Biology subjects

Sweeney, B.

Publications and source records attributed to Sweeney, B..

6 recordsLinked to original sources

bioRxiv2026

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT

Rfam is a comprehensive database of non-coding RNA (ncRNA) families providing curated sequence alignments, consensus secondary structures, and covariance models for thousands of RNA families. The database is essential for identifying structured non-coding RNAs in newly sequenced genomes and understanding RNA structure-function relationships. Here we present computational protocols for automated ncRNA annotation of viral genomes, and for programmatic interaction with Rfam through its RESTful API. We showcase genome-wide RNA structure visualization from a genome sequence and from a multiple sequence alignment by generating comprehensive 2D structure diagrams using newly developed features in R2DT. We also present practical examples for retrieving family metadata, downloading alignments, accessing secondary structures, and searching user sequences from the Rfam API. These methods enable researchers in virology and RNA biology to integrate Rfam data into custom bioinformatics pipelines, comparative analyses, and machine learning workflows.

bioinformatics↗

bioRxiv2025

GOFlowLLM - Curating miRNA literature with Large Language Models and flowcharts

The exponential growth of non-coding RNA research--with over 230,000 papers published since 2000--has created an urgent knowledge management crisis in molecular biology. Despite their crucial regulatory roles, microRNAs (miRNAs) face a significant curation bottleneck, with only 1,400 articles manually curated to the Gene Ontology (GO) knowledgebase over a decade. We present GOFlowLLM, an automated curation pipeline powered by reasoning-enabled Large Language Models (LLMs) that follows established GO curation flowcharts to extract and structure miRNA-mediated gene silencing data at scale. When evaluated on existing curation, GOFlowLLM selects the correct GO term in 90% of cases. Curators also agree with 95% of the systems reasoning steps and 90% of the evidence selected. Applied to 6,996 previously uncurated articles, our system identified 2,538 new candidate GO annotations on 1,785 articles in just 58 hours--potentially doubling the available miRNA GO curation. Manual review of a subset of these annotations shows that curators agreed with the selected term in 87% of cases, the models reasoning in 92% of cases, and the extracted evidence in 93%. GOFlowLLM demonstrates how LLMs can significantly accelerate biocuration while maintaining high-quality standards by following expert-designed reasoning frameworks. The integration of reasoning traces in our system provides transparent justification for annotations that can be reviewed by human curators, addressing one of the key challenges in adopting AI for scientific curation, potentially transforming how we manage the growing corpus of scientific knowledge in molecular biology. GoFlowLLM is available on github: https://github.com/RNAcentral/GO_Flow_LLM.

bioinformatics↗

bioRxiv2025

First full-genome alignment representative for the genus Pestivirus

The members of the genus Pestivirus in the family Flaviviridae comprise economically important pathogens of life stock like classical swine fever (CSFV) and bovine viral diarrhea virus (BVDV). Intense research over the last years revealed that at least 11 recognized and eight proposed pestivirus species exist. The single-stranded, positive-sense RNA genome encodes for one large polyprotein which is processed by viral and cell-derived proteases into 12 mature proteins. Besides its protein-coding function, the RNA genome also contains RNA secondary structures with critical importance for various stages of the viral life cycle. Some of those RNA secondary structures, like the internal ribosome entry site (IRES) and a 3 stem-loop essential for genome replication, had already been studied for a few individual pestiviruses. In this study, we provide the first genome-wide multiple sequence alignment (MSA) including all known pestivirus species (accepted and tentative). Moreover, we performed a comprehensive analysis of RNA secondary structures phylogenetically conserved across the complete genus. While showing well-described structures, like a 5 stem-loop structure, the IRES element, and the 3 stem loop SL I to be conserved between all pestiviruses, other RNA secondary structures in the 3 untranslated region (UTR) were only conserved in subsets of the species. We identified 29 novel phylogenetically conserved RNA secondary structures in the protein-coding region, with so far unresolved functional importance. The microRNA binding site for miR-17 was previously known in species A, B, and C; in this study, we identified it in ten additional species, but not in species K, S, Q, and R. Another interesting finding is the identification of a putative long-distance RNA interaction between the IRES and the 3 end of the genome. These results together with the now available comprehensive multiple sequence alignment including all 19 pestivirus species, represent a valuable resource for future research and diagnostic purposes.

bioinformatics↗

bioRxiv2024

Rfam 15: RNA families database in 2025

The Rfam database, a widely-used repository of non-coding RNA (ncRNA) families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26, 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronisation with miRBase, resulting in 1, 603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfams coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation, and the development of machine learning models. Rfam is freely available at https://rfam.org. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/614430v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@9b1898org.highwire.dtl.DTLVardef@6bc030org.highwire.dtl.DTLVardef@16b789org.highwire.dtl.DTLVardef@16b8577_HPS_FORMAT_FIGEXP M_FIG Rfam has undergone a major update with the release of 15.0. We have increased the number of genomes in our sequence database Rfamseq by 75%, completed the synchronisation with miRBase and improved 65 families using 3D structures. C_FIG

genomics↗

bioRxiv2024

The evolutionarily conserved PhLP3 is essential for sperm development in Drosophila melanogaster

Phosducin-like proteins (PhLP) are thioredoxin domain-containing proteins that are highly-conserved across unicellular and multicellular organisms. PhLP family proteins are hypothesized to function as co-chaperones in the folding of cytoskeletal proteins. Here, we present the initial molecular, biochemical, and functional characterization of CG4511 as Drosophila melanogaster PhLP3. We cloned the gene into a bacterial expression vector and produced enzymatically active recombinant PhLP3, which showed similar kinetics to previously characterized orthologues. A fly strain homozygous for a P-element insertion in the 5 UTR of the PhLP3 gene exhibited significant downregulation of PhLP3 expression. We found these male flies to be sterile. Microscopic analysis revealed altered testes morphology and impairment of spermiogenesis, leading to a lack of mature sperm. Among the most significant observations was the lack of actin cones during sperm maturation. Excision of the P-element insertion in PhLP3 restored male fertility, spermiogenesis, and seminal vesicle size. Given the high level of conservation of PhLP3, our data suggests PhLP3 may be an important regulator of sperm development across species.

biochemistry↗

bioRxiv2023

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large "cloud" of RNA genomes which - by trial and error - comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.

genomics↗