30. Shahinuzzaman, A.; Chakrabarty, J. K.; Kamal, A. H. M.; Chowdhury, S. M*. Improvement of in solution digestion protocol of methanol-chloroform precipitated cellular proteomics sample. Journal of Proteome Research –submitted, 2019-*Corresponding author

29. Chakrabarty, J. K.; Kamal, A. H. M.; Shahinuzzaman, A.; Chowdhury, S. M*. Inflammatory Proteomic Network Analysis of Polarized Macrophages. Methods in Molecular Biology, Springer Protocols. Submitted (Book Chapter). *-Corresponding author

28. Chakrabarty, J. K., Sadananda, S. C., Bhatt, A., Naik, A., Chowdhury, S. M*. High confidence identification of cross-linked peptides by an enrichment-based dual cleavable cross-linking technology (DUCCT) and data analysis tool Cleave-XL. J. Am. Soc. Mass Spectrom. Accepted 2019.

27. Ricci, Contessa A.; Kamal, Abu Hena Mostafa.; Chakrabarty, Jayanta K.; Fuess, Lauren E.; Mann, Whitney T..; Jinks Lea R.; Brinkhuis, Vanessa.; Chowdhury, Saiful M.; Mydlarz, Laura D. Proteomic investigation of a diseased gorgonian coral indicates disruption of essential cell function and investment in inflammatory and other immune processes-Integr Comp Biol. 2019 Jun 21. pii: icz107.

26. Kamal, A.H.M.; Aloor, Jim J.; Fessler, M. B.; Chowdhury, S.M*.-Crosslinking Proteomics Indicates Effects of Simvastatin on the TLR2 interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade”-Mol Cell Proteomics. 2019 Sep;18(9):1732-1744.-*Corresponding author

25. Fang, Z.; Baghdady, Y. Z.; Schug, K. A.; Chowdhury, S. M.* Evaluation of Different Stationary Phases in the Separation of Inter-crosslinked Peptides. –J Proteome Res. 2019 Apr 5;18(4):1916-1925.*-Corresponding author

24. Wanigasekara, M. S. K.; Huang X.; , Chakrabarty, J. K.; Bugarin, A; Chowdhury, S. M*. Arginine-Selective Chemical Labeling Approach for Identification and Enrichment of Reactive Arginine Residues in Proteins. ACS Omega, 2018, 3 (10), pp 14229–14235. –*Corresponding author

23. Perry, B.; Andrew, A.; Kamal, A. H. M.; Card, D.; Schield, D.; Pasquesi, G.; Pellegrino, M.; Mackessy, S.; Chowdhury, S. M.; Secor, S.; Castoe, T. Multi-species comparisons of snakes suggest that insulin and stress response signaling modulate post-feeding intestinal regeneration.Proc Biol Sci. 2019 Jul 10;286(1906):20190910.

22. Kamal, A. H. M.; Fessler, M. B.; Chowdhury, S. M*. Comparative and network-based proteomic analysis of low dose ethanol- and lipopolysaccharide-induced macrophages. PloS one 2018, 13, e0193104. –*Corresponding author

21. Kamal, A. H. M.; Chakrabarty, J. K.; Udden, S. M. N.; Zaki, M. H.; Chowdhury, S. M. Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages. Scientific reports 2018, 8, 164. *-Corresponding author

20. Mahbub, M. M.; Chowdhury, S. M*.; Christensen, S. M*. Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8. Mobile DNA 2017, 8, 16. *-Corresponding author

19. Bhawal, R. P.; Shahinuzzaman, A. D.; Chowdhury, S. M*. Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry. Journal of the American Society for Mass Spectrometry 2017, 28, 704-707.-Emerging investigator Focus, * -Corresponding Author

18. Chakrabarty, J. K.; Naik, A. G.; Fessler, M. B.; Munske, G. R.; Chowdhury, S. M*. Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking. Analytical chemistry 2016, 88, 10215-10222. * -Corresponding Author

17. Wanigasekara, M. S.; Chowdhury, S. M. Evaluation of chemical labeling methods for identifying functional arginine residues of proteins by mass spectrometry. Analytica chimica acta 2016, 935, 197-206. * -Corresponding Author

16. Chowdhury, Saiful M; Zhu, Xuewei; Aloor, Jim J; Azzam, Kathleen M; Gabor, Kristin A; Ge, William; Addo, Kezia A; Tomer, Kenneth B; Parks, John S; Fessler, Michael B; Proteomic analysis of ABCA1-null macrophages reveals a role for stomatin like protein-2 in raft composition and Toll like Receptor signaling. Molecular & Cellular Proteomics - mcp. M114. 045179 -2015

15. Bhawal, Ruchika P; Sadananda, Sandhya C; Bugarin, Alejandro; Laposa, Brian; Chowdhury, Saiful M; Mass spectrometry cleavable strategy for identification and differentiation of prenylated peptides - Analytical Chemistry - 2015 - *Corresponding author

14. Bian, S; Chowdhury, SM*; Profiling Protein-Protein Interactions and Protein Structures Using Chemical Cross-linking and Mass Spectrometry - Austin J Biomed Eng, 1(4) - 1017 - 2014-*Corresponding author

13. Chowdhury, Saiful M; Munske, Gerhard R; Yang, Jonathon; Zhukova, Daria; Nguyen, Hamilton; Bruce, James E; Solid phase N terminal peptide enrichment study by optimizing trypsin proteolysis on homoarginine modified proteins by mass spectrometry - Rapid Communications in Mass Spectrometry - 28(6) P 635-644 - 2014. -*Corresponing author

12. Du X, Chowdhury, S. M, Manes, M. Wu S, Cumblidge, UM, Adkins, J. N., Anderson, G. A., Smith, R. D. – Xlink-Identifier: An automated data analysis platforms for confident identification of chemically cross-linked peptides using tandem mass spectrometry –J Proteome Res. 2011 Mar 4;10(3):923-31.

11. Shi L, Chowdhury S. M., Smallwood H.S., Yoon H., Mottaz-Brewer H.M., Norbeck A.D., McDermott J.E., Clauss TR.W., Heffron F, Smith R.D., Adkins J.N. Proteomics investigation of the time course responses of RAW 264.7 macrophages to infection with salmonella enterica –– Infect Immun 2009, 77, (8), 3227-33. Featured in Biological Science Division research highlights in PNNL. Link: http://www.pnl.gov/science/highlights/highlight.asp?id=656.

10. Chowdhury, S. M., Du. X, Tolić, N, Wu S, Moore, R. J., Mayer, M. U.,. Smith, R. D., Adkins, J. N. - Identification of cross-linked peptides containing a click-based enrichment group using sequential CID and ETD tandem mass spectrometry – Anal Chem 2009, 81, (13), 5524-32 – high-lighted in online news of Journal of Proteome Research. Link: http://pubs.acs.org/action/showStoryContent?doi=10.1021%2Fon.2009.06.29.395768.

9. Chowdhury, S. M., Shi, L, Yoon, H, Rommereim, L. M., Norbeck, A. D., Auberry K. J., Moore, R. J., Adkins J. N., Heffron, F. and Smith, R. D. - A method for investigating protein-protein interactions related to Salmonella Typhimurium pathogenesis”– J. Proteome Res., 2009, 8 (3), pp 1504–1514 – Ranked 15 in Top 20 most read articles in JPR for the March of 2009.

8. Du, X; Rorie, J; Chowdhury, S; Adkins, J; Anderson, G; Smith, R; Identification of Protein-Protein Interactions Using Chemical Cross-linking and CID and ETD Tandem Mass Spectrometry - MOLECULAR & CELLULAR PROTEOMICS - S33-S33 - 2009

7. Chowdhury, Saiful M; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J; Mayer, M Uljana; Smith, Richard D; Adkins, Joshua N; Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry - Analytical chemistry 81(13) - 5524-5532 - 2009

6. Rodland, K. D., Adkins, J. N., Ansong, C, Chowdhury, S, Manes, N. P., Shi, L., Yoon, H., Smith, R. D., Heffron, F. - Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella - Future Microbiology, 2008 3(6), 625-634. – Review

5. Chowdhury, S. M.; Munske, G. R.; Ronald, R. C.; Bruce, J. E., Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thio-ether bonds in peptides. Journal of Am. Soc. Mass Spectrom 2007, 18(3):493-501.

4. Chowdhury, S. M.; Munske, G. R.; Tang, X; Bruce, J. E., Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers. Anal. Chem. 2006, 78 (24):8183 -8193.

3. Chowdhury, S. M.; Munske, G. R.; Siems, W. F.; Bruce, J. E., A new maleimide-bound acid-cleavable solid-support reagent for profiling phosphorylation. Rapid Commun Mass Spectrom 2005, 19(7):899-909

2. Wnuk, S. F.; Chowdhury, S. M.; Garcia, P. I., Jr.; Robins, M. J., Stereodefined synthesis of O3'-labeled uracil nucleosides. 3'-[(17)O]-2'-Azido-2'-deoxyuridine 5'-diphosphate as a probe for the mechanism of inactivation of ribonucleotide reductases. J Org Chem 2002, 67(6):1816-9.

1. Hossain, M. A.; Mustafa, A. I.; Amin, M. N.; Chowdhury, S. M.- Studies on the quality of three selected varieties of rapeseed and mustard oils and oil cakes, Dhaka University Journal of Science (1997), 45(1), 23-29. Publisher: Dhaka University, CODEN: DJOSEM ISSN: 1022-2502.