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Items: 1 to 50 of 128

1.

Oxygen and Conformation Dependent Protein Oxidation and Aggregation by Porphyrins in Hepatocytes and Light-Exposed Cells.

Maitra D, Carter EL, Richardson R, Rittié L, Basrur V, Zhang H, Nesvizhskii AI, Osawa Y, Wolf MW, Ragsdale SW, Lehnert N, Herrmann H, Omary MB.

Cell Mol Gastroenterol Hepatol. 2019 Jun 4. pii: S2352-345X(19)30072-4. doi: 10.1016/j.jcmgh.2019.05.010. [Epub ahead of print]

2.

Constitutive release of CPS1 in bile and its role as a protective cytokine during acute liver injury.

Park MJ, D'Alecy LG, Anderson MA, Basrur V, Feng Y, Brady GF, Kim DI, Wu J, Nesvizhskii AI, Lahann J, Lukacs NW, Fontana RJ, Omary MB.

Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):9125-9134. doi: 10.1073/pnas.1822173116. Epub 2019 Apr 12.

PMID:
30979808
3.

The Landscape of Circular RNA in Cancer.

Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, Wu YM, Dhanasekaran SM, Engelke CG, Cao X, Robinson DR, Nesvizhskii AI, Chinnaiyan AM.

Cell. 2019 Feb 7;176(4):869-881.e13. doi: 10.1016/j.cell.2018.12.021.

PMID:
30735636
4.

DeltaMass: Automated Detection and Visualization of Mass Shifts in Proteomic Open-Search Results.

Avtonomov DM, Kong A, Nesvizhskii AI.

J Proteome Res. 2019 Feb 1;18(2):715-720. doi: 10.1021/acs.jproteome.8b00728. Epub 2018 Dec 17.

PMID:
30523686
5.

Functions of the COPII gene paralogs SEC23A and SEC23B are interchangeable in vivo.

Khoriaty R, Hesketh GG, Bernard A, Weyand AC, Mellacheruvu D, Zhu G, Hoenerhoff MJ, McGee B, Everett L, Adams EJ, Zhang B, Saunders TL, Nesvizhskii AI, Klionsky DJ, Shavit JA, Gingras AC, Ginsburg D.

Proc Natl Acad Sci U S A. 2018 Aug 14;115(33):E7748-E7757. doi: 10.1073/pnas.1805784115. Epub 2018 Jul 31.

6.

p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis.

Anwar T, Arellano-Garcia C, Ropa J, Chen YC, Kim HS, Yoon E, Grigsby S, Basrur V, Nesvizhskii AI, Muntean A, Gonzalez ME, Kidwell KM, Nikolovska-Coleska Z, Kleer CG.

Nat Commun. 2018 Jul 18;9(1):2801. doi: 10.1038/s41467-018-05078-8.

7.

HSC70 is a chaperone for wild-type and mutant cardiac myosin binding protein C.

Glazier AA, Hafeez N, Mellacheruvu D, Basrur V, Nesvizhskii AI, Lee LM, Shao H, Tang V, Yob JM, Gestwicki JE, Helms AS, Day SM.

JCI Insight. 2018 Jun 7;3(11). pii: 99319. doi: 10.1172/jci.insight.99319. eCollection 2018 Jun 7.

8.

PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of Hoxa9 and Meis1 in acute myeloid leukemia.

Ropa J, Saha N, Chen Z, Serio J, Chen W, Mellacheruvu D, Zhao L, Basrur V, Nesvizhskii AI, Muntean AG.

Oncotarget. 2018 Apr 24;9(31):22123-22136. doi: 10.18632/oncotarget.25204. eCollection 2018 Apr 24.

9.

The Ewing Sarcoma Secretome and Its Response to Activation of Wnt/beta-catenin Signaling.

Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER.

Mol Cell Proteomics. 2018 May;17(5):901-912. doi: 10.1074/mcp.RA118.000596. Epub 2018 Jan 31.

10.

IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry.

Avtonomov DM, Polasky DA, Ruotolo BT, Nesvizhskii AI.

Anal Chem. 2018 Feb 6;90(3):2369-2375. doi: 10.1021/acs.analchem.7b04999. Epub 2018 Jan 16.

11.

RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1.

Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, Govindarajoo B, Zhang Y, Sun Y, Dou Y, Basrur V, Elenitoba-Johnson KS, Nesvizhskii AI, Ceron J, Lee CY, Borggrefe T, Kovall RA, Rual JF.

EMBO J. 2017 Nov 2;36(21):3232-3249. doi: 10.15252/embj.201796525. Epub 2017 Oct 13.

12.

The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.

13.

Nuclear lamina genetic variants, including a truncated LAP2, in twins and siblings with nonalcoholic fatty liver disease.

Brady GF, Kwan R, Ulintz PJ, Nguyen P, Bassirian S, Basrur V, Nesvizhskii AI, Loomba R, Omary MB.

Hepatology. 2018 May;67(5):1710-1725. doi: 10.1002/hep.29522. Epub 2018 Mar 24.

14.

GSK3β controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug.

Kao SH, Wang WL, Chen CY, Chang YL, Wu YY, Wang YT, Wang SP, Nesvizhskii AI, Chen YJ, Hong TM, Yang PC.

Oncogene. 2017 Oct 19;36(42):5916. doi: 10.1038/onc.2017.302. Epub 2017 Sep 4.

PMID:
28869596
15.

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses.

Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R.

Nat Methods. 2017 Sep;14(9):921-927. doi: 10.1038/nmeth.4398. Epub 2017 Aug 21.

16.

PIQED: automated identification and quantification of protein modifications from DIA-MS data.

Meyer JG, Mukkamalla S, Steen H, Nesvizhskii AI, Gibson BW, Schilling B.

Nat Methods. 2017 Jun 29;14(7):646-647. doi: 10.1038/nmeth.4334. No abstract available.

17.

ProHits-viz: a suite of web tools for visualizing interaction proteomics data.

Knight JDR, Choi H, Gupta GD, Pelletier L, Raught B, Nesvizhskii AI, Gingras AC.

Nat Methods. 2017 Jun 29;14(7):645-646. doi: 10.1038/nmeth.4330. No abstract available.

18.

Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.

Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6581-6586. doi: 10.1073/pnas.1701263114. Epub 2017 Jun 12.

19.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

20.

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.

Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI.

Nat Methods. 2017 May;14(5):513-520. doi: 10.1038/nmeth.4256. Epub 2017 Apr 10.

21.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

22.

New targeted approaches for the quantification of data-independent acquisition mass spectrometry.

Bruderer R, Sondermann J, Tsou CC, Barrantes-Freer A, Stadelmann C, Nesvizhskii AI, Schmidt M, Reiter L, Gomez-Varela D.

Proteomics. 2017 May;17(9). doi: 10.1002/pmic.201700021.

23.

A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.

24.

Data Independent Acquisition analysis in ProHits 4.0.

Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC.

J Proteomics. 2016 Oct 21;149:64-68. doi: 10.1016/j.jprot.2016.04.042. Epub 2016 Apr 29.

25.

BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.

Avtonomov DM, Raskind A, Nesvizhskii AI.

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.

26.

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers.

Tsou CC, Tsai CF, Teo GC, Chen YJ, Nesvizhskii AI.

Proteomics. 2016 Aug;16(15-16):2257-71. doi: 10.1002/pmic.201500526. Epub 2016 Jul 22.

27.

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam MN, Griss J, Tabb DL.

Anal Chem. 2016 Jun 7;88(11):5733-41. doi: 10.1021/acs.analchem.6b00021. Epub 2016 May 24.

28.

MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency.

Zhang H, Gayen S, Xiong J, Zhou B, Shanmugam AK, Sun Y, Karatas H, Liu L, Rao RC, Wang S, Nesvizhskii AI, Kalantry S, Dou Y.

Cell Stem Cell. 2016 Apr 7;18(4):481-94. doi: 10.1016/j.stem.2016.02.004. Epub 2016 Mar 17.

29.

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.

Shanmugam AK, Nesvizhskii AI.

J Proteome Res. 2015 Dec 4;14(12):5169-78. doi: 10.1021/acs.jproteome.5b00504. Epub 2015 Nov 24.

30.

Two-pass alignment improves novel splice junction quantification.

Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI.

Bioinformatics. 2016 Jan 1;32(1):43-9. doi: 10.1093/bioinformatics/btv642. Epub 2015 Oct 30.

31.

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H.

J Proteomics. 2015 Nov 3;129:108-120. doi: 10.1016/j.jprot.2015.09.013. Epub 2015 Sep 15.

32.

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI.

J Proteomics. 2015 Nov 3;129:121-126. doi: 10.1016/j.jprot.2015.07.036. Epub 2015 Aug 4.

33.

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

Kitata RB, Dimayacyac-Esleta BR, Choong WK, Tsai CF, Lin TD, Tsou CC, Weng SH, Chen YJ, Yang PC, Arco SD, Nesvizhskii AI, Sung TY, Chen YJ.

J Proteome Res. 2015 Sep 4;14(9):3658-69. doi: 10.1021/acs.jproteome.5b00477. Epub 2015 Aug 6.

34.

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME.

Mol Endocrinol. 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16.

35.

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.

J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.

36.

The landscape of antisense gene expression in human cancers.

Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X, Wu YM, Robinson D, Wang R, Chen G, Beer DG, Nesvizhskii AI, Chinnaiyan AM.

Genome Res. 2015 Jul;25(7):1068-79. doi: 10.1101/gr.180596.114. Epub 2015 Jun 10.

37.

Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens.

Dytfeld D, Rosebeck S, Kandarpa M, Mayampurath A, Mellacheruvu D, Alonge MM, Ngoka L, Jasielec J, Richardson PG, Volchenboum S, Nesvizhskii AI, Sreekumar A, Jakubowiak AJ.

Br J Haematol. 2015 Jul;170(1):66-79. doi: 10.1111/bjh.13394. Epub 2015 Mar 30.

38.

Targeting the MLL complex in castration-resistant prostate cancer.

Malik R, Khan AP, Asangani IA, Cieślik M, Prensner JR, Wang X, Iyer MK, Jiang X, Borkin D, Escara-Wilke J, Stender R, Wu YM, Niknafs YS, Jing X, Qiao Y, Palanisamy N, Kunju LP, Krishnamurthy PM, Yocum AK, Mellacheruvu D, Nesvizhskii AI, Cao X, Dhanasekaran SM, Feng FY, Grembecka J, Cierpicki T, Chinnaiyan AM.

Nat Med. 2015 Apr;21(4):344-52. doi: 10.1038/nm.3830. Epub 2015 Mar 30.

39.

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics.

Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y, Chen YJ.

Nat Commun. 2015 Mar 27;6:6622. doi: 10.1038/ncomms7622.

40.

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.

Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19.

41.

Analysis of Protein Stability by the Cycloheximide Chase Assay.

Kao SH, Wang WL, Chen CY, Chang YL, Wu YY, Wang YT, Wang SP, Nesvizhskii AI, Chen YJ, Hong TM, Yang PC.

Bio Protoc. 2015 Jan 5;5(1). pii: e1374. doi: 10.21769/BioProtoc.1374.

42.

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

Fermin D, Avtonomov D, Choi H, Nesvizhskii AI.

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.

43.

Proteogenomics: concepts, applications and computational strategies.

Nesvizhskii AI.

Nat Methods. 2014 Nov;11(11):1114-25. doi: 10.1038/nmeth.3144. Review.

44.

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS.

Shanmugam AK, Yocum AK, Nesvizhskii AI.

J Proteome Res. 2014 Sep 5;13(9):4113-9. doi: 10.1021/pr500496p. Epub 2014 Jul 28.

45.

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas.

Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS.

Am J Pathol. 2014 May;184(5):1331-42. doi: 10.1016/j.ajpath.2014.01.036. Epub 2014 Mar 22.

46.

The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response.

Johnson C, Kweon HK, Sheidy D, Shively CA, Mellacheruvu D, Nesvizhskii AI, Andrews PC, Kumar A.

PLoS Genet. 2014 Mar 6;10(3):e1004183. doi: 10.1371/journal.pgen.1004183. eCollection 2014 Mar.

47.

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.

Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H.

J Proteomics. 2014 Apr 4;100:37-43. doi: 10.1016/j.jprot.2013.10.023. Epub 2013 Oct 26.

48.

Reconstructing targetable pathways in lung cancer by integrating diverse omics data.

Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM.

Nat Commun. 2013;4:2617. doi: 10.1038/ncomms3617.

49.

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.

J Proteome Res. 2013 Dec 6;12(12):5666-80. doi: 10.1021/pr400611h. Epub 2013 Nov 14.

50.

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.

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