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

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

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Protein Classifier for Thyroid Nodules Learned from Rapidly Acquired Proteotypes

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  • In oncology: 11
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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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High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

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A high density map for navigating the human Polycomb complexome

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

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

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

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

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

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  • Site-wide: 37,617
  • In systems biology: 699
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  • Site-wide: 107,070
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  • Site-wide: 209,511

Complex-centric proteome profiling by SEC-SWATH-MS

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  • Site-wide: 38,282
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  • Site-wide: 166,200
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Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

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  • Site-wide: 38,634
  • In cancer biology: 1,095
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PGC1a and Exercise Adaptations in Zebrafish

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  • Site-wide: 41,231
  • In physiology: 182
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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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  • Site-wide: 42,238
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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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  • Site-wide: 42,366
  • In bioinformatics: 4,505
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Molecular architecture of the human tRNA ligase complex

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  • Site-wide: 44,240
  • In biochemistry: 1,093
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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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  • Site-wide: 46,003
  • In systems biology: 885
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Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

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  • Site-wide: 54,070
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  • Site-wide: 204,446

Rapid profiling of protein complex re-organization in perturbed systems

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  • Site-wide: 56,351
  • In systems biology: 1,141
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  • Site-wide: 87,010

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

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  • Site-wide: 58,548
  • In systems biology: 1,172
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  • Site-wide: 88,861
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  • Site-wide: 77,633

Meiotic Nuclear Pore Complex Remodeling Provides Key Insights into Nuclear Basket Organization

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  • Site-wide: 62,675
  • In cell biology: 2,740
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Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis

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  • Site-wide: 63,941
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A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS

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  • Site-wide: 66,546
  • In systems biology: 1,320
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Mitochondrial translation and dynamics synergistically extend lifespan in C. elegans through HLH-30

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  • In cell biology: 2,907
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The polyQ expansion modulates the configuration and phosphorylation of huntingtin

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  • In neuroscience: 9,801
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Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

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  • Site-wide: 70,255
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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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  • Site-wide: 70,575
  • In biochemistry: 1,891
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Resource misallocation as a mediator of fitness costs in antibiotic resistance.

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  • Site-wide: 76,305
  • In microbiology: 4,674
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Arabidopsis Proteome and the Mass Spectral Assay Library

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  • Site-wide: 77,661
  • In plant biology: 1,866
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  • Site-wide: 182,438

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

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  • Site-wide: 78,977
  • In systems biology: 1,587
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  • Site-wide: 170,085

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

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  • Site-wide: 83,110
  • In biophysics: 2,948
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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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  • In biochemistry: 2,369
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Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria

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  • Site-wide: 88,272
  • In systems biology: 1,819
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Breast cancer classification based on proteotypes obtained by SWATH mass spectrometry

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  • Site-wide: 90,266
  • In cancer biology: 2,690
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  • Site-wide: 144,108
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  • Site-wide: 145,434

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

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  • Site-wide: 96,367
  • In biochemistry: 2,711
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Integrated multi-omics reveals anaplerotic insufficiency in methylmalonyl-CoA mutase deficiency

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  • Site-wide: 99,598
  • In pediatrics: 208
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SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution

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  • Site-wide: 99,819
  • In evolutionary biology: 4,602
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Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

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

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

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  • In cell biology: 5,711
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Sensitive detection and structural characterisation of UV-induced cross-links in protein-RNA complexes using CLIR-MS

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Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration

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Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer

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Integrative analysis allows a global and precise identification of functional miRNA target genes in mESCs

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PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER.

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7q11.23 CNV alters protein synthesis and REST-mediated neuronal intrinsic excitability

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  • In neuroscience: 21,296
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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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  • Site-wide: 146,742
  • In cancer biology: 4,482
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Novel biochemical, structural and systems insights into inflammatory signaling revealed by contextual interaction proteomics

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  • Site-wide: 150,152
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Integrative solution structure of a PTBP1-viral IRES complex reveals strong compaction and ordering with residual conformational flexibility

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All driven by energy demand? Integrative comparison of metabolism of Enterococcus faecalis wildtype and a glutamine synthase mutant

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Proteomic Dynamics of Breast Cancers Identifies Potential Therapeutic Protein Targets

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Deep Domain Adversarial Neural Network for the Deconvolution of Cell Type Mixtures in Tissue Proteome Profiling

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