Publications by authors named "B Cosma"
Article Synopsis
- Current methods for predicting bacterial gene functions are limited due to a lack of database matches for novel proteins, necessitating improved prediction techniques.
- A new tool called SAFPred has been developed, utilizing protein embeddings from advanced language models to enhance gene function prediction in bacteria while incorporating their unique operon structures.
- SAFPred demonstrated superior performance over traditional methods and identified 11 potential novel toxins in enterococci, which could have important health implications.
Background: Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short read lengths specific to next-generation sequencing (NGS), third-generation sequencers are known to produce more error-prone reads, thereby generating a new set of challenges for assembly algorithms and pipelines. However, the introduction of HiFi reads, which offer substantially reduced error rates, has provided a promising solution for more accurate assembly outcomes.
View Article and Find Full Text PDFMotivation: Today, we know the function of only a small fraction of the protein sequences predicted from genomic data. This problem is even more salient for bacteria, which represent some of the most phylogenetically and metabolically diverse taxa on Earth. This low rate of bacterial gene annotation is compounded by the fact that most function prediction algorithms have focused on eukaryotes, and conventional annotation approaches rely on the presence of similar sequences in existing databases.
View Article and Find Full Text PDFBackground: Many preterm infants are significantly growth restricted at hospital discharge and are at increased risk for long-term growth failure.
Aims: To compare growth and weight gain composition after term between preterm infants who were growth retarded and those who were not.
Study Design: An observational longitudinal study was conducted.
A method is described for extraction of chlorinated hydrocarbons (DDTs and PCBs) from fish samples with sulphuric acid of various concentrations. The results are better than those obtained by an official method using Soxhiet extraction with n-hexane, especially with 9.5-13M sulphuric acid.
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