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Items: 42

1.

Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM.

Sci Rep. 2019 Jun 6;9(1):8324. doi: 10.1038/s41598-019-43552-5.

2.

Phosphorylation of G3BP1-S149 does not influence stress granule assembly.

Panas MD, Kedersha N, Schulte T, Branca RM, Ivanov P, Anderson P.

J Cell Biol. 2019 Jul 1;218(7):2425-2432. doi: 10.1083/jcb.201801214. Epub 2019 Jun 6.

PMID:
31171631
3.

Breast cancer quantitative proteome and proteogenomic landscape.

Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B; Consortia Oslo Breast Cancer Research Consortium (OSBREAC), Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J.

Nat Commun. 2019 Apr 8;10(1):1600. doi: 10.1038/s41467-019-09018-y.

4.

Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.

Srinivas V, Lebrette H, Lundin D, Kutin Y, Sahlin M, Lerche M, Eirich J, Branca RMM, Cox N, Sjöberg BM, Högbom M.

Nature. 2018 Nov;563(7731):416-420. doi: 10.1038/s41586-018-0653-6. Epub 2018 Oct 31.

5.

Accumulation of endogenous peptides triggers a pathogen stress response in Arabidopsis thaliana.

Kmiec B, Branca RMM, Berkowitz O, Li L, Wang Y, Murcha MW, Whelan J, Lehtiö J, Glaser E, Teixeira PF.

Plant J. 2018 Nov;96(4):705-715. doi: 10.1111/tpj.14100.

PMID:
30242930
6.

Ether cross-link formation in the R2-like ligand-binding oxidase.

Griese JJ, Branca RMM, Srinivas V, Högbom M.

J Biol Inorg Chem. 2018 Aug;23(6):879-886. doi: 10.1007/s00775-018-1583-3. Epub 2018 Jun 26.

7.

Publisher Correction: Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J.

Nat Commun. 2018 May 8;9(1):1852. doi: 10.1038/s41467-018-04279-5.

8.

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J.

Nat Commun. 2018 Mar 2;9(1):903. doi: 10.1038/s41467-018-03311-y. Erratum in: Nat Commun. 2018 May 8;9(1):1852.

9.

Synaptic markers of cognitive decline in neurodegenerative diseases: a proteomic approach.

Bereczki E, Branca RM, Francis PT, Pereira JB, Baek JH, Hortobágyi T, Winblad B, Ballard C, Lehtiö J, Aarsland D.

Brain. 2018 Feb 1;141(2):582-595. doi: 10.1093/brain/awx352. Erratum in: Brain. 2019 Jun 1;142(6):e24.

10.

Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase.

Maugeri PT, Griese JJ, Branca RM, Miller EK, Smith ZR, Eirich J, Högbom M, Shafaat HS.

J Am Chem Soc. 2018 Jan 31;140(4):1471-1480. doi: 10.1021/jacs.7b11966. Epub 2018 Jan 22.

11.

Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin.

Teixeira PF, Masuyer G, Pinho CM, Branca RMM, Kmiec B, Wallin C, Wärmländer SKTS, Berntsson RP, Ankarcrona M, Gräslund A, Lehtiö J, Stenmark P, Glaser E.

J Mol Biol. 2018 Feb 2;430(3):348-362. doi: 10.1016/j.jmb.2017.11.011. Epub 2017 Nov 26.

PMID:
29183787
12.

A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts.

Kmiec B, Branca RMM, Murcha MW, Lehtiö J, Glaser E, Teixeira PF.

Mol Plant. 2018 Feb 5;11(2):342-345. doi: 10.1016/j.molp.2017.11.008. Epub 2017 Nov 26. No abstract available.

13.

Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells.

Reithmeier A, Panizza E, Krumpel M, Orre LM, Branca RMM, Lehtiö J, Ek-Rylander B, Andersson G.

BMC Cancer. 2017 Sep 15;17(1):650. doi: 10.1186/s12885-017-3616-7.

14.

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J.

Sci Rep. 2017 Jul 3;7(1):4513. doi: 10.1038/s41598-017-04798-z.

15.

Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics.

Kifer I, Branca RM, Ben-Dor A, Zhai L, Xu P, Lehtio J, Yakhini Z.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):272-281. doi: 10.1109/TCBB.2015.2452901.

PMID:
28368805
16.

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.

Teixeira PF, Kmiec B, Branca RM, Murcha MW, Byzia A, Ivanova A, Whelan J, Drag M, Lehtiö J, Glaser E.

Nat Chem Biol. 2017 Jan;13(1):15-17. doi: 10.1038/nchembio.2227. Epub 2016 Oct 31.

PMID:
27820795
17.

Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.

Maleki S, Kjellqvist S, Paloschi V, Magné J, Branca RM, Du L, Hultenby K, Petrini J, Fuxe J; MIBAVA Leducq Consortium, Lehtiö J, Franco-Cereceda A, Eriksson P, Björck HM.

Sci Rep. 2016 Oct 25;6:35712. doi: 10.1038/srep35712.

18.

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.

Zhou Y, Frings O, Branca RM, Boekel J, le Sage C, Fredlund E, Agami R, Orre LM.

Oncogene. 2017 Feb 9;36(6):731-745. doi: 10.1038/onc.2016.242. Epub 2016 Aug 1.

19.

Alterations in the membrane-associated proteome fraction of alveolar macrophages in sarcoidosis.

Kjellin H, Silva E, Branca RM, Eklund A, Jakobsson PJ, Grunewald J, Lehtiö J, Wheelock ÅM.

Sarcoidosis Vasc Diffuse Lung Dis. 2016 Mar 29;33(1):17-28.

PMID:
27055832
20.

Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor.

Griese JJ, Kositzki R, Schrapers P, Branca RM, Nordström A, Lehtiö J, Haumann M, Högbom M.

J Biol Chem. 2015 Oct 16;290(42):25254-72. doi: 10.1074/jbc.M115.675223. Epub 2015 Aug 31.

21.

Secretome protein signature of human gastrointestinal stromal tumor cells.

Berglund E, Daré E, Branca RM, Akcakaya P, Fröbom R, Berggren PO, Lui WO, Larsson C, Zedenius J, Orre L, Lehtiö J, Kim J, Bränström R.

Exp Cell Res. 2015 Aug 1;336(1):158-70. doi: 10.1016/j.yexcr.2015.05.004. Epub 2015 May 14.

PMID:
25983130
22.

A flowchart to analyze protease activity in plant mitochondria.

Teixeira PF, Branca RM, Kmiec B, Glaser E.

Methods Mol Biol. 2015;1305:123-30. doi: 10.1007/978-1-4939-2639-8_8.

PMID:
25910730
23.

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Zhu Y, Hultin-Rosenberg L, Forshed J, Branca RM, Orre LM, Lehtiö J.

Mol Cell Proteomics. 2014 Jun;13(6):1552-62. doi: 10.1074/mcp.M113.031203. Epub 2014 Apr 1.

24.

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, Forshed J, Käll L, Lehtiö J.

Nat Methods. 2014 Jan;11(1):59-62. doi: 10.1038/nmeth.2732. Epub 2013 Nov 17.

PMID:
24240322
25.

Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference.

Sandberg A, Branca RM, Lehtiö J, Forshed J.

J Proteomics. 2014 Jan 16;96:133-44. doi: 10.1016/j.jprot.2013.10.035. Epub 2013 Nov 5.

26.

Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein.

Griese JJ, Roos K, Cox N, Shafaat HS, Branca RM, Lehtiö J, Gräslund A, Lubitz W, Siegbahn PE, Högbom M.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17189-94. doi: 10.1073/pnas.1304368110. Epub 2013 Oct 7.

27.

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts.

Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, Lehtiö J, Whelan J, Stenmark P, Glaser E.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3761-9. doi: 10.1073/pnas.1307637110. Epub 2013 Sep 16.

28.

Quantitative proteomics profiling of primary lung adenocarcinoma tumors reveals functional perturbations in tumor metabolism.

Pernemalm M, De Petris L, Branca RM, Forshed J, Kanter L, Soria JC, Girard P, Validire P, Pawitan Y, van den Oord J, Lazar V, Påhlman S, Lewensohn R, Lehtiö J.

J Proteome Res. 2013 Sep 6;12(9):3934-43. doi: 10.1021/pr4002096. Epub 2013 Aug 13.

29.

Mammalian target of rapamycin (mTor) mediates tau protein dyshomeostasis: implication for Alzheimer disease.

Tang Z, Bereczki E, Zhang H, Wang S, Li C, Ji X, Branca RM, Lehtiö J, Guan Z, Filipcik P, Xu S, Winblad B, Pei JJ.

J Biol Chem. 2013 May 31;288(22):15556-70. doi: 10.1074/jbc.M112.435123. Epub 2013 Apr 12.

30.

Defining, comparing, and improving iTRAQ quantification in mass spectrometry proteomics data.

Hultin-Rosenberg L, Forshed J, Branca RM, Lehtiö J, Johansson HJ.

Mol Cell Proteomics. 2013 Jul;12(7):2021-31. doi: 10.1074/mcp.M112.021592. Epub 2013 Mar 7.

31.

A combined proteomic and transcriptomic approach shows diverging molecular mechanisms in thoracic aortic aneurysm development in patients with tricuspid- and bicuspid aortic valve.

Kjellqvist S, Maleki S, Olsson T, Chwastyniak M, Branca RM, Lehtiö J, Pinet F, Franco-Cereceda A, Eriksson P.

Mol Cell Proteomics. 2013 Feb;12(2):407-25. doi: 10.1074/mcp.M112.021873. Epub 2012 Nov 26.

32.

In vitro oxidative inactivation of human presequence protease (hPreP).

Teixeira PF, Pinho CM, Branca RM, Lehtiö J, Levine RL, Glaser E.

Free Radic Biol Med. 2012 Dec 1;53(11):2188-95. doi: 10.1016/j.freeradbiomed.2012.09.039. Epub 2012 Oct 3.

33.

Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway.

Arabi A, Ullah K, Branca RM, Johansson J, Bandarra D, Haneklaus M, Fu J, Ariës I, Nilsson P, Den Boer ML, Pokrovskaja K, Grandér D, Xiao G, Rocha S, Lehtiö J, Sangfelt O.

Nat Commun. 2012;3:976. doi: 10.1038/ncomms1975.

34.

Tumor proteomics by multivariate analysis on individual pathway data for characterization of vulvar cancer phenotypes.

Sandberg A, Lindell G, Källström BN, Branca RM, Danielsson KG, Dahlberg M, Larson B, Forshed J, Lehtiö J.

Mol Cell Proteomics. 2012 Jul;11(7):M112.016998. doi: 10.1074/mcp.M112.016998. Epub 2012 Apr 12.

35.

Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ).

Forshed J, Johansson HJ, Pernemalm M, Branca RM, Sandberg A, Lehtiö J.

Mol Cell Proteomics. 2011 Oct;10(10):M111.010264. doi: 10.1074/mcp.M111.010264. Epub 2011 Jul 6.

36.

Phosphoproteomic profiling of NSCLC cells reveals that ephrin B3 regulates pro-survival signaling through Akt1-mediated phosphorylation of the EphA2 receptor.

Ståhl S, Branca RM, Efazat G, Ruzzene M, Zhivotovsky B, Lewensohn R, Viktorsson K, Lehtiö J.

J Proteome Res. 2011 May 6;10(5):2566-78. doi: 10.1021/pr200037u. Epub 2011 Apr 11.

PMID:
21413766
37.

Proteomic study of thyroid tumors reveals frequent up-regulation of the Ca2+ -binding protein S100A6 in papillary thyroid carcinoma.

Sofiadis A, Dinets A, Orre LM, Branca RM, Juhlin CC, Foukakis T, Wallin G, Höög A, Hulchiy M, Zedenius J, Larsson C, Lehtiö J.

Thyroid. 2010 Oct;20(10):1067-76. doi: 10.1089/thy.2009.0400.

PMID:
20629554
38.

Concentration-dependent front velocity of the autocatalytic hydrogenase reaction.

Bodó G, Branca RM, Tóth A, Horváth D, Bagyinka C.

Biophys J. 2009 Jun 17;96(12):4976-83. doi: 10.1016/j.bpj.2009.03.024.

40.

Oxygen and temperature-dependent structural and redox changes in a novel cytochrome c(4) from the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina.

Branca RM, Bodó G, Várkonyi Z, Debreczeny M, Osz J, Bagyinka C.

Arch Biochem Biophys. 2007 Nov 15;467(2):174-84. Epub 2007 Aug 29.

PMID:
17931594
41.

Cross-crystallization method used for the crystallization and preliminary diffraction analysis of a novel di-haem cytochrome c4.

Tomcová I, Branca RM, Bodó G, Bagyinka C, Smatanová IK.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt 8):820-4. Epub 2006 Jul 26.

42.

Theoretical calculations on hydrogenase kinetics: explanation of the lag phase and the enzyme concentration dependence of the activity of hydrogenase uptake.

Osz J, Bodó G, Branca RM, Bagyinka C.

Biophys J. 2005 Sep;89(3):1957-64. Epub 2005 Jun 10. Erratum in: Biophys J. 2006 Jan 15;90(2):709.

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