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 Istvan Albert, and was edited by Istvan Albert,
The 2025 ISCB Overton Prize Award: Dr James Zou (academic.oup.com)
The ISCB Overton Prize is awarded to a scientist for their significant contributions to computational biology. This year, at the 33rd annual conference on Intelligent Systems for Molecular Biology and the 24th European Conference on Computational Biology, the International Society for Computational Biology has the pleasure of honoring Dr James Zou with this award!
submitted by: Istvan Albert
Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification (academic.oup.com)
We introduce a new method and corresponding user-friendly software tool for long-read transcript quantification called oarfish. Our model incorporates a novel coverage score, which affects the conditional probability of fragment assignment in the underlying probabilistic model. We demonstrate, in both simulated and experimental data, that by accounting for this coverage information, Oarfish is able to produce more accurate quantification estimates than existing long-read quantification tools.
submitted by: Istvan Albert
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment (academic.oup.com)
We introduce a new and modified pseudoalignment scheme that partitions each reference into “virtual colors [...] We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. [...] demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing.
submitted by: Istvan Albert
Automated assignment grading with large language models: insights from a bioinformatics course (academic.oup.com)
We present the results of a practical evaluation of LLM-based graders for written assignments in the 2024/25 iteration of the Introduction to Bioinformatics course at the University of Ljubljana.
Later in the paper 92% of students used LLMs to write the assignments. Thus as the authors themselves recognized:
Over 92% of students reported using such tools, with 90% using ChatGPT for solving programming tasks and answering essay-style questions and 46% using Copilot for code generation in programming tasks. Inevitably, in some cases, this devolves into LLMs grading the output of other LLMs.
Also the paper is way, way too long to read.
submitted by: Istvan Albert
Want to get the Biostar Herald in your email? Who wouldn't? Sign up righ'ere: toggle subscription
