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The single-cell pathology landscape of breast cancer.

Jackson HW, Fischer JR, Zanotelli VRT, Ali HR, Mechera R, Soysal SD, Moch H, Muenst S, Varga Z, Weber WP, Bodenmiller B.

Nature. 2020 Jan 20. doi: 10.1038/s41586-019-1876-x. [Epub ahead of print]


Uncovering axes of variation among single-cell cancer specimens.

Chen WS, Zivanovic N, van Dijk D, Wolf G, Bodenmiller B, Krishnaswamy S.

Nat Methods. 2020 Jan 13. doi: 10.1038/s41592-019-0689-z. [Epub ahead of print]


Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy.

Klufa J, Bauer T, Hanson B, Herbold C, Starkl P, Lichtenberger B, Srutkova D, Schulz D, Vujic I, Mohr T, Rappersberger K, Bodenmiller B, Kozakova H, Knapp S, Loy A, Sibilia M.

Sci Transl Med. 2019 Dec 11;11(522). pii: eaax2693. doi: 10.1126/scitranslmed.aax2693.


Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.

Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O.

Cell Rep. 2019 Oct 1;29(1):202-211.e6. doi: 10.1016/j.celrep.2019.08.077.


Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B.

Mol Cell. 2019 Jun 6;74(5):1086-1102.e5. doi: 10.1016/j.molcel.2019.04.021. Epub 2019 May 14.


A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.

Wagner J, Rapsomaniki MA, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal SD, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes KJ, Rodríguez Martínez M, Weber WP, Bodenmiller B.

Cell. 2019 May 16;177(5):1330-1345.e18. doi: 10.1016/j.cell.2019.03.005. Epub 2019 Apr 11.


IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer.

Corrò C, Healy ME, Engler S, Bodenmiller B, Li Z, Schraml P, Weber A, Frew IJ, Rechsteiner M, Moch H.

J Pathol. 2019 Jul;248(3):377-389. doi: 10.1002/path.5267. Epub 2019 Apr 11.


In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay.

Schulz D, Severin Y, Zanotelli VRT, Bodenmiller B.

Sci Rep. 2019 Feb 13;9(1):1925. doi: 10.1038/s41598-018-38127-9.


A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry.

Damond N, Engler S, Zanotelli VRT, Schapiro D, Wasserfall CH, Kusmartseva I, Nick HS, Thorel F, Herrera PL, Atkinson MA, Bodenmiller B.

Cell Metab. 2019 Mar 5;29(3):755-768.e5. doi: 10.1016/j.cmet.2018.11.014. Epub 2019 Jan 31.


Learning time-varying information flow from single-cell epithelial to mesenchymal transition data.

Krishnaswamy S, Zivanovic N, Sharma R, Pe'er D, Bodenmiller B.

PLoS One. 2018 Oct 29;13(10):e0203389. doi: 10.1371/journal.pone.0203389. eCollection 2018.


Correction to: Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer.

Kündig P, Giesen C, Jackson H, Bodenmiller B, Papassotirolopus B, Freiberger SN, Aquino C, Opitz L, Varga Z.

J Transl Med. 2018 Jul 2;16(1):180. doi: 10.1186/s12967-018-1553-0.


Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer.

Kündig P, Giesen C, Jackson H, Bodenmiller B, Papassotirolopus B, Freiberger SN, Aquino C, Opitz L, Varga Z.

J Transl Med. 2018 May 8;16(1):118. doi: 10.1186/s12967-018-1495-6. Erratum in: J Transl Med. 2018 Jul 2;16(1):180.


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 Syst. 2018 Apr 25;6(4):531. doi: 10.1016/j.cels.2018.04.004. No abstract available.


High-Dimensional Phenotyping Identifies Age-Emergent Cells in Human Mammary Epithelia.

Pelissier Vatter FA, Schapiro D, Chang H, Borowsky AD, Lee JK, Parvin B, Stampfer MR, LaBarge MA, Bodenmiller B, Lorens JB.

Cell Rep. 2018 Apr 24;23(4):1205-1219. doi: 10.1016/j.celrep.2018.03.114.


Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

Chevrier S, Crowell HL, Zanotelli VRT, Engler S, Robinson MD, Bodenmiller B.

Cell Syst. 2018 May 23;6(5):612-620.e5. doi: 10.1016/j.cels.2018.02.010. Epub 2018 Mar 28.


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 12;9(1):632. doi: 10.1038/s41467-018-03005-5.


Ruthenium counterstaining for imaging mass cytometry.

Catena R, Montuenga LM, Bodenmiller B.

J Pathol. 2018 Apr;244(4):479-484. doi: 10.1002/path.5049. Epub 2018 Mar 6.


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 Syst. 2018 Jan 24;6(1):25-36.e5. doi: 10.1016/j.cels.2017.12.001. Epub 2017 Dec 27. Erratum in: Cell Syst. 2018 Apr 25;6(4):531.


The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.


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 Sep;14(9):873-876. doi: 10.1038/nmeth.4391. Epub 2017 Aug 7.


An Immune Atlas of Clear Cell Renal Cell Carcinoma.

Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B.

Cell. 2017 May 4;169(4):736-749.e18. doi: 10.1016/j.cell.2017.04.016.


Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry.

Lun XK, Zanotelli VR, Wade JD, Schapiro D, Tognetti M, Dobberstein N, Bodenmiller B.

Nat Biotechnol. 2017 Feb;35(2):164-172. doi: 10.1038/nbt.3770. Epub 2017 Jan 16.


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 J. 2016 Aug 15;35(16):1810-21. doi: 10.15252/embj.201694071. Epub 2016 Jul 11.


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 Biol. 2016 Jun 29;17(1):142. doi: 10.1186/s13059-016-1006-0.


Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications.

Bodenmiller B.

Cell Syst. 2016 Apr 27;2(4):225-38. doi: 10.1016/j.cels.2016.03.008. Epub 2016 Apr 27. Review.


Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species.

Catena R, Özcan A, Zivanovic N, Bodenmiller B.

Cytometry A. 2016 May;89(5):491-7. doi: 10.1002/cyto.a.22848. Epub 2016 Mar 28.


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 Sep 24;163(1):202-17. doi: 10.1016/j.cell.2015.08.056. Epub 2015 Sep 17.


Automatic single cell segmentation on highly multiplexed tissue images.

Schüffler PJ, Schapiro D, Giesen C, Wang HA, Bodenmiller B, Buhmann JM.

Cytometry A. 2015 Oct;87(10):936-42. doi: 10.1002/cyto.a.22702. Epub 2015 Jul 2.


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 Jun 12;290(24):14963-78. doi: 10.1074/jbc.M114.627794. Epub 2015 Apr 16.


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;10(2):316-33. doi: 10.1038/nprot.2015.020. Epub 2015 Jan 22.


Unraveling cell populations in tumors by single-cell mass cytometry.

Di Palma S, Bodenmiller B.

Curr Opin Biotechnol. 2015 Feb;31:122-9. doi: 10.1016/j.copbio.2014.07.004. Epub 2014 Aug 11. Review.


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 Jul 1;111(26):E2770-7. doi: 10.1073/pnas.1408792111. Epub 2014 Jun 16.


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 Aug 7;55(3):422-435. doi: 10.1016/j.molcel.2014.05.012. Epub 2014 Jun 12.


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 Apr;11(4):417-22. doi: 10.1038/nmeth.2869. Epub 2014 Mar 2.


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. 2013 Nov 5;85(21):10107-16. doi: 10.1021/ac400996x. Epub 2013 Sep 17.


A practical guide to multiplexed mass cytometry.

Zivanovic N, Jacobs A, Bodenmiller B.

Curr Top Microbiol Immunol. 2014;377:95-109. doi: 10.1007/82_2013_335.


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 Feb 14;152(4):791-805. doi: 10.1016/j.cell.2013.01.033.


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 Jan 31;3(1):16-22. doi: 10.1016/j.celrep.2012.11.025. Epub 2012 Dec 27.


Proteomics meets the scientific method.

Picotti P, Bodenmiller B, Aebersold R.

Nat Methods. 2013 Jan;10(1):24-7. doi: 10.1038/nmeth.2291. No abstract available.


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 Sep;30(9):858-67.


A platinum-based covalent viability reagent for single-cell mass cytometry.

Fienberg HG, Simonds EF, Fantl WJ, Nolan GP, Bodenmiller B.

Cytometry A. 2012 Jun;81(6):467-75. doi: 10.1002/cyto.a.22067. Epub 2012 May 10.


Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry.

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

Cell. 2011 Feb 18;144(4):539-50. doi: 10.1016/j.cell.2011.01.012.


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 21;3(153):rs4. doi: 10.1126/scisignal.2001182.


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 3;330(6009):1385-9. doi: 10.1126/science.1195618. Erratum in: Science. 2011 Jan 21;331(6015):284.


Phosphoproteome resource for systems biology research.

Bodenmiller B, Aebersold R.

Methods Mol Biol. 2011;694:307-22. doi: 10.1007/978-1-60761-977-2_19.


Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics.

Bodenmiller B, Aebersold R.

Methods Enzymol. 2010;470:317-34. doi: 10.1016/S0076-6879(10)70013-6. Epub 2010 Mar 1.


Mapping of phosphorylation sites by LC-MS/MS.

Gerrits B, Bodenmiller B.

Methods Mol Biol. 2010;658:127-36. doi: 10.1007/978-1-60761-780-8_7.


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 25;463(7284):1048-53. doi: 10.1038/nature08787.


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 1;106(35):14831-6. doi: 10.1073/pnas.0900742106. Epub 2009 Aug 19.


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 15;23(16):1929-43. doi: 10.1101/gad.532109.

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