proteomics

The immunogenic 33-mer gliadin peptide attenuates flagellin-induced TLR5/NF-κB signaling

The paper investigates how 33-mer gliadin nanostructures affect TLR5/NF-κB signaling in Caco-2 cells, showing they inhibit flagellin-induced activation.

Five decades of human H1N1 evolution reveal conserved glycan receptor specificity

This study examines the evolution of H1N1 influenza viruses over five decades, revealing conserved glycan receptor specificity despite amino acid changes in the hemagglutinin.

A Multi-Omic Phenobank Reveals Axes of Glioblastoma Growth, Invasion, and Therapeutic Vulnerability

The paper establishes a multi-omic PDX resource linking GBM invasion phenotypes to molecular programs and therapeutic responses, identifying two invasion modes and a neurodevelopmental factor associated with tumor growth and survival.

Revisiting Hydractiniidae (Hydrozoa): Mitogenomic Insights into the Diversity, Systematics and Life-Cycle Evolution of North Atlantic and Arctic Species

This study uses mitogenomic and morphological data to reassess hydractiniid diversity, species boundaries, and life-cycle evolution in North Atlantic and Arctic species.

Trastuzumab deruxtecan kills skin and uveal melanoma in vivo by HER2-independent payload release

This study shows trastuzumab deruxtecan (T-DXd) effectively kills melanoma in vivo, even when HER2 is not expressed, due to extracellular cathepsin L-mediated payload release.

How Bacterial Growth-Phase Reshapes Synthetic Gene Circuit Function

This study develops a mathematical model to predict synthetic gene circuit function during bacterial stationary phase by measuring transcription and translation dynamics over time.

A monoallelic immunopeptidome atlas of 10 prevalent canine DLA-88 alleles

The paper generates a monoallelic immunopeptidome atlas for 10 prevalent canine DLA-88 alleles, identifying 32,702 peptides and revealing allele-specific binding motifs and conserved antigen-processing signatures.

Pre-neuronal origins of monoamine and acetylcholine synthesis and transport

This study identifies the evolutionary origins of neurotransmitter synthesis and transport in fungi, showing these functions predate neurons and are linked to lysosomal processes in opisthokonts.

Single Cell Proteomics reveals partial uncoupling of the Glycerol-3-Phosphate shuttle to compensate for Electron Transport Chain dysfunction in Alexander Disease GFAP mutations

The paper uses single-cell proteomics to show that GFAP mutations in Alexander disease lead to ETC dysfunction and metabolic adaptation via the G3P shuttle.

In Vitro Assessment of Chemically Modified Probiotic Bacteria as Receptor-Mimic Decoys for Cholera Toxin B Subunit

This study develops GM1-receptor-mimic probiotic bacteria that bind and sequester cholera toxin B subunit in vitro, reducing its binding to host cells.

Radiotherapy Reshapes the 3D Genome in Medulloblastoma Cells

This study examines how radiotherapy affects the 3D genome of medulloblastoma cells, identifying molecular and structural changes associated with radiation response.

Host-secreted lactate during respiratory viral infection diminishes macrophage antibacterial activity through metabolic reprogramming

This study shows that host-secreted lactate from viral-infected airway epithelial cells reduces macrophage antibacterial activity by reprogramming their metabolism.

p70 ribosomal protein S6 Kinase (p70S6K) as a potential peripheral biomarker for autistic symptoms in 16p11.2 deletion and duplication syndromes

The paper identifies reduced p70S6K levels in PBMCs of individuals with 16p11.2 deletion and duplication syndromes, correlating with autistic symptom severity.

In silico subtractive genomics and reverse vaccinology approach reveal outer membrane proteins OMP47 and LptD as dual-purpose drug and vaccine targets in Pasteurella multocida Pm70

AI-Driven Design of Next-Generation Immunoinformatics Multi-Epitope Subunit Vaccine Targeting the Most Virulent Mpox Proteome: A Structural and Kinetic Validation Framework

This paper develops an AI-driven vaccine design framework for Mpox, yielding three multi-epitope constructs validated for structural stability, immune binding, and expression efficiency.

TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides

TopFor automates the generation of AMBER-compatible parameters for noncanonical amino acids in peptides, enabling efficient MD simulations and integration into peptide discovery workflows.

Genomic and proteomic insights into the virulence of a native Heterorhabditis indica-Photorhabdus akhurstii complex active against Spodoptera spp.

This study characterizes a native Heterorhabditis indica-Photorhabdus akhurstii complex and identifies virulence factors contributing to its insecticidal activity against Spodoptera species.

Proteomics reveal temperature-coupled cobalamin homeostasis and pathogenicity in Pseudomonas aeruginosa

This study uses proteomics to show that Pseudomonas aeruginosa adjusts its cobalamin homeostasis and pathogenicity in response to temperature changes, revealing temperature-dependent shifts in metabolic strategies.

FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

CHORUS: A proteome-scale atlas of membrane protein interaction interfaces predicted from sequence

CHORUS predicts membrane protein interaction interfaces from sequence, outperforming existing methods and providing a proteome-scale atlas of interactions.

Perturb-Seqr: Signature Search Engine Integrating Connectivity Mapping Resources

Perturb-Seqr integrates multiple Connectivity Mapping datasets to enable drug and target discovery by searching for gene expression signatures of drug and gene perturbations.

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

An improved Trypanosoma vivax genome assembly confirms the distinct organisation of its variant antigen repertoire

The paper presents an improved T. vivax genome assembly, revealing distinct VSG gene organization and expression mechanisms compared to T. brucei.

Non-canonical alternate interactors of SARS CoV-2 Spike protein implicated in placental susceptibilty

The paper identifies CD147, EGFR, and LDLR as non-canonical interactors of SARS-CoV-2 spike protein in placenta, associated with increased susceptibility to vertical transmission.

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

Chronic stress remodels gut bacterial ecology and polysaccharide metabolism with neuroendocrine consequences despite unchanged behavior

This study shows chronic stress alters gut bacterial function and metabolism, affecting neuroendocrine pathways without changing behavior in mice.

A domesticated prophage enzyme links bacterial metabolism, episymbiosis and phage fitness

The paper identifies a prophage-encoded enzyme that links bacterial metabolism, episymbiosis, and phage fitness by remodeling host structures and promoting symbiotic interactions.

Cytos MPS: an automated multimodal pooled screening platform for protein, morphology and transcriptomics

Cytos MPS integrates CRISPR guide identity, morphology, transcriptomics, and protein data to reveal multimodal phenotypes from perturbations.

Bovine serum albumin interaction modulates the cellular potency of the BUB1 inhibitor BAY-1816032: fluorescence, molecular docking, and mesothelioma cell evidence

This study investigates how bovine serum albumin interacts with the BUB1 inhibitor BAY-1816032, showing that albumin binding reduces its cellular potency in mesothelioma cells.

Staphylococcus aureus GpsB, Stk, and VraSR form a cell wall surveillance network to maintain cell envelope integrity and mediate antibiotic resistance

This study identifies GpsB, Stk, and VraSR as forming a cell wall surveillance network in S. aureus that maintains cell envelope integrity and contributes to antibiotic resistance.