378 documents found, page 1 of 38

Comparative assessment of protein large language models for enzyme commission n...

Background: Protein large language models (LLM) have been used to extract representations of enzyme sequences to predict their function, which is encoded by enzyme commission (EC) numbers. However, a comprehensive comparison of different LLMs for this task is still lacking, leaving questions about their relative performance. Moreover, protein sequence alignments (e.g. BLASTp or DIAMOND) are often combined with ...

Cellular and biochemical alterations induced by diesel oil in the brown alga Sa...

The effect of the in vitro acute exposure to diesel oil (0.001%, 0.01%, 0.1%, and 1%, v/v) has been evaluated in the brown seaweed Sargassum cymosum var. stenoplhyllum by determining the contents of photosynthetic pigments, phenolic compounds, and morphological and cellular changes. In vitro cultures of S. cymosum were exposed to diesel oil for 30min, 1h, 12h, and 24h under laboratory-controlled conditions. Chl...

TROPPO: tissue-specific reconstruction and phenotype prediction using omics data

The increasing availability of high-throughput technologies in systems biology has advanced predictive tools like genome-scale metabolic models. Despite this progress, integrating omics data to create accurate, context-specific metabolic models for different tissues or cells remains challenging. A significant issue is that many existing tools rely on proprietary software, which limits accessibility. We introduc...

Implementing metabolic transformation algorithms and their application in agein...

This work presents the Python-based implementation and validation of the Metabolic Transformation Algorithm (MTA) and its robust counterpart (rMTA), originally developed in MATLAB. MTA/rMTA facilitates the identification of therapeutic metabolic interventions by simulating gene knockouts and evaluating their potential to redirect metabolic fluxes toward healthier phenotypes. The transition to Python capitalizes...

Co-creating a Mpox Elimination Campaign in the WHO European Region: The Central...

Viral genetics and transmission dynamics in the second wave of mpox outbreak in...

Orogenital and anal infection by Chlamydia trachomatis, Neisseria gonorrhoeae, ...

Background: Men who have sex with men (MSM) are at risk for sexually transmitted infections (STIs), but more data on extragenital carriage are needed. Aim: We assessed the genital and extragenital prevalence of bacterial and other STIs in MSM in a Lisbon sexual health clinic. Methods: We screened oral, anal, and urine samples of MSM visiting the GAT-CheckpointLX clinic June 2017-December 2021 for Chlamydia trac...

Bias-Motivated Physical or Verbal Violence Among Men Who Have Sex with Men: Fin...

BioISO: an objective-oriented application for assisting the curation of genome-...

As the reconstruction of Genome-Scale Metabolic Models (GEMs) becomes standard practice in systems biology, the number of organisms having at least one metabolic model is peaking at an unprecedented scale. The automation of laborious tasks, such as gap-finding and gap-filling, allowed the development of GEMs for poorly described organisms. However, the quality of these models can be compromised by the automatio...

Computationally-designed miniproteins showing neutralization activity against S...

As the COVID-19 pandemic demonstrated, the need for robust antiviral therapies against SARS-CoV-2 remains substantial. A promising strategy to meet this demand is through the development of proteins tailored for enhanced binding affinity to crucial viral targets, such as epitopes located on their fusion proteins. Among these targets is the Spike proteins receptor binding domain (RBD), which interacts with the h...