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Items: 1 to 50 of 84

1.

Multi-omics characterization of a diet-induced obese model of non-alcoholic steatohepatitis.

Ægidius HM, Veidal SS, Feigh M, Hallenborg P, Puglia M, Pers TH, Vrang N, Jelsing J, Kornum BR, Blagoev B, Rigbolt KTG.

Sci Rep. 2020 Jan 24;10(1):1148. doi: 10.1038/s41598-020-58059-7.

2.

A draft genome sequence of the elusive giant squid, Architeuthis dux.

da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP.

Gigascience. 2020 Jan 1;9(1). pii: giz152. doi: 10.1093/gigascience/giz152.

3.

Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells.

Barrio-Hernandez I, Jafari A, Rigbolt KTG, Hallenborg P, Sanchez-Quiles V, Skovrind I, Akimov V, Kratchmarova I, Dengjel J, Kassem M, Blagoev B.

Genome Res. 2020 Jan;30(1):127-137. doi: 10.1101/gr.248286.119. Epub 2019 Dec 12.

PMID:
31831592
4.

Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.

Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J.

Syst Med (New Rochelle). 2019 Mar 28;2(1):1-9. doi: 10.1089/sysm.2018.0013. eCollection 2019.

5.

Phosphoproteomic and Functional Analyses Reveal Sperm-specific Protein Changes Downstream of Kappa Opioid Receptor in Human Spermatozoa.

Urizar-Arenaza I, Osinalde N, Akimov V, Puglia M, Candenas L, Pinto FM, Muñoa-Hoyos I, Gianzo M, Matorras R, Irazusta J, Blagoev B, Subiran N, Kratchmarova I.

Mol Cell Proteomics. 2019 Mar 15;18(Suppl 1):S118-S131. doi: 10.1074/mcp.RA118.001133. Epub 2019 Jan 8.

PMID:
30622161
6.

UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites.

Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B.

Nat Struct Mol Biol. 2018 Jul;25(7):631-640. doi: 10.1038/s41594-018-0084-y. Epub 2018 Jul 2.

PMID:
29967540
7.

Data on mass spectrometry-based proteomics for studying the involvement of CYLD in the ubiquitination events downstream of EGFR activation.

Sanchez-Quiles V, Osinalde N, Akimov V, Kratchmarova I, Blagoev B.

Data Brief. 2018 Apr 25;18:1856-1863. doi: 10.1016/j.dib.2018.04.049. eCollection 2018 Jun.

8.

Fundamental constraints in synchronous muscle limit superfast motor control in vertebrates.

Mead AF, Osinalde N, Ørtenblad N, Nielsen J, Brewer J, Vellema M, Adam I, Scharff C, Song Y, Frandsen U, Blagoev B, Kratchmarova I, Elemans CP.

Elife. 2017 Nov 22;6. pii: e29425. doi: 10.7554/eLife.29425.

9.

StUbEx PLUS-A Modified Stable Tagged Ubiquitin Exchange System for Peptide Level Purification and In-Depth Mapping of Ubiquitination Sites.

Akimov V, Olsen LCB, Hansen SVF, Barrio-Hernandez I, Puglia M, Jensen SS, Solov'yov IA, Kratchmarova I, Blagoev B.

J Proteome Res. 2018 Jan 5;17(1):296-304. doi: 10.1021/acs.jproteome.7b00566. Epub 2017 Nov 1.

PMID:
29091453
10.

Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor.

Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B.

Mol Cell Proteomics. 2017 Aug;16(8):1433-1446. doi: 10.1074/mcp.M116.066423. Epub 2017 Jun 1.

11.

Data on interleukin (IL)-2- and IL-15-dependent changes in IL-2Rβ and IL-2Rγ complexes.

Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I.

Data Brief. 2017 Mar 2;11:499-506. doi: 10.1016/j.dib.2017.02.030. eCollection 2017 Apr.

12.

Biogenic nanosized iron oxides obtained from cultivation of iron bacteria from the genus Leptothrix.

Nedkov I, Slavov L, Angelova R, Blagoev B, Kovacheva D, Abrashev MV, Iliev M, Groudeva V.

J Biol Phys. 2016 Oct;42(4):587-600. Epub 2016 Aug 30.

13.

Characterization of Receptor-Associated Protein Complex Assembly in Interleukin (IL)-2- and IL-15-Activated T-Cell Lines.

Osinalde N, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Blagoev B, Kratchmarova I.

J Proteome Res. 2017 Jan 6;16(1):106-121. doi: 10.1021/acs.jproteome.6b00233. Epub 2016 Aug 18.

PMID:
27463037
14.

MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3.

Hallenborg P, Siersbæk M, Barrio-Hernandez I, Nielsen R, Kristiansen K, Mandrup S, Grøntved L, Blagoev B.

Cell Death Dis. 2016 Jun 30;7(6):e2289. doi: 10.1038/cddis.2016.188.

15.

S-nitrosylation of the Mitochondrial Chaperone TRAP1 Sensitizes Hepatocellular Carcinoma Cells to Inhibitors of Succinate Dehydrogenase.

Rizza S, Montagna C, Cardaci S, Maiani E, Di Giacomo G, Sanchez-Quiles V, Blagoev B, Rasola A, De Zio D, Stamler JS, Cecconi F, Filomeni G.

Cancer Res. 2016 Jul 15;76(14):4170-82. doi: 10.1158/0008-5472.CAN-15-2637. Epub 2016 May 23.

16.

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking.

Francavilla C, Papetti M, Rigbolt KT, Pedersen AK, Sigurdsson JO, Cazzamali G, Karemore G, Blagoev B, Olsen JV.

Nat Struct Mol Biol. 2016 Jun;23(6):608-18. doi: 10.1038/nsmb.3218. Epub 2016 May 2.

PMID:
27136326
17.

Nuclear Phosphoproteomic Screen Uncovers ACLY as Mediator of IL-2-induced Proliferation of CD4+ T lymphocytes.

Osinalde N, Mitxelena J, Sánchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Zubiaga AM, Blagoev B, Kratchmarova I.

Mol Cell Proteomics. 2016 Jun;15(6):2076-92. doi: 10.1074/mcp.M115.057158. Epub 2016 Apr 11.

18.

Changes in Gab2 phosphorylation and interaction partners in response to interleukin (IL)-2 stimulation in T-lymphocytes.

Osinalde N, Sánchez-Quiles V, Blagoev B, Kratchmarova I.

Sci Rep. 2016 Mar 30;6:23530. doi: 10.1038/srep23530.

19.

p53 regulates expression of uncoupling protein 1 through binding and repression of PPARγ coactivator-1α.

Hallenborg P, Fjære E, Liaset B, Petersen RK, Murano I, Sonne SB, Falkerslev M, Winther S, Jensen BA, Ma T, Hansen JB, Cinti S, Blagoev B, Madsen L, Kristiansen K.

Am J Physiol Endocrinol Metab. 2016 Jan 15;310(2):E116-28. doi: 10.1152/ajpendo.00119.2015. Epub 2015 Nov 17.

20.

SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes.

Osinalde N, Sánchez-Quiles V, Akimov V, Blagoev B, Kratchmarova I.

Data Brief. 2015 Aug 22;5:53-8. doi: 10.1016/j.dib.2015.08.007. eCollection 2015 Dec.

21.

Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts.

Le Bihan MC, Barrio-Hernandez I, Mortensen TP, Henningsen J, Jensen SS, Bigot A, Blagoev B, Butler-Browne G, Kratchmarova I.

J Proteome Res. 2015 Aug 7;14(8):3348-61. doi: 10.1021/acs.jproteome.5b00397. Epub 2015 Jun 29.

PMID:
26074025
22.

PPARγ ligand production is tightly linked to clonal expansion during initiation of adipocyte differentiation.

Hallenborg P, Petersen RK, Feddersen S, Sundekilde U, Hansen JB, Blagoev B, Madsen L, Kristiansen K.

J Lipid Res. 2014 Dec;55(12):2491-500. doi: 10.1194/jlr.M050658. Epub 2014 Oct 13.

23.

Phosphorylation site dynamics of early T-cell receptor signaling.

Chylek LA, Akimov V, Dengjel J, Rigbolt KT, Hu B, Hlavacek WS, Blagoev B.

PLoS One. 2014 Aug 22;9(8):e104240. doi: 10.1371/journal.pone.0104240. eCollection 2014.

24.

Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics.

Osinalde N, Sanchez-Quiles V, Akimov V, Guerra B, Blagoev B, Kratchmarova I.

Proteomics. 2015 Jan;15(2-3):520-31. doi: 10.1002/pmic.201400194. Epub 2014 Sep 30.

PMID:
25142963
25.

StUbEx: Stable tagged ubiquitin exchange system for the global investigation of cellular ubiquitination.

Akimov V, Henningsen J, Hallenborg P, Rigbolt KT, Jensen SS, Nielsen MM, Kratchmarova I, Blagoev B.

J Proteome Res. 2014 Sep 5;13(9):4192-204. doi: 10.1021/pr500549h. Epub 2014 Aug 15.

PMID:
25093938
26.

Analysis of secreted proteins using SILAC.

Henningsen J, Blagoev B, Kratchmarova I.

Methods Mol Biol. 2014;1188:313-26. doi: 10.1007/978-1-4939-1142-4_22.

PMID:
25059621
27.

SILAC-based temporal phosphoproteomics.

Francavilla C, Hekmat O, Blagoev B, Olsen JV.

Methods Mol Biol. 2014;1188:125-48. doi: 10.1007/978-1-4939-1142-4_10.

PMID:
25059609
28.

JMJD1C demethylates MDC1 to regulate the RNF8 and BRCA1-mediated chromatin response to DNA breaks.

Watanabe S, Watanabe K, Akimov V, Bartkova J, Blagoev B, Lukas J, Bartek J.

Nat Struct Mol Biol. 2013 Dec;20(12):1425-33. doi: 10.1038/nsmb.2702. Epub 2013 Nov 17.

PMID:
24240613
29.

The chromatin scaffold protein SAFB1 renders chromatin permissive for DNA damage signaling.

Altmeyer M, Toledo L, Gudjonsson T, Grøfte M, Rask MB, Lukas C, Akimov V, Blagoev B, Bartek J, Lukas J.

Mol Cell. 2013 Oct 24;52(2):206-20. doi: 10.1016/j.molcel.2013.08.025. Epub 2013 Sep 19.

30.

Functional proteomics defines the molecular switch underlying FGF receptor trafficking and cellular outputs.

Francavilla C, Rigbolt KT, Emdal KB, Carraro G, Vernet E, Bekker-Jensen DB, Streicher W, Wikström M, Sundström M, Bellusci S, Cavallaro U, Blagoev B, Olsen JV.

Mol Cell. 2013 Sep 26;51(6):707-22. doi: 10.1016/j.molcel.2013.08.002. Epub 2013 Sep 5.

31.

Separate developmental programs for HLA-A and -B cell surface expression during differentiation from embryonic stem cells to lymphocytes, adipocytes and osteoblasts.

Sabir HJ, Nehlin JO, Qanie D, Harkness L, Prokhorova TA, Blagoev B, Kassem M, Isa A, Barington T.

PLoS One. 2013;8(1):e54366. doi: 10.1371/journal.pone.0054366. Epub 2013 Jan 18.

32.

Agonism and antagonism at the insulin receptor.

Knudsen L, Hansen BF, Jensen P, Pedersen TÅ, Vestergaard K, Schäffer L, Blagoev B, Oleksiewicz MB, Kiselyov VV, De Meyts P.

PLoS One. 2012;7(12):e51972. doi: 10.1371/journal.pone.0051972. Epub 2012 Dec 27.

33.

Quantitative phosphoproteomics to characterize signaling networks.

Rigbolt KT, Blagoev B.

Semin Cell Dev Biol. 2012 Oct;23(8):863-71. doi: 10.1016/j.semcdb.2012.05.006. Epub 2012 Jun 5. Review.

PMID:
22677334
34.

Stable isotope labelling with amino acids in cell culture for human embryonic stem cell proteomic analysis.

Harkness L, Prokhorova TA, Kassem M, Blagoev B.

Methods Mol Biol. 2012;873:297-305. doi: 10.1007/978-1-61779-794-1_20.

PMID:
22528364
35.

Mdm2 controls CREB-dependent transactivation and initiation of adipocyte differentiation.

Hallenborg P, Feddersen S, Francoz S, Murano I, Sundekilde U, Petersen RK, Akimov V, Olson MV, Lozano G, Cinti S, Gjertsen BT, Madsen L, Marine JC, Blagoev B, Kristiansen K.

Cell Death Differ. 2012 Aug;19(8):1381-9. doi: 10.1038/cdd.2012.15. Epub 2012 Mar 2.

36.

Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics.

Akimov V, Rigbolt KT, Nielsen MM, Blagoev B.

Mol Biosyst. 2011 Dec;7(12):3223-33. doi: 10.1039/c1mb05185g. Epub 2011 Sep 28.

PMID:
21956701
37.

Interleukin-2 signaling pathway analysis by quantitative phosphoproteomics.

Osinalde N, Moss H, Arrizabalaga O, Omaetxebarria MJ, Blagoev B, Zubiaga AM, Fullaondo A, Arizmendi JM, Kratchmarova I.

J Proteomics. 2011 Dec 10;75(1):177-91. doi: 10.1016/j.jprot.2011.06.007. Epub 2011 Jun 23.

PMID:
21722762
38.

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

Rigbolt KT, Vanselow JT, Blagoev B.

Mol Cell Proteomics. 2011 Aug;10(8):O110.007450. doi: 10.1074/mcp.O110.007450. Epub 2011 May 20.

39.

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.

Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B.

Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570.

40.

Systematic in vivo RNAi analysis identifies IAPs as NEDD8-E3 ligases.

Broemer M, Tenev T, Rigbolt KT, Hempel S, Blagoev B, Silke J, Ditzel M, Meier P.

Mol Cell. 2010 Dec 10;40(5):810-22. doi: 10.1016/j.molcel.2010.11.011.

41.

Mapping protein-protein interactions by quantitative proteomics.

Dengjel J, Kratchmarova I, Blagoev B.

Methods Mol Biol. 2010;658:267-78. doi: 10.1007/978-1-60761-780-8_16.

PMID:
20839110
42.

Proteome-wide quantitation by SILAC.

Rigbolt KT, Blagoev B.

Methods Mol Biol. 2010;658:187-204. doi: 10.1007/978-1-60761-780-8_11.

PMID:
20839105
43.

Dynamics of the skeletal muscle secretome during myoblast differentiation.

Henningsen J, Rigbolt KT, Blagoev B, Pedersen BK, Kratchmarova I.

Mol Cell Proteomics. 2010 Nov;9(11):2482-96. doi: 10.1074/mcp.M110.002113. Epub 2010 Jul 14.

44.

PTP1B targets the endosomal sorting machinery: dephosphorylation of regulatory sites on the endosomal sorting complex required for transport component STAM2.

Stuible M, Abella JV, Feldhammer M, Nossov M, Sangwan V, Blagoev B, Park M, Tremblay ML.

J Biol Chem. 2010 Jul 30;285(31):23899-907. doi: 10.1074/jbc.M110.115295. Epub 2010 May 26.

45.

GABAB receptor constituents revealed by tandem affinity purification from transgenic mice.

Bartoi T, Rigbolt KT, Du D, Köhr G, Blagoev B, Kornau HC.

J Biol Chem. 2010 Jul 2;285(27):20625-33. doi: 10.1074/jbc.M109.049700. Epub 2010 Apr 20.

46.

Quantitative analysis of HGF and EGF-dependent phosphotyrosine signaling networks.

Hammond DE, Hyde R, Kratchmarova I, Beynon RJ, Blagoev B, Clague MJ.

J Proteome Res. 2010 May 7;9(5):2734-42. doi: 10.1021/pr100145w.

PMID:
20222723
47.

Regulation of epidermal growth factor receptor trafficking by lysine deacetylase HDAC6.

Deribe YL, Wild P, Chandrashaker A, Curak J, Schmidt MHH, Kalaidzidis Y, Milutinovic N, Kratchmarova I, Buerkle L, Fetchko MJ, Schmidt P, Kittanakom S, Brown KR, Jurisica I, Blagoev B, Zerial M, Stagljar I, Dikic I.

Sci Signal. 2009 Dec 22;2(102):ra84. doi: 10.1126/scisignal.2000576.

PMID:
20029029
48.

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.

Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M.

J Proteome Res. 2010 Jan;9(1):393-403. doi: 10.1021/pr900721e.

PMID:
19888749
49.

Receptor tyrosine kinase signaling: a view from quantitative proteomics.

Dengjel J, Kratchmarova I, Blagoev B.

Mol Biosyst. 2009 Oct;5(10):1112-21. doi: 10.1039/b909534a. Epub 2009 Aug 6. Review.

PMID:
19756300
50.

Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells.

Prokhorova TA, Rigbolt KT, Johansen PT, Henningsen J, Kratchmarova I, Kassem M, Blagoev B.

Mol Cell Proteomics. 2009 May;8(5):959-70. doi: 10.1074/mcp.M800287-MCP200. Epub 2009 Jan 17.

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