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Items: 1 to 20 of 124

1.

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.

PMID:
30065114
2.

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.

3.

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. [Epub ahead of print]

4.

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.

5.

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.

PMID:
29386236
6.

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.

PMID:
29278491
7.

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.

8.

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.

9.

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.

PMID:
28902428
10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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