The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from GenoMax, Istvan Albert, and was edited by Istvan Albert,
BioAgents: Bridging the gap in bioinformatics analysis with multi-agent systems | Scientific Reports (www.nature.com)
We thus propose a multi-agent system built on small language models, fine-tuned on bioinformatics data, and enhanced with retrieval augmented generation (RAG).
To better understand the challenges faced by practitioners, we analyzed 68,000 question-answer (QA) pairs from Biostars, extracting the associated tags and categorizing each question.
We surveyed expert bioinformaticians on workflow questions derived from Biostars data, comparing their reasoning and logic against outputs from BioAgents.
We then created three levels of questions (easy, medium, and hard) increasing in complexity (i.e., number of steps and knowledge required) derived from questions in Biostars
submitted by: Istvan Albert
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets | Genome Biology | Full Text (genomebiology.biomedcentral.com)
CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets
submitted by: GenoMax
A high-coverage genome from a 200,000-year-old Denisovan (www.biorxiv.org)
Here, we present a second high-quality Denisovan genome, reconstructed from a molar found at Denisova Cave. It belonged to a man who lived ∼200,000 years ago in a small Denisovan group. This group mixed with early Neandertals and was then replaced by Denisovans who had mixed with later Neandertals. We show that in addition Denisovans received gene flow from hominins that diverged before the split of the ancestors of Denisovans and modern humans.
submitted by: Istvan Albert
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