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Items: 34

1.

Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells.

Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim MS, Pandey A.

Proteomics. 2019 Aug;19(15):e1800315. doi: 10.1002/pmic.201800315. Epub 2019 Jun 26.

PMID:
30983154
2.

Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation.

Alexander EJ, Ghanbari Niaki A, Zhang T, Sarkar J, Liu Y, Nirujogi RS, Pandey A, Myong S, Wang J.

Proc Natl Acad Sci U S A. 2018 Dec 4;115(49):E11485-E11494. doi: 10.1073/pnas.1811997115. Epub 2018 Nov 15.

3.

Identification of long-lived synaptic proteins by proteomic analysis of synaptosome protein turnover.

Heo S, Diering GH, Na CH, Nirujogi RS, Bachman JL, Pandey A, Huganir RL.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3827-E3836. doi: 10.1073/pnas.1720956115. Epub 2018 Apr 2.

4.

Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis.

Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M.

Elife. 2017 Nov 10;6. pii: e31012. doi: 10.7554/eLife.31012.

5.

Human adenine nucleotide translocases physically and functionally interact with respirasomes.

Lu YW, Acoba MG, Selvaraju K, Huang TC, Nirujogi RS, Sathe G, Pandey A, Claypool SM.

Mol Biol Cell. 2017 Jun 1;28(11):1489-1506. doi: 10.1091/mbc.E17-03-0195. Epub 2017 Apr 12.

6.

Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis.

Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A.

Leukemia. 2017 Jul;31(7):1513-1524. doi: 10.1038/leu.2017.61. Epub 2017 Feb 17.

PMID:
28210003
7.

Toward Postgenomics Ophthalmology: A Proteomic Map of the Human Choroid-Retinal Pigment Epithelium Tissue.

Dammalli M, Murthy KR, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Nair B, Gowda H, Keshava Prasad TS.

OMICS. 2017 Feb;21(2):114-122. doi: 10.1089/omi.2016.0170.

PMID:
28186866
8.

Homer1a drives homeostatic scaling-down of excitatory synapses during sleep.

Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL.

Science. 2017 Feb 3;355(6324):511-515. doi: 10.1126/science.aai8355. Epub 2017 Feb 2.

9.

Secretome analysis of diarrhea-inducing strains of Escherichia coli.

Nirujogi RS, Muthusamy B, Kim MS, Sathe GJ, Lakshmi PT, Kovbasnjuk ON, Prasad TS, Wade M, Jabbour RE.

Proteomics. 2017 Mar;17(6). doi: 10.1002/pmic.201600299. Epub 2017 Mar 6.

10.

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.

Genome Res. 2017 Jan;27(1):133-144. doi: 10.1101/gr.201368.115. Epub 2016 Nov 15.

11.

Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling.

Ugolino J, Ji YJ, Conchina K, Chu J, Nirujogi RS, Pandey A, Brady NR, Hamacher-Brady A, Wang J.

PLoS Genet. 2016 Nov 22;12(11):e1006443. doi: 10.1371/journal.pgen.1006443. eCollection 2016 Nov.

12.

A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology?

Murthy KR, Dammalli M, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Subbannayya Y, Mishra UK, Nair B, Gowda H, Prasad TS.

OMICS. 2016 Sep;20(9):510-9. doi: 10.1089/omi.2016.0100.

PMID:
27631190
13.

Phosphotyrosine profiling of curcumin-induced signaling.

Sathe G, Pinto SM, Syed N, Nanjappa V, Solanki HS, Renuse S, Chavan S, Khan AA, Patil AH, Nirujogi RS, Nair B, Mathur PP, Prasad TSK, Gowda H, Chatterjee A.

Clin Proteomics. 2016 Jun 15;13:13. doi: 10.1186/s12014-016-9114-0. eCollection 2016.

14.

Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans.

Mitchell CJ, Kim MS, Zhong J, Nirujogi RS, Bose AK, Pandey A.

Mol Oncol. 2016 Jun;10(6):910-20. doi: 10.1016/j.molonc.2016.03.003. Epub 2016 Mar 25.

15.

Dysregulation of splicing proteins in head and neck squamous cell carcinoma.

Radhakrishnan A, Nanjappa V, Raja R, Sathe G, Chavan S, Nirujogi RS, Patil AH, Solanki H, Renuse S, Sahasrabuddhe NA, Mathur PP, Prasad TS, Kumar P, Califano JA, Sidransky D, Pandey A, Gowda H, Chatterjee A.

Cancer Biol Ther. 2016;17(2):219-29. doi: 10.1080/15384047.2016.1139234. Epub 2016 Feb 6.

16.

Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling.

Li R, Liao G, Nirujogi RS, Pinto SM, Shaw PG, Huang TC, Wan J, Qian J, Gowda H, Wu X, Lv DW, Zhang K, Manda SS, Pandey A, Hayward SD.

PLoS Pathog. 2015 Dec 29;11(12):e1005346. doi: 10.1371/journal.ppat.1005346. eCollection 2015 Dec.

17.

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.

BMC Syst Biol. 2015 Nov 6;9:75. doi: 10.1186/s12918-015-0225-4.

18.

Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer.

Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A.

Mol Cell Proteomics. 2015 Nov;14(11):2887-900. doi: 10.1074/mcp.M115.050484. Epub 2015 Sep 1.

19.

Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia.

Zahari MS, Wu X, Pinto SM, Nirujogi RS, Kim MS, Fetics B, Philip M, Barnes SR, Godfrey B, Gabrielson E, Nevo E, Pandey A.

Sci Rep. 2015 Sep 2;5:13660. doi: 10.1038/srep13660.

20.

Activating Mutations in PIK3CA Lead to Widespread Modulation of the Tyrosine Phosphoproteome.

Zahari MS, Wu X, Blair BG, Pinto SM, Nirujogi RS, Jelinek CA, Malhotra R, Kim MS, Park BH, Pandey A.

J Proteome Res. 2015 Sep 4;14(9):3882-3891. doi: 10.1021/acs.jproteome.5b00302. Epub 2015 Aug 20.

21.

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.

OMICS. 2015 May;19(5):283-93. doi: 10.1089/omi.2015.0029.

PMID:
25933257
22.

Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats.

Nirujogi RS, Wright JD Jr, Manda SS, Zhong J, Na CH, Meyerhoff J, Benton B, Jabbour R, Willis K, Kim MS, Pandey A, Sekowski JW.

Proteomics. 2015 Jan;15(2-3):487-99. doi: 10.1002/pmic.201400371.

PMID:
25403869
23.

Quantitative phosphoproteomic analysis of IL-33-mediated signaling.

Pinto SM, Nirujogi RS, Rojas PL, Patil AH, Manda SS, Subbannayya Y, Roa JC, Chatterjee A, Prasad TS, Pandey A.

Proteomics. 2015 Jan;15(2-3):532-44. doi: 10.1002/pmic.201400303.

24.

Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous-cell carcinoma.

Syed N, Barbhuiya MA, Pinto SM, Nirujogi RS, Renuse S, Datta KK, Khan AA, Srikumar K, Prasad TS, Kumar MV, Kumar RV, Chatterjee A, Pandey A, Gowda H.

Proteomics. 2015 Jan;15(2-3):374-82. doi: 10.1002/pmic.201400379.

25.

Activation of diverse signalling pathways by oncogenic PIK3CA mutations.

Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A.

Nat Commun. 2014 Sep 23;5:4961. doi: 10.1038/ncomms5961.

26.

Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project.

Manda SS, Nirujogi RS, Pinto SM, Kim MS, Datta KK, Sirdeshmukh R, Prasad TS, Thongboonkerd V, Pandey A, Gowda H.

J Proteome Res. 2014 Jul 3;13(7):3166-77. doi: 10.1021/pr401123v. Epub 2014 Jun 24.

PMID:
24960282
27.

Brain proteomics of Anopheles gambiae.

Dwivedi SB, Muthusamy B, Kumar P, Kim MS, Nirujogi RS, Getnet D, Ahiakonu P, De G, Nair B, Gowda H, Prasad TS, Kumar N, Pandey A, Okulate M.

OMICS. 2014 Jul;18(7):421-37. doi: 10.1089/omi.2014.0007. Epub 2014 Jun 17.

28.

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.

Nature. 2014 May 29;509(7502):575-81. doi: 10.1038/nature13302.

29.

Proteomic analysis of human osteoarthritis synovial fluid.

Balakrishnan L, Nirujogi RS, Ahmad S, Bhattacharjee M, Manda SS, Renuse S, Kelkar DS, Subbannayya Y, Raju R, Goel R, Thomas JK, Kaur N, Dhillon M, Tankala SG, Jois R, Vasdev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TsK, Mohan S, Gowda H, Shankar S, Pandey A.

Clin Proteomics. 2014 Feb 17;11(1):6. doi: 10.1186/1559-0275-11-6.

30.

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.

Clin Proteomics. 2014 Feb 3;11(1):5. doi: 10.1186/1559-0275-11-5.

31.

Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients.

Balakrishnan L, Bhattacharjee M, Ahmad S, Nirujogi RS, Renuse S, Subbannayya Y, Marimuthu A, Srikanth SM, Raju R, Dhillon M, Kaur N, Jois R, Vasudev V, Ramachandra Y, Sahasrabuddhe NA, Prasad TsK, Mohan S, Gowda H, Shankar S, Pandey A.

Clin Proteomics. 2014 Jan 6;11(1):1. doi: 10.1186/1559-0275-11-1.

32.

Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis.

Prasad TS, Verma R, Kumar S, Nirujogi RS, Sathe GJ, Madugundu AK, Sharma J, Puttamallesh VN, Ganjiwale A, Myneedu VP, Chatterjee A, Pandey A, Harsha H, Narayana J.

Clin Proteomics. 2013 Jul 19;10(1):8. doi: 10.1186/1559-0275-10-8.

33.

Proteomic analysis of human follicular fluid: a new perspective towards understanding folliculogenesis.

Ambekar AS, Nirujogi RS, Srikanth SM, Chavan S, Kelkar DS, Hinduja I, Zaveri K, Prasad TS, Harsha HC, Pandey A, Mukherjee S.

J Proteomics. 2013 Jul 11;87:68-77. doi: 10.1016/j.jprot.2013.05.017. Epub 2013 May 24.

PMID:
23707233
34.

Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani.

Nirujogi RS, Pawar H, Renuse S, Kumar P, Chavan S, Sathe G, Sharma J, Khobragade S, Pande J, Modak B, Prasad TS, Harsha HC, Patole MS, Pandey A.

J Proteomics. 2014 Jan 31;97:48-61. doi: 10.1016/j.jprot.2013.04.021. Epub 2013 May 9.

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