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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.
Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.
Prasad TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A. Prasad TS, et al. Among authors: Kelkar DS. Genome Res. 2017 Jan;27(1):133-144. doi: 10.1101/gr.201368.115. Epub 2016 Nov 15. Genome Res. 2017. PMID: 28003436 Free PMC article.
A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry.
Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA, Kim MS, Renuse S, Pinto SM, Sharma R, Pawar H, Sekhar NR, Mohanty AK, Getnet D, Yang Y, Zhong J, Dash AP, MacCallum RM, Delanghe B, Mlambo G, Kumar A, Keshava Prasad TS, Okulate M, Kumar N, Pandey A. Chaerkady R, et al. Genome Res. 2011 Nov;21(11):1872-81. doi: 10.1101/gr.127951.111. Epub 2011 Jul 27. Genome Res. 2011. PMID: 21795387 Free PMC article.
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.
Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A. Kelkar DS, et al. Mol Cell Proteomics. 2011 Dec;10(12):M111.011627. doi: 10.1074/mcp.M111.011445. Epub 2011 Oct 3. Mol Cell Proteomics. 2011. PMID: 21969609 Free PMC article.
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. Among authors: Kelkar DS. BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4. BMC Syst Biol. 2015. PMID: 26542228 Free PMC article.
Proteomics of human aqueous humor.
Murthy KR, Rajagopalan P, Pinto SM, Advani J, Murthy PR, Goel R, Subbannayya Y, Balakrishnan L, Dash M, Anil AK, Manda SS, Nirujogi RS, Kelkar DS, Sathe GJ, Dey G, Chatterjee A, Gowda H, Chakravarti S, Shankar S, Sahasrabuddhe NA, Nair B, Somani BL, Prasad TS, Pandey A. Murthy KR, et al. Among authors: Kelkar DS. OMICS. 2015 May;19(5):283-93. doi: 10.1089/omi.2015.0029. OMICS. 2015. PMID: 25933257
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.
Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry.
Nagarajha Selvan LD, Kaviyil JE, Nirujogi RS, Muthusamy B, Puttamallesh VN, Subbannayya T, Syed N, Radhakrishnan A, Kelkar DS, Ahmad S, Pinto SM, Kumar P, Madugundu AK, Nair B, Chatterjee A, Pandey A, Ravikumar R, Gowda H, Prasad TS. Nagarajha Selvan LD, et al. Clin Proteomics. 2014 Feb 3;11(1):5. doi: 10.1186/1559-0275-11-5. Clin Proteomics. 2014. PMID: 24484775 Free PMC article.
A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.
Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GS, Venugopal A, Sekhar NR, Kelkar DS, Nemade H, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A. Pawar H, et al. Proteomics. 2012 Mar;12(6):832-44. doi: 10.1002/pmic.201100505. Proteomics. 2012. PMID: 22539434
Temporal analysis of neural differentiation using quantitative proteomics.
Chaerkady R, Kerr CL, Marimuthu A, Kelkar DS, Kashyap MK, Gucek M, Gearhart JD, Pandey A. Chaerkady R, et al. J Proteome Res. 2009 Mar;8(3):1315-26. doi: 10.1021/pr8006667. J Proteome Res. 2009. PMID: 19173612 Free PMC article.
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