Dr. Erich Brunner

Dr. Erich Brunner

Y55-K-54

+41 44 635 31 59

List of publications

(* equal contribution, ⁺corresponding author)

Giulia Moro*, Izaskun Mallona⁺*, Malwine J. Barz, Joël Maillard, Michael David Brügger, Hassan Fazilaty, Quentin Szabo, Tomas Valenta, Kristina Handler, Fiona Kerlin, Lorenz Bastian, Claudia D. Baldus, Andreas E. Moor, Robert Zinzen, Mark D. Robinson, Erich Brunner⁺ & Konrad Basler. RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing. Nature Communications. volume 16, Article number: 10991 (2025). https://doi.org/10.1038/s41467-025-66248-z

Brunner E⁺*, Yagi R*, Debrunner M, Beck-Schneider D, Burger A, Escher E, Mosimann C, Hausmann G, Basler K⁺. CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Sci Alliance. 2019 Jun 13;2(3). pii: e201800267. doi: 10.26508/lsa.201800267. Print 2019 Jun.

Spletter ML, Barz C, Yeroslaviz A, Zhang X, Lemke SB, Bonnard A, Brunner E, Cardone G, Basler K, Habermann BH, Schnorrer F. A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle. Elife. 2018 May 30;7. pii: e34058. doi: 10.7554/eLife.34058. [Epub ahead of print]

Franz A, Brunner E, Basler K. Generation of genome-modified Drosophila cell lines using SwAP Fly. 2017 Aug 2017

Marty F, Rago G, Smith DF, Gao X, Eijkel GB, MacAleese L, Bonn M, Brunner E, Basler K, Heeren RMA. Combining ToF-SIMS imaging mass spectrometry and CARS microspectroscopy reveals lipid patterns reminiscent of gene expression patterns in the wing imaginal disc of Drosophila melanogaster. Anal. Chem. 2017 Jul 20. doi: 10.1021/acs.analchem.7b00125. [Epub ahead of print]

Franz A, Shlyueva D, Brunner E, Stark A, Basler K. Probing the canonicity of the Wnt/wingless signaling pathway. PLOS Genetics. 2017 Apr 3;13(4):e1006700. doi: 10.1371/journal.pgen.1006700. eCollection 2017 Apr. PMID:28369070

Subasic D, Brümmer A, Wu Y, Pinto SM, Imig J, Keller M, Jovanovic M, Lightfoot HL, Nasso S, Goetze S, Brunner E, Hall J, Aebersold R, Zavolan M, Hengartner MO. Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Res. 2015 Jul 31. [Epub ahead of print]

Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E⁺, Brun V⁺. DIGESTIF: A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments. J Proteome Res. 2014 Dec 30. [Epub ahead of print]

Qeli E, Omasits. U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH. Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. J Proteomics, 2014 May 27. pii: S1874-3919(14)00272-3. doi: 10.1016/j.jprot.2014.05.011. [Epub ahead of print]

Marty F*, Rockel-Bauer C*, Simigdala N, Brunner E, Basler K. Large-scale imaginal disc sorting: a protocol for “omics”-approaches. Methods 2014 Apr 12. pii: S1046-2023(14)00149-2. doi: 10.1016/j.ymeth.2014.04.005. [Epub ahead of print]

Gerber F, Marty F, Eijkel GB, Basler K, Brunner E, Furrer R, and Heeren RMA. Multi order correction algorithms to remove image distortions from mass spectrometry imaging datasets. Anal. Chem., 2013 DOI: 10.1021/ac402018e • Publication Date (Web): 04 Oct 2013

Handke B, Poernbacher I, Goetze S, Ahrens CH, Omasits U, Marty F, Simigdala N, Meyer I, Wollscheid B, Brunner E, Hafen E, Lehner CF. The hemolymph proteome of fed and starved Drosophila larvae. 2013 PLoS One. 2013 Jun 20;8(6):e67208. doi: 10.1371/journal.pone.0067208.

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 K, Mering C, Weiss M, Zheng X. The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics. 2012 Feb;12(3):340-5. doi: 10.1002/pmic.201290014.

Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nature Rev Mol Cell Biol. 2010 Nov;11(11):789-801. Epub 2010 Oct 14.

Song H, Goetze S, Bischof J, Spichiger-Haeusermann C, Kuster M, Brunner E, Basler K. (2010) Coop functions as a corepressor of Pangolin and antagonizes Wingless signaling. Genes Dev. 2010 May;24(9):881-6.

Gluderer G, Brunner E, Germann M, Jovaisaite V, Li C, Rentsch CA, Hafen E, Stocker H. (2010) Madm (Mlf1 adapter molecule) cooperates with Bunched A to promote growth in Drosophila. J Biol. 2010. 9(1):9. Epub 2010 Feb 11.

Ahrens CH, Brunner E, Basler K. (2009) Quantitative proteomics: A central technology for systems biology. J Proteomics. 10;73(4):820-7

Goetze, S*, Qeli E*, Mosimann C*, Staes A, Gerrits B, Roschitzki B, Van Damme P. Mohanty S, Niederer EM, Laczko E, Lange V, Hafen E, Aebersold R, Basler K, Ahrens CH, Gevaert K, Brunner E⁺. (2009) Identification and Functional Characterization of N-terminally acetylated Proteins in Drosophila melanogaster. PloS Biol. 7(11): e1000236. doi:10.1371/journal.pbio.1000236.

Köhler K, Brunner E, Guan X, Boucke K, Greber UF, Mohanty S, Barth JMI, Wenk MR, Hafen E. (2009) A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy. Oct;5(7):980-90. Epub 2009 Oct 22.

Grobei MA, Qeli E, Brunner E, Rehrauer H, Zhang R, Roschitzki B, Basler K, Ahrens CH, Ueli Grossniklaus U. (2009) Shotgun proteomics analysis of the Arabidopsis thaliana mature pollen provides new insights into pollen development and function. Genome Res. June 22, 2009, doi:10.1101/gr.089060.108.

Schrimpf S, Weiss M, Reiter L, Ahrens C, Jovanovic M, Malström J, Brunner E, Mohanty S, Hunziker PE, Aebersold R, von Mering C, Hengartner M. (2009) Comparative functional characterization of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLOS Biol. Mar 3;7(3):e48. [Epub ahead of print].

Rutishauser D, Mertz KD, Moos R, Brunner E, Rülicke T, Calella AM, Aguzzi A. (2009) The comprehensive native interactome of a fully functional tagged prion protein. PLOS One. 4(2):e4446. Epub 2009 Feb 11.

Sandra LN, Brunner E, King NL, Deutsch EW, Stein SE, The Flybase Consortium, Aebersold R, Hafen E. (2009) The Drosophila melanogaster PeptideAtlas facilitates improved fly proteomics and genome annotation. BMC Bioinformatics, Feb 11;10(1):59. [Epub ahead of print]

Ahrens CA*, Brunner E*, Hafen E, Aebersold R, Basler K. (2007) A proteome catalog of Drosophila melanogaster: An essential resource for targeted quantitative proteomics. Fly 1(3):e1-e5.

Brunner E*⁺, Ahrens CH*⁺, Mohanty S*, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R⁺. (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology 25(5):576-83. Epub 2007 Apr 22.

Zhao J, Leonhard C, Brunner E, Heitz PU, Odermatt B. (2006) Molecular characterization of well-differentiated human thyroid carcinomas by cDNA arrays. Int J Oncol. 29:1041-51.

Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C and Aebersold R. (2006) Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J Proteome Res. 5:2241-9.

Schrimpf SP, Meskenaite V, Brunner E, Rutishauser D, Walther P, Eng J, Aebersold R, Sonderegger P. (2005) Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics 5:2531-2541.

Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 6:R9. Epub 2004 Dec 10.

Heitz PU, Zhao J, Leonard-Meier Ch, Gemsenjager E, Odermatt B, Brunner E. (2003) Differential gene expression signatures in well differentiated thyroid carcinomas. Verh Dtsch Ges Pathol. 87:185-7.

Kramps T*, Peter O*, Brunner E*, Nellen D, Froesch B, Chatterjee S, Murone M, Zullig S, Basler K. (2002) Wnt/wingless signaling requires BCL9/legless-mediated recruitment of pygopus to the nuclear beta-catenin-TCF complex. Cell 109, 47-60.

Brunner E*, Brunner D*, Fu WM, Hafen E, Basler K. (1999) The dominant mutation Glazed is a gain-of-function allele of wingless that, similar to loss of APC, interferes with normal eye development. Dev. Biol. 206, 178-188.

Brunner E*, Peter O*, Schweizer L, Basler K. (1997) pangolin encodes a Lef-1 homologue that acts downstream of Armadillo to transduce the Wingless signal in Drosophila. Nature 385, 829-33.

Book chapters

Brunner E, Gerrits B, Scott M, Roschitzki B. (2007) Differential display and protein quantification. EXS Book-Review. (Baginsky and Fernie Plant Systems Biology) 97:115-40.

Editorials

Ahrens CH, Schrimpf SP, Brunner E, Aebersold R. Model organism proteomics. J Proteomics. Special Issue, 2010 Oct 10;73(11):2051-3. Epub 2010 Sep 9.