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List of works by Bernd Bodenmiller

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

scientific article published on 31 January 2019

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

scientific article published on 11 April 2019

A luminal flavoprotein in endoplasmic reticulum-associated degradation

scientific article

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

scientific article published on 10 May 2012

A practical guide to multiplexed mass cytometry

scientific article published on 01 January 2014

A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids

scientific article published on 01 December 2020

AirLab: a cloud-based platform to manage and share antibody-based single-cell research

scientific article published on 29 June 2016

An Immune Atlas of Clear Cell Renal Cell Carcinoma

scientific article

An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells

scientific article published on 19 February 2007

An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures

scientific article published on 29 May 2008

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

scientific article published on 14 May 2019

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Automated identification of stratifying signatures in cellular subpopulations

scientific article

Automatic single cell segmentation on highly multiplexed tissue images.

scientific article

CellCycleTRACER accounts for cell cycle and volume in mass cytometry data

scientific article published on 12 February 2018

Channel crosstalk correction in suspension and imaging mass cytometry

Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis

scientific article

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases

scientific article published on 28 July 2009

Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification

scientific article published on February 2009

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.

scientific article published on 23 March 2018

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

scientific article

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

scientific article published on 2 July 2018

Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data

scientific article published on 26 December 2020

Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling

scientific journal article

Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome

scientific article

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

scientific article published on 28 March 2016

Fast chemical imaging at high spatial resolution by laser ablation inductively coupled plasma mass spectrometry.

scientific article

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

scientific article

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

scientific article published on 01 December 2019

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

scientific article published in April 2018

High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States and Uncovers Interlineage Relationships

scientific article published on 21 July 2020

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

scientific article

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

scientific article published on 11 April 2019

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

scientific article published in Scientific Reports

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

scientific article published on 16 January 2017

Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence

scientific article

Kinome-wide decoding of network-attacking mutations rewiring cancer signaling

scientific article

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

scientific article published in PLoS ONE

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

scientific article published on 8 May 2018

Mapping of phosphorylation sites by LC-MS/MS

scientific article published on 01 January 2010

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition

scientific article published on 30 November 2020

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

scientific article published on 01 October 2019

Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

scientific article published on 27 April 2016

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

scientific article

Orm family proteins mediate sphingolipid homeostasis

scientific article

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm

scientific article

PhosphoPep--a database of protein phosphorylation sites in model organisms

scientific article published on December 2008

PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

scientific article

Phosphoproteome resource for systems biology research

scientific article published in January 2011

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast

scientific article

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

scientific article published on February 2011

Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion

scientific article published on 11 July 2016

Profiling cell signaling networks at single-cell resolution

scientific article published on 04 March 2020

Proteomics meets the scientific method.

scientific article

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

scientific article

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

scientific article published on 01 March 2010

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

scientific article

Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis

scientific article

Reproducible isolation of distinct, overlapping segments of the phosphoproteome

Rewiring of genetic networks in response to DNA damage.

scientific article

Ruthenium Counterstaining for Imaging Mass Cytometry

scientific article

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

scientific article published on 26 December 2017

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

scientific article published in April 2018

Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data

scientific article published on 27 January 2020

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling

scientific article published on October 2007

Target of Rapamycin Complex 2 Regulates Actin Polarization and Endocytosis via Multiple Pathways

scientific article published on 16 April 2015

The Human Cell Atlas

scientific article

The Human Cell Atlas

The Human Cell Atlas White Paper

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity

scientific article

The single-cell pathology landscape of breast cancer

scientific article published on 20 January 2020

T‐cell recovery and evidence of persistent immune activation 12 months after severe <scp>COVID</scp>‐19

scientific article published in 2022

Uncovering axes of variation among single-cell cancer specimens

scientific article published on 13 January 2020

Unraveling cell populations in tumors by single-cell mass cytometry

scientific article

Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A

scientific journal article

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data.

scientific article published on 07 August 2017