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A draft map of the human proteome.
Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A. Kim MS, et al. Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302. Nature. 2014. PMID: 24870542 Free PMC article.
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling.
Zhong J, Sharma J, Raju R, Palapetta SM, Prasad TS, Huang TC, Yoda A, Tyner JW, van Bodegom D, Weinstock DM, Ziegler SF, Pandey A. Zhong J, et al. Database (Oxford). 2014 Feb 25;2014:bau007. doi: 10.1093/database/bau007. Print 2014. Database (Oxford). 2014. PMID: 24573880 Free PMC article.
Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis.
Sahasrabuddhe NA, Huang TC, Ahmad S, Kim MS, Yang Y, Ghosh B, Leach SD, Gowda H, Somani BL, Chaerkady R, Pandey A. Sahasrabuddhe NA, et al. J Proteomics. 2014 Aug 28;108:306-15. doi: 10.1016/j.jprot.2014.04.027. Epub 2014 Apr 24. J Proteomics. 2014. PMID: 24769236
A multi-omic analysis of human naïve CD4+ T cells.
Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. Mitchell CJ, et al. BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4. BMC Syst Biol. 2015. PMID: 26542228 Free PMC article.
Ablation of Dicer leads to widespread perturbation of signaling pathways.
Sahasrabuddhe NA, Huang TC, Kumar P, Yang Y, Ghosh B, Leach SD, Chaerkady R, Pandey A. Sahasrabuddhe NA, et al. Biochem Biophys Res Commun. 2015 Jul 31;463(3):389-94. doi: 10.1016/j.bbrc.2015.05.077. Epub 2015 May 30. Biochem Biophys Res Commun. 2015. PMID: 26032504 Free PMC article.
Identification of miR-145 targets through an integrated omics analysis.
Huang TC, Renuse S, Pinto S, Kumar P, Yang Y, Chaerkady R, Godsey B, Mendell JT, Halushka MK, Civin CI, Marchionni L, Pandey A. Huang TC, et al. Mol Biosyst. 2015 Jan;11(1):197-207. doi: 10.1039/c4mb00585f. Epub 2014 Oct 30. Mol Biosyst. 2015. PMID: 25354783 Free PMC article.
Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.
Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Kelkar DS, et al. Mol Cell Proteomics. 2014 Nov;13(11):3184-98. doi: 10.1074/mcp.M114.038299. Epub 2014 Jul 24. Mol Cell Proteomics. 2014. PMID: 25060758 Free PMC article.
Proteomics for understanding miRNA biology.
Huang TC, Pinto SM, Pandey A. Huang TC, et al. Proteomics. 2013 Feb;13(3-4):558-67. doi: 10.1002/pmic.201200339. Epub 2012 Dec 27. Proteomics. 2013. PMID: 23125164 Free PMC article. Review.
Identifying targets of miR-143 using a SILAC-based proteomic approach.
Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A. Yang Y, et al. Mol Biosyst. 2010 Oct;6(10):1873-82. doi: 10.1039/c004401f. Epub 2010 Jun 14. Mol Biosyst. 2010. PMID: 20544124 Free PMC article.
Regulation of lipid metabolism by Dicer revealed through SILAC mice.
Huang TC, Sahasrabuddhe NA, Kim MS, Getnet D, Yang Y, Peterson JM, Ghosh B, Chaerkady R, Leach SD, Marchionni L, Wong GW, Pandey A. Huang TC, et al. J Proteome Res. 2012 Apr 6;11(4):2193-205. doi: 10.1021/pr2009884. Epub 2012 Feb 28. J Proteome Res. 2012. PMID: 22313051 Free PMC article.
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