NICED : Scientists

Research Experience

Dr. Kaushik Kumar Dey is an accomplished interdisciplinary scientist whose research integrates mass spectrometry - based proteomics and metabolomics with neurobiology, infectious disease biology, and systems biology. His overarching goal is to combine advanced proteomics with translational systems medicine to identify diagnostic and mechanistic biomarkers for major human diseases, including neurodegenerative disorders, cancer, and antimicrobial resistance (AMR). His work brings together deep expertise in quantitative proteomics/metabolomics, bioinformatics, and multi-omics integration to explore molecular mechanisms underlying complex biological systems.
Currently serving as Scientist (Proteomics) at the ICMR-National Institute for Research in Bacterial Infections (NIRBI), Dr. Dey is leading efforts to establish a national hub for advanced proteomics research focused on infectious diseases and AMR. His laboratory is implementing cutting-edge proteomics and systems biology workflows using high-resolution mass spectrometry platforms to investigate host-pathogen interactions and molecular pathways driving bacterial pathogenesis. Beyond developing analytical pipelines, he plays a pivotal role in training researchers and scientific staff, mentoring young investigators, and supporting ICMR's intramural and extramural research programs, fostering translational collaborations that link proteomic discovery to clinical relevance.
From 2016 to 2024, Dr. Dey pursued an extensive postdoctoral fellowship with Prof. Junmin Peng and Dr. Liqin Zhu at St. Jude Children's Research Hospital (USA), where he developed and applied state-of-the-art mass spectrometry workflows to study Alzheimer's disease (AD). His pioneering work combined deep proteome, phosphoproteome, and metabolome profiling across human brain, cerebrospinal fluid (CSF), and serum, revealing dynamic signaling networks, mitochondrial dysfunction, and sex-specific molecular signatures underlying AD progression. Through integrative multi-omics analyses, he identified a mitochondrial-centered molecular signature that advanced the mechanistic understanding of neurodegeneration and laid the groundwork for precision therapeutic strategies.
Dr. Dey earned his Ph.D. in Cancer Biology under Prof. Mahitosh Mandal at the Indian Institute of Technology Kharagpur (IIT KGP). His doctoral research employed comparative mass spectrometry-based proteomics to identify early diagnostic biomarkers and elucidate the oncogenic role of S100A7 in oral squamous cell carcinoma (OSCC). His work uncovered key molecular drivers of oral tumorigenesis through the p38/MAPK and RAB2A signaling pathways, resulting in several high-impact publications and national recognitions, including ICMR Senior Research Fellowships. His discoveries contributed to developing molecular diagnostic markers and potential therapeutic targets for oral cancer.Before his academic career, Dr. Dey gained industrial R&D experience at Avesthagen Limited (Biopharma Group), where he contributed to the process development of recombinant therapeutics and monoclonal antibodies, including Bevacizumab, Rituximab, and Darbepoetin. His expertise covered upstream and downstream bioprocessing, chromatography-based purification, and analytical assay validation, providing a strong translational and regulatory foundation that complements his academic pursuits.
Through a career spanning industry, academia, and government research, Dr. Dey continues to drive innovation in multi-omics discovery and systems biology. His multidisciplinary expertise, translational vision, and leadership in establishing advanced proteomics capabilities position him as a key contributor to India's efforts in precision diagnostics, biomarker discovery, and omics-driven biomedical innovation.
 

Research Interest

My research focuses on integrating mass spectrometry-based proteomics and metabolomics with systems biology to address critical challenges in antimicrobial resistance (AMR) and neurodegenerative diseases. At ICMR-NIBRI, Kolkata, my goal is to advance multiomics-driven discovery and translational applications in infection biology, AMR surveillance, and neuroinflammation. I aim to establish a comprehensive multiomics research hub at NIBRI that bridges infection biology, AMR, and neurodegeneration through proteomics-enabled precision medicine and translational biomarker discovery, in alignment with ICMR's national health priorities.

Key Focus Areas

1. AMR Mechanisms and Functional Biomarkers:Profiling host-pathogen proteome and metabolome to identify molecular mechanisms underlying antibiotic tolerance, persistence, and reversible resistance.
2. Host-Pathogen Multiomics:Integrating proteomics, metabolomics, and lipidomics to reveal molecular signatures of emerging and re-emerging infections relevant to India.
3. Epigenetic and Post-Translational Modifications:Investigating histone and protein PTMs that regulate immune response, bacterial persistence, and pathogen adaptation.
4. AMR-Neurodegeneration Interface:Exploring infection-induced neuroinflammation and shared molecular pathways linking chronic infection, immune dysregulation, and neurodegenerative disorders such as Alzheimer's and Parkinson's disease.
5. Translational Applications:Developing LC-MS-based, culture-independent diagnostic and biomarker platforms for infection detection, drug susceptibility testing, and early-stage neurodegenerative disease screening.
    

Membership/ Fellow of Professional Societies/ Associations

1. AssociateMemberofAmericanAssociationforCancerResearch(AACR
2. LifeMemberIndianassociationofCancerResearch(IACR)
3. Annual Member AmericanSocietyforMassSpectrometry(ASMS
4. LifeandElectedMemberIndianSocietyforMassSpectrometry(ISMAS)
5. LifeMemberProteomicsSocietyofIndia(PSI)
6. Member HumanProteomeorganization (HUPO)
7. Life Member Indian Academy of Neurosciences (IAN)
8. Life member The Society of Biological Chemists (SBC)
    

Honors, Awards, and Fellowships

1. Young Scientist Award(2025) - International Conference on Advances in Systems Biology (ICASB-2025), Doctor Hari Singh Gour Vishwavidyalaya (Central University), Sagar, Madhya Pradesh, India.
2. SERB-ANRF Travel Fellowship (2024) - XLII Annual Meeting of Indian Academy of Neurosciences, Bengaluru, India.International Travel Grant(2023) - 46th Annual Meeting of the Japan Neuroscience Society, Japan.
3. Ramalingaswami Re-Entry Fellowship (2022) - Department of Biotechnology (DBT), Government of India, New Delhi, India.
4. National Institute Travel Grant(2015) :34th Annual Convention of Indian Association for Cancer Research (IACR), IIT Kharagpur, Jaipur, India.
5. Independent Senior Research Fellowship (2014-2016): Indian Council of Medical Research (ICMR), New Delhi, India).
6. International Institute Travel Grant(2014): AACR Annual Meeting, IIT Kharagpur, San Diego, USA.
7. DST International Travel Grant(2012): 5th Oncology Biomarker Summit, Department of Science and Technology, Zurich, Switzerland.
    

Publications

1. Kaushik Kumar Dey*, Jay M. Yarbro, Danting Liu, Xian Han, Zhen Wang, Yun Jiao, Zhiping Wu, Shu Yang, DongGeun Lee, Abhijit Dasgupta, Zuo-Fei Yuan, Xusheng Wang, Liqin Zhu, and Junmin Peng*. Deep serum proteome profiling identifies sex-influenced patterns in a murine model of Alzheimer's disease. Journal of Proteome Research, 22(12), 3487-3502, 2023. https://doi.org/10.1021/acs.jproteome.3c00689 (JIF: 4.46).
2. Cheng Tian, Liyuan Li, Qingfei Pan, Beisi Xu, Yizhen Li, Li Fan, Anthony Brown, Michelle Morrison, Kaushik Dey, Jun J. Yang, Jiyang Yu, Evan S. Glazer, Liqin Zhu. Spatiotemporal regulation of cholangiocarcinoma growth and dissemination by peritumoral myofibroblasts in a Vcam1-dependent manner. Oncogene, 42, 476-488, 2023. https://doi.org/10.1038/s41388-023-02639-0 (JIF: 8.75).
3. Xiaojun Sun*, Huan Sun*, Xian Han, Ping-Chung Chen, Yun Jiao, Zhiping Wu, Xue Zhang, Zhen Wang, Mingming Niu, Kaiwen Yu, Danting Liu, Kaushik Kumar Dey, Ariana Mancieri, Yingxue Fu, Ji-Hoon Cho, Yuxin Li, Suresh Poudel, Tess C. Branon, Alice Y. Ting, Junmin Peng*. Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling. Analytical Chemistry, 94(13), 5325-5334, 2022. https://doi.org/10.1021/acs.analchem.1c05212 (JIF: 8.00).
4. Bing Bai*, David Vanderwall*, Yuxin Li, Xusheng Wang, Suresh Poudel, Hong Wang, Kaushik Kumar Dey, Ping-Chung Chen, Ka Yang, Junmin Peng. Proteomic Landscape of Alzheimer's Disease: Novel Insights into Pathogenesis and Biomarker Discovery. Molecular Neurodegeneration, 16(1), 1-16, 2021. https://doi.org/10.1186/s13024-021-00474-z (JIF: 18.18).
5. Kaushik Kumar Dey*, Hong Wang*, Yuxin Li, Mingming Niu, Ji-Hoon Cho, Xusheng Wang, Bing Bai, Yun Jiao, Surendhar Reddy Chepyala, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Junmin Peng. Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer's disease. Molecular Neurodegeneration, 15(1), 1-20, 2020. https://doi.org/10.1186/s13024-020-00384-6 (JIF: 18.18).
6. Danting Liu, Shu Yang, Kanisha Kavdia, Jeffrey M. Sifford, Zhiping Wu, Boer Xie, Zhen Wang, Vishwajeeth R. Pagala, Hong Wang, Kaiwen Yu, Kaushik K. Dey, Anthony A. High, Thomas G. Beach, and Junmin Peng. Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry.Journal of Proteome Research, 2020, 20(1), 337-345. https://doi.org/10.1021/acs.jproteome.0c00426 (JIF: 4.46).
7. Bing Bai*, Xusheng Wang*, Yuxin Li*, Ping-Chung Chen*, Kaiwen Yu, Kaushik Kumar Dey, Jay M. Yarbro, Xian Han, Brianna M. Lutz, Shuquan Rao, Yun Jiao, Jeffrey M. Sifford, Jonghee Han, Minghui Wang, Haiyan Tan, Timothy I. Shaw, Ji-Hoon Cho, Suiping Zhou, Hong Wang, Mingming Niu, Ariana Mancieri, Kaitlynn A. Messler, Xiaojun Sun, Zhiping Wu, Vishwajeeth Pagala, Anthony A. High, Wenjian Bi, Hui Zhang, Hongbo Chi, Vahram Haroutunian, Bin Zhang, Thomas G. Beach, Gang Yu, and Junmin Peng (*Equal Contribution). Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression.Neuron, 2020, 105(6), 975-991. https://doi.org/10.1016/j.neuron.2019.12.015 (JIF: 18.69).
8. Zhen Wang*, Kanisha Kavdia*, Kaushik Kumar Dey, Vishwajeeth R. Pagala, Kiran Kodali, Danting Liu, Dong Geun Lee, Huan Sun, Surendhar Reddy Chepyala, Ji-Hoon Cho, Anthony A. High, and Junmin Peng (*Equal Contribution). High-throughput and Deep-Proteome Profiling by 16-plex Tandem Mass Tag Labeling Coupled with Two-Dimensional Chromatography and Mass Spectrometry.JoVE (Journal of Visualized Experiments), 2020, e61684, 1-18. https://dx.doi.org/10.3791/61684 (JIF: 1.40).
9. Kaushik Kumar Dey*, Hong Wang*, Mingming Niu, Bing Bai, Xusheng Wang, Yuxin Li, Ji-Hoon Cho, Haiyan Tan, Ashutosh Mishra, Anthony A. High, Ping-Chung Chen, Zhiping Wu, Thomas G. Beach, and Junmin Peng (*Equal Contribution). Deep Undeleted Human Serum Proteome Profiling Toward Biomarker Discovery for Alzheimer's Disease.Clinical Proteomics, 2019, 16(1), 1-12. https://doi.org/10.1186/s12014-019-9237-1 (JIF: 5.00).
10. Ipsita Pal, Y. Rajesh, Payel Banik, Goutam Dey, Kaushik Kumar Dey, Rashmi Bharti, Deboki Naskar, Sandipan Chakraborty, Sudip K. Ghosh, Swadesh K. Das, Luni Emdad, Subhas Chandra Kundu, Paul B. Fisher, and Mahitosh Mandal. Prevention of Epithelial to Mesenchymal Transition in Colorectal Carcinoma by Regulation of the E-Cadherin-β-Catenin-Vinculin Axis.Cancer Letters, 2019, 452, 254-263. https://doi.org/10.1016/j.canlet.2019.03.008 (JIF: 8.67).
11. Y Rajesh, Anupam Banerjee, Ipsita Pal, Angana Biswas, Subhayan Das, Kaushik Kumar Dey, Neelkamal Kapoor, Ananta Kumar Ghosh, Pralay Mitra, Mahitosh Mandal. Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management.Biochimica et Biophysica Acta (BBA) - General Subjects, 2019, 1863(7), 1196-1209. https://doi.org/10.1016/j.bbagen.2019.04.015 (JIF: 3.94)
12. Boer Xie*, Yuanyuan Wang*, Drew R. Jones*, Kaushik Kumar Dey, Xusheng Wang, Yuxin Li, Ji-Hoon Cho, Haiyan Tan, Junmin Peng. Isotope Labeling-assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling.Analytical Chemistry, 2018, 90(14), 8538-8545. https://doi.org/10.1021/acs.analchem.8b01591 (JIF: 8.08)
13. Aditya Parekh, Subhayan Das, Sheetal Parida, Chandan Das, Debabrata Dutta, Sanjaya Mallick, Pei-Hsun Wu, B. N. Prashanth Kumar, Rashmi Bharti, Goutam Dey, Kacoli Banerjee, Shashi Rajput, Deblina Bharadwaj, Ipsita Pal, Kaushik K Dey, Y Rajesh, Bikash Jena, Angana Biswas, Payel Banik, Anjan Pradhan, Swadesh Das, Amit Das, Santanu Dhara, Paul Fisher, Denis Wirtz, Gordon Mills, Mahitosh Mandal. Multi-nucleated cells use ROS to induce breast cancer chemo-resistance in vitro and in vivo.Oncogene, 2018, 37(33), 4546-4561. https://doi.org/10.1038/s41388-018-0272-6 (JIF: 8.75)
14. Rashmi Bharti, Goutam Dey, Indranil Banerjee, Kaushik Kumar Dey, Sheetal Parida, Prashanth B. N. Kumar, Chandan Kanta Das, Ipsita Pal, Manabendra Mukherjee, Mridula Misra, Anjan K. Pradhan, Luni Emdad, Swadesh K. Das, Paul B. Fisher, Mahitosh Mandal. Somatostatin receptor targeted liposomes with Diacerein inhibit IL-6 for breast cancer therapy.Cancer Letters, 2016, 388, 292-302. https://doi.org/10.1016/j.canlet.2016.12.021 (JIF: 8.67)
15. Sheetal Parida, Chitranjit Maiti, Y Rajesh, Kaushik K Dey, Ipsita Pal, Rusha Patra, Dibakar Dhara, Pranab Kumar Dutta, Mahitosh Mandal. Gold nanorod embedded reduction responsive block copolymer micelle-triggered drug delivery combined with photo thermal ablation for targeted cancer therapy.Biochimica et Biophysica Acta (BBA) - General Subjects, 2017, 1861(1), 3039-3052. https://doi.org/10.1016/j.bbagen.2016.10.004 (JIF: 3.94)
16. Kaushik K Dey*, Rashmi Bharti, Goutam Dey, Ipsita Pal, Y Rajesh, Sandip Chavan, Subhayan Das, Chandan Kanta Das, Bikash Chandra Jena, Priyanka Halder, Jay Gopal Ray, Indranil Kulavi, Mahitosh Mandal*. S100A7 has an oncogenic role in oral squamous cell carcinoma by activating p38/MAPK and RAB2A signaling pathway.Cancer Gene Therapy, 2016, 11, 382-391. https://doi.org/10.1038/cgt.2016.43 (Joint Corresponding Author) (JIF: 5.85)
17. Ipsita Pal, Kaushik Kumar Dey, Madhuri Chaurasia, Sheetal Parida, Subhayan Das, Y Rajesh, Kulbhushan Sharma, Tamohan Chaudhuri, Mahitosh Mandal. Cooperative effect of BI-69A11 and Celecoxib enhances radio sensitization by modulating DNA damage repair in colon carcinoma.Tumor Biology, 2016, 37(5), 6389-6402. https://doi.org/10.1007/s13277-015-4399-6 (JIF: 3.65)
18. Kaushik Kumar Dey, Ipsita Pal, Rashmi Bharti, Goutam Dey, B. N. Prashanth Kumar, Shashi Rajput, Aditya Parekh, Sheetal Parida, Priyanka Halder, Indranil Kulavi, Mahitosh Mandal. Identification of RAB2A and PRDX1 as the potential biomarkers for Oral Squamous Cell Carcinoma using mass spectrometry based comparative proteomics approach.Tumor Biology, 2015, 36(12), 9829-9837. https://doi.org/10.1007/s13277-015-3758-7 (JIF: 3.65)
19. Ipsita Pal, Sheetal Parida, B. N. Prashanth Kumar, Payel Banik, Kaushik Kumar Dey, Sandipan Chakraborty, Sujit Bhutia, Mahitosh Mandal. Blockade of autophagy enhances pro-apoptotic potential of BI-69A11, a novel Akt inhibitor, in colon carcinoma.European Journal of Pharmacology, 2015, 765, 217-227. https://doi.org/10.1016/j.ejphar.2015.08.039 (JIF: 4.43)
20. Dey G, Bharti R, Dhanarajan G, Das S, Dey KK, Kumar B. N., Sen R, Mandal M. Marine lipopeptide Iturin A inhibits Akt mediated GSK3β and FoxO3a signaling and triggers apoptosis in breast cancer.Scientific Reports, 2015, 5(1), 1-14. https://doi.org/10.1038/srep10316 (JIF: 4.99)
21. Pal I, Sarkar S, Rajput S, Dey KK, Chakraborty S, Dash R, Das S. K., Sarkar D, Barile E, De S. K., Pellecchia M, Fisher P. B., Mandal M. BI-69A11 enhances susceptibility of colon cancer cells to mda-7/IL-24-induced growth inhibition by targeting Akt.British Journal of Cancer, 2014, 111(1), 101-111. https://doi.org/10.1038/bjc.2014.227 (JIF: 7.64)
22. B. N. Prashanth Kumar, Shashi Rajput, Kaushik Kumar Dey, Subhasis Das, Abhijit Majumder, Mahitosh Mandal. Celecoxib alleviates tamoxifen-instigated angiogenic effects by ROS-dependent VEGF-A/VEGFR2 autocrine signaling.BMC Cancer, 2013, 13, 273. https://doi.org/10.1186/1471-2407-13-273 (JIF: 4.63)
23. Rajput S, Kumar B. N., Dey KK, Pal I, Parekh A, Mandal M. Molecular targeting of Akt by thymoquinone promotes G1 arrest through translation inhibition of cyclin D1 and induces apoptosis in breast cancer cells.Life Sciences, 2013, 93, 783-790. https://doi.org/10.1016/j.lfs.2013.09.009 (JIF: 6.78)
24. Das S, Dey KK, Dey G, Pal I, Majumder A, Maiti Choudhury S, Kundu S. C., Mandal M. Antineoplastic and apoptotic potential of traditional medicines thymoquinone and diosgenin in squamous cell carcinoma.PLoS One, 2012, 7(10), e46641. https://doi.org/10.1371/journal.pone.0046641 (JIF: 3.75)
25. Das S, Dey KK, Bharti R, Maiti Choudhury S, Maiti S, Mandal M. PKI 166 induced redox signaling and apoptosis through activation of p53, MAP kinase and caspase pathway in epidermoid carcinoma.Journal of Experimental Therapeutics and Oncology, 2012, 10(2), 139-153. https://doi.org/10.3727/096504012X13500414679808 (JIF: 1.1)
     

Book Chapters

1. Kaushik Kumar Dey*, Huan Sun*, Zhen Wang, Mingming Niu, Hong Wang, Yun Jiao, Xiaojun Sun, Yuxin Li, and Junmin Peng (*Equal Contribution). Proteomic Profiling of Cerebrospinal Fluid by 16-Plex TMT-Based Mass Spectrometry.Methods in Molecular Biology, 2022, 21-37. https://doi.org/10.1007/978-1-0716-1936-0_3 (JIF: 1.16)

 

Patents

1. Patent:Detection of Alzheimer's Disease Using Specific Biomarkers, United States Patent Application No. US20230085163A1, Published on March 23, 2023 and currently pending review by the United States Patent and Trademark Office (USPTO). This invention discloses a mass spectrometry-based method for the detection and classification of Alzheimer's disease using protein biomarkers identified in cerebrospinal fluid and blood, aiming to improve early diagnosis and precision therapeutic strategies; Inventor: Junmin Peng, Hong Wang, Kaushik Kumar Dey