CellCycleTRACER accounts for cell cycle and volume in mass cytometry data.

Rapsomaniki MA, Lun XK, Woerner S, Laumanns M, Bodenmiller B, Martínez MR
Nat Commun, 2018 Feb
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Ruthenium Counterstaining for Imaging Mass Cytometry.

Catena R, Montuenga LM, Bodenmiller B
J Pathol, 2018 Feb
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Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B
Cell Systems, 2018 Jan
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histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data.

Schapiro D, Jackson HW, Raghuraman S, Fischer JR, Zanotelli VRT, Schulz D, Giesen C, Catena R, Varga Z, Bodenmiller B
Nat Methods, 2017 Jul
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An Immune Atlas of Clear Cell Renal Cell Carcinoma

Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch, Maries van den Broek, Christian Beisel, Michael Beda Stadler, Craig Gedye, Bernhard Reis, Dana Pe?er, Bernd Bodenmiller
Cell, 2017 May
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Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry

Xiao-Kang Lun, Vito R T Zanotelli, James D Wade, Denis Schapiro, Marco Tognetti, Nadine Dobberstein, Bernd Bodenmiller
Nat Biotechnology, 2017 Jan
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Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion

Malmersjö S, Di Palma S, Diao J, Lai Y, Pfuetzner RA, Wang AL, McMahon MA, Hayer A, Porteus M, Bodenmiller B, Brunger AT, Meyer T
EMBO Journal, 2016 Aug
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AirLab: A cloud-based platform to manage and share antibody-based single-cell research

Catena R, Özcan A, Jacobs A, Chevrier S, Bodenmiller B.
Genome Biology, 2016 Jun
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Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

Bodenmiller B
Cell Systems, 2016 Apr
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Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species.

Catena R, Özcan A, Zivanovic N, Bodenmiller B.
Cytometry A, 2016 Mar
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Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling.

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R.
Cell, 2015 Sept
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Automatic single cell segmentation on highly multiplexed tissue images.

Schüffler PJ, Schapiro D, Giesen C, Wang HA, Bodenmiller B, Buhmann JM.
Cytometry A, 2015 Jul
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Target of rapamycin complex 2 regulates actin polarization and endocytosis via multiple pathways.

Rispal D, Eltschinger S, Stahl M, Vaga S, Bodenmiller B, Abraham Y, Filipuzzi I, Movva NR, Aebersold R, Helliwell SB, Loewith R.
J Biol Chem, 2015 Apr
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Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Zunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe’er D, Nolan GP.
Nat Protoc., 2015 Feb
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Unraveling cell populations in tumors by single-cell mass cytometry.

Di Palma S, Bodenmiller B.
Curr Opin Biotechnol., 2014 Aug
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Automated identification of stratifying signatures in cellular subpopulations.

Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP.
Proc Natl Acad Sci U S A. , 2014
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The Calcineurin Signaling Network Evolves via Conserved Kinase-Phosphatase Modules that Transcend Substrate Identity.

Goldman A, Roy J, Bodenmiller B, Wanka S, Landry CR, Aebersold R, Cyert MS.
Mol Cell, 2014
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Fast chemical imaging at high spatial resolution by laser ablation inductively coupled plasma mass spectrometry.

Wang HA, Grolimund D, Giesen C, Borca CN, Shaw-Stewart JR, Bodenmiller B, Günther D.
Anal Chem. , 2014
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A practical guide to multiplexed mass cytometry.

Zivanovic N, Jacobs A, Bodenmiller B.
Curr Top Microbiol Immunol., 2014
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Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry.

Giesen C, Wang HA, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, Schüffler PJ, Grolimund D, Buhmann JM, Brandt S, Varga Z, Wild PJ, Günther D, Bodenmiller B.
Nat Methods, 2014
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Proteomics meets the scientific method.

Picotti P, Bodenmiller B, Aebersold R.
Nat Methods, 2013
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Yeast Endosulfines Control Entry into Quiescence and Chronological Life Span by Inhibiting Protein Phosphatase 2A.

Bontron S, Jaquenoud M, Vaga S, Talarek N, Bodenmiller B, Aebersold R, De Virgilio C.
Cell Rep, 2013
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Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling.

Wippich F, Bodenmiller B, Trajkovska MG, Wanka S, Aebersold R, Pelkmans L.
Cell, 2013
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Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.

Bodenmiller B, Zunder ER, Finck R, Chen TJ, Savig ES, Bruggner RV, Simonds EF, Bendall SC, Sachs K, Krutzik PO, Nolan GP.
Nat Biotechnol, 2012
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A platinum-based covalent viability reagent for single cell mass cytometry

Fienberg HG, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B
Cytometry A, 2012
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Phosphoproteome resource for systems biology research.

Bodenmiller B, Aebersold R.
Methods Mol Biol., 2011
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Laurell E, Beck K, Krupina K, Theerthagiri G, Bodenmiller B, Horvath P, Aebersold R, Antonin W, Kutay U.

Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry.
Cell, 2011 Feb
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Mapping of phosphorylation sites by LC-MS/MS.

Gerrits B, Bodenmiller B.
Methods Mol Biol, 2010
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Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics.

Bodenmiller B, Aebersold R.
Methods Enzymol, 2010
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Orm family proteins mediate sphingolipid homeostasis.

Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS.
Nature, 2010 Feb
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Rewiring of genetic networks in response to DNA damage.

Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T.
Science, 2010 Dec
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Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.

Bodenmiller B*, Wanka S*, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R.
Sci Signal, 2010 Dec
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Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome.

Domon B*, Bodenmiller B*, Carapito C*, Hao Z, Huehmer A, Aebersold R.
J Proteome Res, 2009 Jun
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A luminal flavoprotein in endoplasmic reticulum-associated degradation.

Riemer J, Appenzeller-Herzog C, Johansson L, Bodenmiller B, Hartmann-Petersen R, Ellgaard L.
Proc Natl Acad Sci U S A., 2009 Sep
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Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis.

Sumara G, Formentini I, Collins S, Sumara I, Windak R, Bodenmiller B, Ramracheya R, Caille D, Jiang H, Platt KA, Meda P, Aebersold R, Rorsman P, Ricci R.
Cell, 2009 Jan
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Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases.

Tan CS*, Bodenmiller B*, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R.
Sci Signal, 2009 Jul
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Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.

Huber A*, Bodenmiller B*, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R.
Genes Dev, 2009 Aug
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Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.

Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R.
Cell, 2009 Aug
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Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence.

Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI.
Mol Cell Proteomics, 2008 Jan
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An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures.

Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B.
Mol Cell Proteomics, 2008 Nov
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Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

Tress ML, Bodenmiller B, Aebersold R, Valencia A.
Genome Biol, 2008
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Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification.

Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI.
J Proteome Res, 2009 Feb
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Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.
BMC Bioinformatics, 2008 Dec
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PhosphoPep–a database of protein phosphorylation sites in model organisms.

Bodenmiller B*, Campbell D*, Gerrits B*, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R.
Nat Biotech, 2008 Dec
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PhosphoPep–a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.

Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon PT, Pedrioli PG, Panse C, Lee HK, Schlapbach R, Aebersold R.
Mol Syst Bi, 2007
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Reproducible isolation of distinct, overlapping segments of the phosphoproteome.

Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R.
Nat Methods, 2007 Mar
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SuperHirn – a novel tool for high resolution LC-MS-based peptide/protein profiling.

Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M.
Proteomics, 2007 Oct
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An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells.

Bodenmiller B, Mueller LN, Pedrioli PG, Pflieger D, Jünger MA, Eng JK, Aebersold R, Tao WA.
Mol Biosyst, 2007 Apr
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Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry.

Tao WA, Wollscheid B, O’Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R.
Nat Methods, 2005 Aug
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