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Items: 27


Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism.

Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W.

Mol Syst Biol. 2018 Mar 1;14(3):e7962. doi: 10.15252/msb.20177962.


Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis.

Nintemann SJ, Vik D, Svozil J, Bak M, Baerenfaller K, Burow M, Halkier BA.

Front Plant Sci. 2017 Nov 29;8:2028. doi: 10.3389/fpls.2017.02028. eCollection 2017.


Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation.

Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E10018-E10027. doi: 10.1073/pnas.1708433114. Epub 2017 Oct 30.


A Cautionary Tale on the Inclusion of Variable Posttranslational Modifications in Database-Dependent Searches of Mass Spectrometry Data.

Svozil J, Baerenfaller K.

Methods Enzymol. 2017;586:433-452. doi: 10.1016/bs.mie.2016.11.007. Epub 2017 Jan 10.


Meselect - A Rapid and Effective Method for the Separation of the Main Leaf Tissue Types.

Svozil J, Gruissem W, Baerenfaller K.

Front Plant Sci. 2016 Nov 15;7:1701. eCollection 2016.


Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis.

Baerenfaller K, Shu H, Hirsch-Hoffmann M, Fütterer J, Opitz L, Rehrauer H, Hennig L, Gruissem W.

Plant Cell Environ. 2016 Nov;39(11):2557-2569. doi: 10.1111/pce.12811. Epub 2016 Sep 30.


Proteasome targeting of proteins in Arabidopsis leaf mesophyll, epidermal and vascular tissues.

Svozil J, Gruissem W, Baerenfaller K.

Front Plant Sci. 2015 May 28;6:376. doi: 10.3389/fpls.2015.00376. eCollection 2015.


Large-Scale Proteomics of the Cassava Storage Root and Identification of a Target Gene to Reduce Postharvest Deterioration.

Vanderschuren H, Nyaboga E, Poon JS, Baerenfaller K, Grossmann J, Hirsch-Hoffmann M, Kirchgessner N, Nanni P, Gruissem W.

Plant Cell. 2014 May;26(5):1913-1924. Epub 2014 May 29.


Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A.

Svozil J, Hirsch-Hoffmann M, Dudler R, Gruissem W, Baerenfaller K.

Mol Cell Proteomics. 2014 Jun;13(6):1523-36. doi: 10.1074/mcp.M113.036269. Epub 2014 Apr 13.


Arabidopsis proteomics: a simple and standardizable workflow for quantitative proteome characterization.

Rödiger A, Agne B, Baerenfaller K, Baginsky S.

Methods Mol Biol. 2014;1072:275-88. doi: 10.1007/978-1-62703-631-3_20.


Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level.

Motohashi R, Rödiger A, Agne B, Baerenfaller K, Baginsky S.

Plant Physiol. 2012 Dec;160(4):2189-201. doi: 10.1104/pp.112.204032. Epub 2012 Oct 1.


Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit.

Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W.

Mol Syst Biol. 2012;8:606. doi: 10.1038/msb.2012.39.


pep2pro: the high-throughput proteomics data processing, analysis, and visualization tool.

Hirsch-Hoffmann M, Gruissem W, Baerenfaller K.

Front Plant Sci. 2012 Jun 11;3:123. doi: 10.3389/fpls.2012.00123. eCollection 2012.


The HUPO initiative on Model Organism Proteomes, iMOP.

Jones AM, Aebersold R, Ahrens CH, Apweiler R, Baerenfaller K, Baker M, Bendixen E, Briggs S, Brownridge P, Brunner E, Daube M, Deutsch EW, Grossniklaus U, Heazlewood J, Hengartner MO, Hermjakob H, Jovanovic M, Lawless C, Lochnit G, Martens L, Ravnsborg C, Schrimpf SP, Shim YH, Subasic D, Tholey A, Wijk Kv, Mering Cv, Weiss M, Zheng X.

Proteomics. 2012 Feb;12(3):340-5. doi: 10.1002/pmic.201290014.


Plastid proteome assembly without Toc159: photosynthetic protein import and accumulation of N-acetylated plastid precursor proteins.

Bischof S, Baerenfaller K, Wildhaber T, Troesch R, Vidi PA, Roschitzki B, Hirsch-Hoffmann M, Hennig L, Kessler F, Gruissem W, Baginsky S.

Plant Cell. 2011 Nov;23(11):3911-28. doi: 10.1105/tpc.111.092882. Epub 2011 Nov 29.


Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF).

Reiland S, Finazzi G, Endler A, Willig A, Baerenfaller K, Grossmann J, Gerrits B, Rutishauser D, Gruissem W, Rochaix JD, Baginsky S.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12955-60. doi: 10.1073/pnas.1104734108. Epub 2011 Jul 18.


Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves.

Gfeller A, Baerenfaller K, Loscos J, Chételat A, Baginsky S, Farmer EE.

Plant Physiol. 2011 Aug;156(4):1797-807. doi: 10.1104/pp.111.181008. Epub 2011 Jun 21.


Integrated proteome and metabolite analysis of the de-etiolation process in plastids from rice (Oryza sativa L.).

Reiland S, Grossmann J, Baerenfaller K, Gehrig P, Nunes-Nesi A, Fernie AR, Gruissem W, Baginsky S.

Proteomics. 2011 May;11(9):1751-63. doi: 10.1002/pmic.201000703. Epub 2011 Mar 23.


pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.

Baerenfaller K, Hirsch-Hoffmann M, Svozil J, Hull R, Russenberger D, Bischof S, Lu Q, Gruissem W, Baginsky S.

Integr Biol (Camb). 2011 Mar;3(3):225-37. doi: 10.1039/c0ib00078g. Epub 2011 Jan 24.


MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data.

Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL.

Plant Physiol. 2011 Jan;155(1):259-70. doi: 10.1104/pp.110.168195. Epub 2010 Nov 12.


Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.

Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S.

Plant Physiol. 2009 Jun;150(2):889-903. doi: 10.1104/pp.109.138677. Epub 2009 Apr 17.


Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S.

Science. 2008 May 16;320(5878):938-41. doi: 10.1126/science.1157956. Epub 2008 Apr 24.


5-Fluorouracil is efficiently removed from DNA by the base excision and mismatch repair systems.

Fischer F, Baerenfaller K, Jiricny J.

Gastroenterology. 2007 Dec;133(6):1858-68. Epub 2007 Sep 14.


A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments.

Grossmann J, Fischer B, Baerenfaller K, Owiti J, Buhmann JM, Gruissem W, Baginsky S.

Proteomics. 2007 Dec;7(23):4245-54.


The Mass Distance Fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry.

Potthast F, Gerrits B, Häkkinen J, Rutishauser D, Ahrens CH, Roschitzki B, Baerenfaller K, Munton RP, Walther P, Gehrig P, Seif P, Seeberger PH, Schlapbach R.

J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Jul 1;854(1-2):173-82. Epub 2007 Apr 25.


Persistent mismatch repair deficiency following targeted correction of hMLH1.

Weiss MB, Vitolo MI, Baerenfaller K, Marra G, Park BH, Bachman KE.

Cancer Gene Ther. 2007 Jan;14(1):98-104. Epub 2006 Nov 3.


Characterization of the "mismatch repairosome" and its role in the processing of modified nucleosides in vitro.

Baerenfaller K, Fischer F, Jiricny J.

Methods Enzymol. 2006;408:285-303.


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