R. Aebersold

Proteomic-based stratification of intermediate-risk prostate cancer patients

The paper identifies an 18-protein signature from proteomic data to stratify intermediate-risk prostate cancer patients into low- and high-risk groups for biochemical recurrence.

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

The paper uses patient-derived organoids and phosphoproteomics to study signaling crosstalk in colorectal cancer and identify off-target effects of kinase inhibitors.

Integrative solution structure of a PTBP1-viral IRES complex reveals strong compaction and ordering with residual conformational flexibility

The paper determines the solution structure of a PTBP1-viral IRES complex using integrative modeling, revealing compaction, ordering, and residual flexibility essential for IRES-mediated translation.

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

The paper identifies two distinct nuclear pore complex remodeling events during budding yeast meiosis, revealing conserved mechanisms of nuclear basket organization.

A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modelling potential

This paper improves a CLIR-MS workflow for protein-RNA cross-linking, increasing detected products and enabling structural restraint analysis.

Molecular architecture of the human tRNA ligase complex

This study presents biochemical and structural analysis of the human tRNA ligase complex, revealing its molecular architecture and catalytic mechanism.

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

This study develops two novel castration-resistant prostate cancer cell lines and characterizes their transcriptomic and proteomic profiles to understand resistance mechanisms.

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

This paper reports the cryo-EM structure of human PRC2 with cofactors JARID2 and AEBP2 bound to a nucleosome containing H2AK119ub1, revealing their roles in PRC2 activity regulation and histone modification crosstalk.

SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution

The paper uses proteomic data to show that paralogues influence protein complex evolution through co-expression patterns and functional divergence.

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

The paper introduces a high-throughput proteomic method to profile protease activity and substrate specificity in native conditions, achieving high throughput and accuracy.

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

This study shows that inhibiting both mitochondrial translation and dynamics in C. elegans synergistically extends lifespan through HLH-30-dependent lysosome biogenesis and autophagy.

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

This paper introduces an accelerated SWATH MS method for protein biomarker discovery in FFPE tissues, showing reduced instrument time and batch effects while maintaining good protein quantification and clinical separation.

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

This study compares two proteomic methods, 2DLC-MS/MS and SWATH-MS, showing they both identify differentially expressed proteins in HGSOC subtypes but differ in workflow complexity and proteome coverage.

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

The paper identifies shared targets of Ypk1, PKA, and Sch9 by comparing phospho-proteomes under chemical inhibition, revealing Ypk1's role in phosphorylating and activating Nth1.

Arabidopsis Proteome and the Mass Spectral Assay Library

The paper generates a comprehensive Arabidopsis proteome atlas and library, then uses DIA-MS to study abscisic acid effects, identifying differentially expressed proteins.

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

This study develops a proteomic workflow for FFPE tissues to stratify prostate cancer and DLBCL samples, identifying MPO as a prognostic marker and showing FFPE's utility for biomarker discovery.

Breast cancer classification based on proteotypes obtained by SWATH mass spectrometry

This study uses SWATH mass spectrometry to classify breast cancer subtypes and identifies key proteins that improve patient stratification for precision medicine.

PGC1a and Exercise Adaptations in Zebrafish

This study shows that PGC1a induces mitochondrial biogenesis and exercise-like adaptations in zebrafish, revealing conserved exercise responses and novel ETC organization.

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

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.

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

The paper shows Nog1 uses ATPase and GTPase activities to coordinate removal of Arx1 and Mrt4 from pre-60S ribosomes, linking PET quality control with ribosomal stalk assembly.

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

The paper characterizes the ATG2A-WIPI4 complex's role in autophagosome biogenesis through structural and biochemical analyses.

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

This study investigates the structure of the Importin4_histone H3/H4_Asf1a complex and identifies key interactions between Importin4 and the histone H3 tail.