proteomics

Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

Network analysis of mouse brain proteomes resolves molecular and cellular endophenotypes of aging and Aβ pathology

This study uses proteomics to identify aging and Aβ-related molecular changes in mouse brains and finds they are conserved in human AD proteomes.

Endothelial protein C receptor is an entry receptor for Langya virus

This study identifies the endothelial protein C receptor (EPCR) as the entry receptor for Langya virus and reveals the molecular basis of its interaction with the viral attachment glycoprotein.

Starve, stress, and mate: Activation of the CCAAT-Binding complex overrides sterility of mating-type heterozygous Candida albicans

The paper identifies the CCAAT-binding complex (CBC) as a key regulator that overrides genetic sterility in Candida albicans by integrating environmental stress signals to enable mating.

Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea

This study identifies surface proteins in Asgard archaea using visual surfaceomics, revealing a peptidophilic cell surface involved in peptide capture and symbiotic interactions.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

Development of a Pan-Proteome Multi-Epitope Vaccine Candidate Against Nipah Virus Using Reverse Vaccinology and Immunoinformatics Approaches

This paper designs a multi-epitope vaccine candidate against Nipah virus using immunoinformatics and reverse vaccinology, identifying VC033_V6_BD_L03 as a lead candidate with high global and regional population coverage.

Amyloid stability and condensate material properties independently govern the hnRNPA2 condensate to fibril transition

This study shows that amyloid structure and condensate stability independently influence the hnRNPA2 condensate-to-fibril transition, revealing a structural framework for this process.

Ribosomal Remodeling and Translational Suppression in the Post-Arrest Heart

This study investigates how cardiac arrest affects myocardial ribosome biology and protein synthesis in pigs and mice, finding increased ribosomal transcripts with ischemic burden and suppressed ribosome activity post-arrest.

TACO: An open, interpretable model for microsecond-scale TCR specificity prediction

TACO predicts TCR specificity against HLA-A*02:01-presented peptides using a statistical model, achieving AUROC 0.67 on held-out data and enabling efficient computational evaluation of TCR-peptide interactions.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

memVar: an integrated resource for interpreting human membrane protein variation in molecular and disease contexts

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

The binding landscape of Ras/effector interactions provides insights on Ras switching and oncogenesis

This study maps the Ras/Nore1A binding landscape under different states and mutations, revealing how oncogenic changes alter interaction dynamics and provide insights for inhibitor design.

Use of Integrative Proteomic Analysis to Uncover Shared Molecular Signatures Across Distinct Forms of Hydrocephalus

This study identifies shared and etiology-specific proteomic signatures across hydrocephalus subtypes using cross-study proteomic analysis of CSF.

Improving phosphoproteomic kinase activity inference by contextual refinement of Kinase Library relationships

The paper improves kinase activity inference by refining kinase-substrate relationships with protein-association evidence, enhancing accuracy and coverage in phosphoproteomic data.

Receptor-proximal phosphoform organization precedes β2 integrin activation

The paper quantifies phosphoform organization near β2 integrins and shows that signaling alters phosphosites while preserving spatial organization of proteins.

Stochastic gene expression drives state switching and phenotypic heterogeneity in RNA repair

The paper shows stochastic RNA repair in E. coli leads to phenotypic heterogeneity and state switching in antibiotic responses.

Polygenic polymorphisms cooperate to drive expansion of HCMV adaptive NK cell and NK-like T cell populations

This study identifies genetic polymorphisms in NKG2C, CD16a, and HLA-E that influence NKG2C expression and ADCC capacity in HCMV-infected individuals.

Massively parallel quantification and prediction of monomeric protein yield in Escherichia coli

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

Interpretable Machine Learning Links Group-Specific Plasma Proteomics to Regional Structural Neuroimaging in Alzheimer's Disease

The paper identifies group-specific plasma proteomic signatures in Alzheimer's disease stages and links them to regional brain structural changes using machine learning and neuroimaging.

Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans

The paper uses computational methods to analyze antioxidant effects on stress response mechanisms in Candida albicans, identifying naringenin and quercetin as potential modulators of Sir2/SIRT3 pathways.

Chronic Sleep Disruption Activates the Transcriptional Unfolded Protein Response and Induces Compartment-Specific Proteomic Changes in Mice

This study shows chronic sleep disruption causes distinct transcriptional and proteomic changes in brain compartments, particularly affecting synaptic function and potentially contributing to Alzheimer's risk.

Inosine Triphosphate Pyrophosphatase as a Candidate Associated with White Matter Abnormalities in Chronic Heart Failure

This study identifies inosine triphosphate pyrophosphatase (ITPA) as a candidate factor linking chronic heart failure and white matter abnormalities through human, animal, and cellular analyses.

Electrostatic control of conformational dynamics drives proton translocation in respiratory Complex I

The paper investigates how electrostatic interactions control conformational changes and proton translocation in Complex I using a combination of experimental and computational methods.

Plant-plant communication in tomato: mechanisms underpinning information transfer between plants

This study investigates plant-plant communication in tomato by analyzing metabolomic and volatile emissions changes in response to herbivory, showing mirror effects in immune system reprogramming between sender and receiver plants.

Linking dynamic photosynthetic traits to biomass: a functional data framework that pinpoints when photosynthesis limits growth

The paper models genotype-specific photosynthetic trait trajectories using functional data analysis to predict biomass, finding that early growth period traits most strongly influence final dry weight.

The intrinsically disordered N-terminal region of eIF5B nucleates RNA-driven phase separation

This study shows that the intrinsically disordered N-terminal region of eIF5B drives RNA-driven phase separation in vitro and validates this in cells.

Squalene as a Candidate Signalling Molecule: Computational Evidence for a Predicted KEAP1 Interaction and Implications for Stress-Induced Altruistic Stem-Cell Niche Protection

This paper investigates the structural feasibility of squalene interacting with the KEAP1 Kelch domain using molecular docking and provides a hypothesis for its role in NRF2 regulation under stress.

The Test Used to Choose Between Pesticide Survival Models Tracks Lesion Persistence, Not Hazard Structure

The paper evaluates pesticide survival models by analyzing lesion persistence, showing that post-exposure death rates better reflect hazard structure than peak-based assumptions.