Author: Ruedi Aebersold

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Preprints

Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

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Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

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Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

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JARID2 and AEBP2 regulate PRC2 activity in the presence of H2A ubiquitination or other histone modifications

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Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells

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Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex

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Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

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Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes

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Multi-Omic Profiling of the Liver Across Diets and Age in a Diverse Mouse Population

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High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

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Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

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A high density map for navigating the human Polycomb complexome

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SECAT: Quantifying differential protein-protein interaction states by network-centric analysis

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Integration of transcriptome, proteome and phosphoproteome data elucidates the genetic control of molecular networks

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System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects

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Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

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Convergent network effects along the axis of gene expression during prostate cancer progression

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Complex-centric proteome profiling by SEC-SWATH-MS

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Ultra-sensitive proteome profiling of FACS-isolated cell populations by data-independent acquisition-MS: Application to human hematopoietic stem and progenitor cells

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DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring

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Comparative ’omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

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PGC1a and Exercise Adaptations in Zebrafish

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Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

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A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS

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Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

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  • In cancer biology: 1,162
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Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

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Mitochondrial translation and dynamics synergistically extend lifespan in C. elegans through HLH-30

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Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle

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Systematic protein complex profiling and differential analysis from co-fractionation mass spectrometry data

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Resource misallocation as a mediator of fitness costs in antibiotic resistance.

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Arabidopsis Proteome and the Mass Spectral Assay Library

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The polyQ expansion modulates the configuration and phosphorylation of huntingtin

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Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis

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MLL1 minimal catalytic complex is a dynamic conformational ensemble susceptible to pharmacological allosteric disruption

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Breast cancer classification based on proteotypes obtained by SWATH mass spectrometry

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  • In cancer biology: 1,715
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Systematic detection of functional proteoform groups from bottom-up proteomic datasets

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Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria

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The GTPase Nog1 couples polypeptide exit tunnel quality control with ribosomal stalk assembly

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Integrative structure investigation on the architecture of human Importin4_histone H3/H4_Asf1a complex and its histone H3 tail binding

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Chemical genetics of AGC-kinases reveals shared targets of Ypk1, Protein Kinase A and Sch9

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Mapping specificity, entropy, allosteric changes and substrates in blood proteases by a high-throughput protease screen

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  • In biochemistry: 2,673
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SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution

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Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes

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Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

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