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SPANX-A/D protein subfamily plays a key role in nuclear organisation, metabolism and flagellar motility of human spermatozoa.

Urizar-Arenaza I, Osinalde N, Akimov V, Puglia M, Muñoa-Hoyos I, Gianzo M, Rodriguez JA, Ganzabal T, Blagoev B, Kratchmarova I, Subiran N.

Sci Rep. 2020 Mar 27;10(1):5625. doi: 10.1038/s41598-020-62389-x.


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.


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.


NADH dehydrogenase complex I is overexpressed in incipient metastatic murine colon cancer cells.

Marquez J, Kratchmarova I, Akimov V, Unda F, Ibarretxe G, Clerigué AS, Osinalde N, Badiola I.

Oncol Rep. 2019 Feb;41(2):742-752. doi: 10.3892/or.2018.6892. Epub 2018 Nov 27.


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.


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.


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.


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.


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.


Targeted mass spectrometry: An emerging powerful approach to unblock the bottleneck in phosphoproteomics.

Osinalde N, Aloria K, Omaetxebarria MJ, Kratchmarova I.

J Chromatogr B Analyt Technol Biomed Life Sci. 2017 Jun 15;1055-1056:29-38. doi: 10.1016/j.jchromb.2017.04.026. Epub 2017 Apr 17. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Temporal profiling and pulsed SILAC labeling identify novel secreted proteins during ex vivo osteoblast differentiation of human stromal stem cells.

Kristensen LP, Chen L, Nielsen MO, Qanie DW, Kratchmarova I, Kassem M, Andersen JS.

Mol Cell Proteomics. 2012 Oct;11(10):989-1007. Epub 2012 Jul 16.


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.


Development of novel monoclonal antibodies that define differentiation stages of human stromal (mesenchymal) stem cells.

Andersen DC, Kortesidis A, Zannettino AC, Kratchmarova I, Chen L, Jensen ON, Teisner B, Gronthos S, Jensen CH, Kassem M.

Mol Cells. 2011 Aug;32(2):133-42. doi: 10.1007/s10059-011-2277-7. Epub 2011 May 23.


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.


Quantitative analysis of the secretion of the MCP family of chemokines by muscle cells.

Henningsen J, Pedersen BK, Kratchmarova I.

Mol Biosyst. 2011 Feb;7(2):311-21. doi: 10.1039/c0mb00209g. Epub 2010 Dec 8.


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.


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.


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.


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.


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.


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.


Stable isotope labeling by amino acids in cell culture (SILAC).

Gruhler S, Kratchmarova I.

Methods Mol Biol. 2008;424:101-11. doi: 10.1007/978-1-60327-064-9_9.


Dissection of the insulin signaling pathway via quantitative phosphoproteomics.

Krüger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M.

Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2451-6. doi: 10.1073/pnas.0711713105. Epub 2008 Feb 11.


Peroxisome proliferator-activated receptor gamma recruits the positive transcription elongation factor b complex to activate transcription and promote adipogenesis.

Iankova I, Petersen RK, Annicotte JS, Chavey C, Hansen JB, Kratchmarova I, Sarruf D, Benkirane M, Kristiansen K, Fajas L.

Mol Endocrinol. 2006 Jul;20(7):1494-505. Epub 2006 Feb 16.


Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6.

Häcker H, Redecke V, Blagoev B, Kratchmarova I, Hsu LC, Wang GG, Kamps MP, Raz E, Wagner H, Häcker G, Mann M, Karin M.

Nature. 2006 Jan 12;439(7073):204-7. Epub 2005 Nov 23.


Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation.

Kratchmarova I, Blagoev B, Haack-Sorensen M, Kassem M, Mann M.

Science. 2005 Jun 3;308(5727):1472-7.


Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics.

Blagoev B, Ong SE, Kratchmarova I, Mann M.

Nat Biotechnol. 2004 Sep;22(9):1139-45. Epub 2004 Aug 15.


Cloning of a novel signaling molecule, AMSH-2, that potentiates transforming growth factor beta signaling.

Ibarrola N, Kratchmarova I, Nakajima D, Schiemann WP, Moustakas A, Pandey A, Mann M.

BMC Cell Biol. 2004 Jan 19;5:2.


Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC).

Ong SE, Kratchmarova I, Mann M.

J Proteome Res. 2003 Mar-Apr;2(2):173-81.


A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling.

Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M.

Nat Biotechnol. 2003 Mar;21(3):315-8. Epub 2003 Feb 10.


Role of adipocyte lipid-binding protein (ALBP) and acyl-coA binding protein (ACBP) in PPAR-mediated transactivation.

Helledie T, Jørgensen C, Antonius M, Krogsdam AM, Kratchmarova I, Kristiansen K, Mandrup S.

Mol Cell Biochem. 2002 Oct;239(1-2):157-64.


Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases.

Pandey A, Blagoev B, Kratchmarova I, Fernandez M, Nielsen M, Kristiansen TZ, Ohara O, Podtelejnikov AV, Roche S, Lodish HF, Mann M.

Oncogene. 2002 Nov 14;21(52):8029-36.


Inhibition of adipocyte differentiation by resistin-like molecule alpha. Biochemical characterization of its oligomeric nature.

Blagoev B, Kratchmarova I, Nielsen MM, Fernandez MM, Voldby J, Andersen JS, Kristiansen K, Pandey A, Mann M.

J Biol Chem. 2002 Nov 1;277(44):42011-6. Epub 2002 Aug 19.


Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M.

Mol Cell Proteomics. 2002 May;1(5):376-86.


A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes.

Kratchmarova I, Kalume DE, Blagoev B, Scherer PE, Podtelejnikov AV, Molina H, Bickel PE, Andersen JS, Fernandez MM, Bunkenborg J, Roepstorff P, Kristiansen K, Lodish HF, Mann M, Pandey A.

Mol Cell Proteomics. 2002 Mar;1(3):213-22.


Opposing effects of fatty acids and acyl-CoA esters on conformation and cofactor recruitment of peroxisome proliferator-activated receptors.

JØrgensen C, Krogsdam AM, Kratchmarova I, Willson TM, Knudsen J, Mandrup S, Kristiansen K.

Ann N Y Acad Sci. 2002 Jun;967:431-9.


A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling.

Pandey A, Ibarrola N, Kratchmarova I, Fernandez MM, Constantinescu SN, Ohara O, Sawasdikosol S, Lodish HF, Mann M.

J Biol Chem. 2002 May 24;277(21):19131-8. Epub 2002 Mar 12.


Modulation of keratinocyte gene expression and differentiation by PPAR-selective ligands and tetradecylthioacetic acid.

Westergaard M, Henningsen J, Svendsen ML, Johansen C, Jensen UB, Schrøder HD, Kratchmarova I, Berge RK, Iversen L, Bolund L, Kragballe K, Kristiansen K.

J Invest Dermatol. 2001 May;116(5):702-12.


Acyl-CoA esters antagonize the effects of ligands on peroxisome proliferator-activated receptor alpha conformation, DNA binding, and interaction with Co-factors.

Elholm M, Dam I, Jorgensen C, Krogsdam AM, Holst D, Kratchmarova I, Gottlicher M, Gustafsson JA, Berge R, Flatmark T, Knudsen J, Mandrup S, Kristiansen K.

J Biol Chem. 2001 Jun 15;276(24):21410-6. Epub 2001 Feb 20.


Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein.

Kratchmarova I, Sosinowski T, Weiss A, Witter K, Vincenz C, Pandey A.

Gene. 2001 Jan 10;262(1-2):267-73.


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