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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.
Development of human protein reference database as an initial platform for approaching systems biology in humans.
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Peri S, et al. Genome Res. 2003 Oct;13(10):2363-71. doi: 10.1101/gr.1680803. Genome Res. 2003. PMID: 14525934 Free PMC article.
Human protein reference database as a discovery resource for proteomics.
Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A. Peri S, et al. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D497-501. doi: 10.1093/nar/gkh070. Nucleic Acids Res. 2004. PMID: 14681466 Free PMC article.
A proteomic analysis of human hemodialysis fluid.
Molina H, Bunkenborg J, Reddy GH, Muthusamy B, Scheel PJ, Pandey A. Molina H, et al. Mol Cell Proteomics. 2005 May;4(5):637-50. doi: 10.1074/mcp.M500042-MCP200. Epub 2005 Feb 20. Mol Cell Proteomics. 2005. PMID: 15723814
A manually curated functional annotation of the human X chromosome.
Harsha HC, Suresh S, Amanchy R, Deshpande N, Shanker K, Yatish AJ, Muthusamy B, Vrushabendra BM, Rashmi BP, Chandrika KN, Padma N, Sharma S, Badano JL, Ramya MA, Shivashankar HN, Peri S, Choudhury DR, Kavitha MP, Saravana R, Niranjan V, Gandhi TK, Ghosh N, Chandran S, Menezes M, Joy M, Mohan SS, Katsanis N, Deshpande KS, Raghothama C, Prasad CK, Pandey A. Harsha HC, et al. Nat Genet. 2005 Apr;37(4):331-2. doi: 10.1038/ng0405-331. Nat Genet. 2005. PMID: 15800640 No abstract available.
Plasma Proteome Database as a resource for proteomics research.
Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN, Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TS, Arun KS, Reddy R, Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi TK, Harsha HC, Mohan SS, Deshpande KS, Sarker M, Pandey A. Muthusamy B, et al. Proteomics. 2005 Aug;5(13):3531-6. doi: 10.1002/pmic.200401335. Proteomics. 2005. PMID: 16041672
SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.
Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A. Kashyap MK, et al. Cancer Biol Ther. 2010 Oct 15;10(8):796-810. doi: 10.4161/cbt.10.8.12914. Epub 2010 Oct 15. Cancer Biol Ther. 2010. PMID: 20686364 Free PMC article.
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway.
Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A. Raju R, et al. Database (Oxford). 2011 Jul 8;2011:bar021. doi: 10.1093/database/bar021. Print 2011. Database (Oxford). 2011. PMID: 21742767 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.
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