2025 · Bioinformatics · Oxford University Press · added 2026-04-21
Motivation: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has be come cost-effective, interpreting these variants—particular Show more
Motivation: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has be come cost-effective, interpreting these variants—particularly collecting literature-based evidence like ACMG/AMP PM3—remains complex and time-consuming. Results: We present AutoPM3, a method that automates PM3 evidence extraction from literatures using open-source large language models (LLMs). AutoPM3 combines a Text2SQL-based variant extractor and a retrieval-augmented generation (RAG) module, enhanced by a variantspecific retriever and fine-tuned LLM, to separately process tables and text. We curated PM3-Bench, a dataset of 1027 variant-publication Show less
2025 · Nucleic acids research · Oxford University Press · added 2026-04-21
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation fr Show more
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation framework based on a modular architecture, for interpreting and prioritizing genetic alterations in cancer patients. A multitude of tools and databases are integrated into Onkopus to provide a comprehensive overview about the consequences of a variant, each with its own semantic, including pathogenicity predictions, allele frequency, biochemical and protein features, Show less
2024 · Nucleic acids research · Oxford University Press · added 2026-04-21
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platf Show more
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platform for clinicians and researchers in the field of rare disease genetics. Supporting data was aggregated from public data sources. We compared REEV with seven other tools for clinical variant evaluation. REEV (semi-)automatically fills individual ACMG criteria facilitating variant interpretation. REEV can store disease and phenotype data related to a case to use these for phenotype Show less
Ivano Bertini, Antonio Rosato · 2003 · Proceedings of the National Academy of Sciences of the United States of America · National Academy of Sciences · added 2026-04-20
Genome sequencing has revolutionized all fields of life sciences. Bioinorganic chemistry is certainly not immune to this influence, which is presenting unprecedented challenges. A new goal for bioinor Show more
Genome sequencing has revolutionized all fields of life sciences. Bioinorganic chemistry is certainly not immune to this influence, which is presenting unprecedented challenges. A new goal for bioinorganic chemistry is the investigation of the linkages between inorganic elements and genomic information. This requires new advancements andor the development of new expertise in fields such as bioinformatics and genetics but also provides a driving force to push forward the exploitation of traditional analytical techniques and spectroscopic tools. The "case study" of metal homeostasis in cells is discussed to provide a flavor of the current evolution of the field. Show less