), 2-5.

11. Jha PK, Valekunja UK, Ray S, Nollet M, Reddy AB. Single-cell transcriptomics and cell-specific proteomics reveal molecular signatures of sleep. Commun Biol. Nature 2022, 5, 846.

12. Puppala A, Rankawat S, Ray S#. Circadian Timekeeping in Anticancer Therapeutics: An Emerging Vista of Chronopharmacology Research. Curr Drug Metab 2021, 22, 998-1008.

13. Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, et al., Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure. mSystems 2021, 6 (5), e00095-21.

14. Lordan R, Rando HM, …, Ray S (as a part of COVID-19 Review Consortium) Casey S Greene. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment. mSystems 2021, 6 (3), e00122-21.

15. Rando HM, Wellhausen W, Ghosh S, ...., Ray S. (as a part of COVID-19 Review Consortium) Casey S Greene. Identification and Development of Therapeutics for COVID-19. mSystems. 2021, 6(6), e0023321.

16. Ch R, Rey G, Ray S, Jha P, et al., Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells. Nat Commun. 2021, 12, 377.

17. Ray S#, Reddy AB. COVID-19 management in light of the circadian clock. Nat Rev Mol Cell Biol. 2020, 21(9), 494-495.

18. Kumar V, Ray S, Aggarwal S, Biswas D, et al., Multiplexed quantitative proteomics provides mechanistic cues for malaria severity and complexity. Commun Biol. Nature 2020, 3(1), 683.

19. Rajarshi K, Khan R, Singh MK, Ranjan T, Ray S*, Ray S. Essential functional molecules associated with SARS-CoV-2 infection: Potential therapeutic targets for COVID-19. Gene. 2021, 768,145313. 

20. Ray S#, Srivastava S. Virtualization of Science Education: A Lesson from the COVID-19 Pandemic. J Proteins Proteom. 2020, 11, 77-80.

21. Ray S, Srivastava S. COVID-19 Pandemic: Hopes from Proteomics and Multi-Omics Research. Omics 2020. 24(8), 457-459.

22. Kumar V, Ray S, Ghantasala S, Srivastava S. An integrated quantitative proteomics workflow for cancer biomarker discovery and validation in plasma. Front Oncol. 2020,10, 543997.

23. Ray S, Valekunja UK, Stangherlin A, Howell SA, et al., Circadian rhythms in the absence of the clock gene Bmal1. Science. 2020, 367(6479), 800-806 [Featured in Science. 2020, 367(6479), 740-741].

24. Ray S#, Lach R, Heesom KJ, Valekunja UK, et al., Phenotypic proteomic profiling identifies a landscape of targets for circadian clock-modulating compounds. Life Sci Alliance. 2019, 2(6), e201900603.

25. Rey G, Milev NB, Valekunja UK, Ch R, Ray S, et al., Metabolic oscillations on the circadian time scale in Drosophila cells lacking clock genes. Mol Syst Biol. 2018, 14(8), e8376 [Featured on journal cover page, and in Mol Syst Biol. 2018,14(9), e8567].

26. Ray S, Patel SK, Venkatesh A, Chatterjee G, et al., Quantitative proteomics analysis of Plasmodium vivax induced alterations in human serum during the acute and convalescent phases of infection. Nature Sci Rep. 2017, 7(1), 4400.

27. Ray S, Patel SK, Venkatesh A, Bhave A, et al., Clinicopathological analysis and multipronged quantitative proteomics reveal oxidative stress and cytoskeletal proteins as possible markers for severe vivax malaria. Nature Sci Rep. 2016, 6, 24557.

28. Ray S, Reddy AB. Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness. Bioessays. 2016, 38(4), 394-405.

29. Venkatesh A, Patel SK, Ray S, Chatterjee G, et al., Proteomics of Plasmodium vivax malaria: progress and potential. Expert Rev Proteomics. 2016, 13(8), 771-782.

30. Ray S, Kumar V, Bhave A, Singh V, et al., Proteomic analysis of Plasmodium falciparum induced alterations in humans from different endemic regions of India to decipher malaria pathogenesis and identify surrogate markers of severity. J Proteomics. 2015, 127(Pt A):103-13.

31. Shah V, Ray S, Srivastava S. Calibration-free concentration analysis of protein biomarkers in human serum using surface plasmon resonance. Talanta 2015, 144, 801-808.

32. Reddy JP, Sinha S, Ray S, Sathe GJ, et al., Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PLoS One. 2015, 10(4), e0120620.

33. Reddy JP, Ray S, Sathe GJ, Gajbhiye A, et al., Comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J Proteomics. 2015, 114, 247-262.

34. Sharma S, Ray S, Mukherjee S, Moiyadi A, Sridhar E, Srivastava S. Multipronged quantitative proteomic analyses indicate modulation of various signal transduction pathways in human meningiomas. Proteomics. 2015, 15(2-3), 394-407.

35. Reddy JP, Ray S, Sathe GJ, Keshava Prasad TS, et al., Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone. Omics. 2015, 19(1), 12-23.

36. Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics. 2015, 15(2-3), 218-231.

37. Reddy PJ*, Ray S*, Srivastava S. The quest of the human proteome and the missing proteins: digging deeper. Omics 2015, 19(5), 276-282.

38. Ray S, Bhave A, Srivastava S. Brainstorming the new avenues for translational proteomics research: first Indo-US bilateral proteomics workshop. Current Proteomics 2015, 12, 75-79.

39. Gupta S*, Reddy JP*, Ray S*, Atak A, et al., Meeting Report: “Proteomics from Discovery to Function:” 6th Annual Meeting of Proteomics Society, India and International Conference-A Milestone for the Indian Proteomics Community. Omics 2015, 19(6): 329-331.

40. Gupta S*, Venkatesh A*, Ray S*, Srivastava S. Challenges and prospects for biomarker research: a current perspective from biomarker research. Biochim Biophys Acta. 2014, 1844(5), 899-908.

41. Ray S, Patel S, Kumar V, Damahe J. Srivastava S. Differential expression of serum/plasma proteins in various infectious diseases: overlapping and inimitable signatures. Proteomics Clin. Appl. 2014, 8, 53-72.

42. Sharma S*, Ray S*, Moiyadi A, Sridhar E, Srivastava S. Quantitative proteomic analysis of meningiomas for the identification of surrogate protein markers. Nature Sci Rep. 2014, 4, 7140.

43. Ray S, Moiyadi A, Srivastava S.  Biorepositories for cancer research in developing countries. Nat Rev Clin Oncol. 2013, 10, 434-436.

44. Srivastava S, Özdemir V, Ray S, et al., E-learning booster in developing world. Nature 2013, 501(7467), 316.

45. Ray S, Renu D, Srivastava R, Gollapalli K, et al., Proteomic investigation of falciparum and vivax malaria for identification of surrogate protein markers. PLoS One 2012, 7(8), e41751.

46. Ray S, Srivastava R, Tripathi K, Vaibhav V, Patankar S, Srivastava S. Serum proteome changes in dengue virus infected patients from a dengue endemic area of India: Towards new molecular targets? Omics 2012, 16(10), 527-536.

47. Ray S, Kamath KS, Srivastava R, Raghu D, et al., Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response. J Proteomics. 2012, 75, 3063-3080.

48. Srivastava R*, Ray S*, Vaibhav V, Gollapalli K, et al., Serum profiling of leptospirosis patients to investigate proteomic alterations. J Proteomics. 2012, 76, 56-68.

49. Gollapalli K, Ray S, Srivastava R, Renu D, et al., Investigation of serum proteome alterations in human glioblastoma multiforme. Proteomics 2012, 12(14), 2378-2390.

50. Ray S, Koshy NR, Diwakar S, Nair B, Srivastava S. Sakshat Labs: India’s virtual proteomics initiative. PLoS Biol. 2012, 10(7): e1001353.

51. Ray S, Koshy NR, Reddy PJ, Srivastava S. Virtual Labs in Proteomics: New E-Learning Tools.  J Proteomics. 2012, 75, 2515-2525.

52. Reddy PJ, Sadhu S, Ray S, Srivastava S. Cancer biomarker detection by surface plasmon resonance biosensors. Clin Lab Med. 2012, 32(1), 47-72.

53. Kamal SM, Warnich L, Ferguson LR, Srivastava S, Ray S, et al., Forward Look: Tenth Anniversary of the Human Genome Sequence and 21st Century Postgenomics Global Health - A Close Up on Africa and Women’s Health. Curr Pharmacogenomics Person Med. 2011, 9(3), 148-155.

54. Ray S, Reddy PJ, Choudhary S, Raghu D, Srivastava S. Emerging nanoproteomics approaches for disease biomarker detection: A current perspective.            J Proteomics. 2011, 74, 2660-2681.

55. Ray S, Ray S, D’souza R, Srivastava S. Nanotechniques and proteomics: An integrated platform for diagnostics, targeted therapeutics and personalized medicine. Curr Pharmacogenomics Person Med. 2011, 9(4), 264-285.

56. Ray S, Reddy PJ, Jain R, Gollapalli K. Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011, 11, 2139-2161.

57. Ray S, Chandra H, Srivastava S. Nanotechniques in proteomics: current status promises and challenges. Biosens Bioelectron. 2010, 25(11), 2389-2401.

58. Ray S, Mehta G, Srivastava S. Label-free detection techniques for protein microarrays: prospects, merits and challenges. Proteomics 2010, 10(4), 731-74

 

B. Book chapters [6]

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1. Banerjee S, Das S, Halder N, Bisht S, Talukdar A, Ray S#. Chronobiological Aspects of Aging, Neurodegeneration, and Inflammation. In: Jha, P.K., Bouaouda, H. (eds) Circadian Rhythms, Sleep and Inflammation. Progress in Inflammation Research, vol 93. Springer, Cham. 2024. https://doi.org/10.1007/978-3-031-74744-1_8.

2. Bhatnagar A, Puppala A, Rankawat S, Ray S#. Role of Circadian Rhythms in Metabolic Syndrome. In: "Metabolic Syndrome from Mechanisms to Interventions" Elsevier 2024, DOI: https://doi.org/10.1016/B978-0-323-85732-1.00006-2, pp 199-218.

3. Ray S#, Srivastava S, Diwakar S, Nair B, Özdemir V. Delivering on the Promise of Bioeconomy in Developing World: Link it with Social Innovation and Education. In: "Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges" Springer 2016, DOI: https://doi.org/10.1007/978-81-322-2837-0_6, pp 73-81.

4. Ray S, Özdemir V. Angel Philanthropy and Crowdfunding to Accelerate Cancer Research in Developing World. In: "Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges" Springer 2016, DOI: https://doi.org/10.1007/978-81-322-2837-0_5, pp 65-71.

5. Gupta S, Ray S, Talukdar A, Sehgal K, Moiyadi A, Srivastava S. Geographic pervasiveness of cancer: Prospects of novel biomarker and therapeutic research in developing countries using OMICs approaches. In: "Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges" Springer 2016, DOI: https://doi.org/10.1007/978-81-322-2837-0_2, pp 9-17.

6. Syed P, Ray S, Gollapalli K, Srivastava S. Serum proteomics for studying disease pathogenesis and identification of disease biomarkers. In: Proteomics: targeted technology, innovations and applications. Caister Academic Press 2014, ISBN: 978-1-908230-46-1, pp 1-17.

 

C. Patents (Granted/filed) [6]

1. Srivastava S, Patankar S, Ray S, Thatte U, Gogtay N, Renu D, et al. Protein Biomarkers for Plasmodium falciparum Malaria [India-Patent No. 512772; Granted, Award Date: 20/02/2024)].

2. Srivastava S, Ray S, Shah GV. Label-Free Method for Detection and Quantification of Protein Biomarkers [India-Patent No. 394414 (Granted, Award Date: 07/04/2022)].

3. Srivastava S, Patankar S, Ray S, Renu D, Dikshit JB, Subramanian K, Gogtay N, Thatte U, Taur S. Protein Biomarkers for Plasmodium vivax Malaria [IPA No. 2195/Mum/2012; Patent Number: 336131 (Granted)].

4. Srivastava S, Srivastava R, Ray S. Protein biomarkers for leptospirosis [IPA No. 1907/MUM/2012; Patent Number: 336123 (Granted)].

5. Srivastava S, Ray S, Shah V. Label-free method for detection and quantification of protein biomarkers [IPA No. 2587/MUM/2015; Publication Date: 05/05/2017].

6. Srivastava S, Kumar V, Ray S. Method for detection of protein biomarkers for different complications of falciparum malaria [Patent Application No. 202021002027; Filing Date: 16/01/2020].

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D. Magazine Editorials [2]

1. Ray S#, Srivastava S. Trends and roadblocks in proteomics research in India. Nature India (Special Issue: Proteomics Research in India) 2015, 6-8, doi: 10.1038/nindia.2015.111.

2. Ray S#, Srivastava S, Nair B, Diwakar S. E-learning resources and virtual labs. Nature India (Special Issue: Proteomics Research in India) 2015, 13-14, doi: 10.1038/nindia.2015.114.